SNPid Chr Pos_RefSeqv1 ProbeAlleles ProbeStrand REF ALT CallAlleles CallStrand Note BS00000713_51 chr1A 1145448 T/C - A G AG + GENE-0014_317 chr1A 1211006 T/G - A C GT - GENE-0014_262 chr1A 1211057 T/C - G A AG + BS00022677_51 chr1A 1211885 A/G - C T CT + RAC875_c95364_259 chr1A 1234396 A/G - C T AG - RAC875_c42700_264 chr1A 1235852 A/G + A G AG + Excalibur_c9509_1180 chr1A 1336994 T/C - G A AG + RAC875_rep_c110533_92 chr1A 1339530 T/C - A G AG + BobWhite_c1361_1187 chr1A 1339768 A/G + G A CT - Kukri_c2408_857 chr1A 1342766 A/G + G A AG + Excalibur_c44612_474 chr1A 1346498 T/C + T C AG - Excalibur_c58555_110 chr1A 3256255 A/G - T C CT + GENE-3142_72 chr1A 3256629 T/C NA NA NA CT NA flanks do not match reference at this position tplb0025b13_2879 chr1A 3386503 T/C - G A AG + tplb0025b13_2372 chr1A 3387617 T/C - G A CT - Kukri_c1818_2380 chr1A 3387764 A/G - C T AG - tplb0025b13_2054 chr1A 3387935 T/C - A G AG + tplb0025b13_1721 chr1A 3388635 A/G - C T CT + tplb0025b13_352 chr1A 3390711 A/G - T C CT + tplb0025b13_150 chr1A 3391831 A/G - T C CT + BS00059422_51 chr1A 3760728 T/C + C T AG - Ku_c28007_1398 chr1A 4500574 A/G + A G AG + BS00023130_51 chr1A 5024234 T/G + T G GT + Kukri_c8390_1102 chr1A 6323705 A/G + G A AG + RAC875_c9457_507 chr1A 6654865 T/C + C T AG - BS00056550_51 chr1A 7294614 A/G + G A AG + CAP12_c1632_462 chr1A 7657609 T/C + T C CT + BS00022355_51 chr1A 7658729 T/C - A G AG + Kukri_c2332_1093 chr1A 7660066 A/G - C T AG - RAC875_c19569_765 chr1A 7660348 A/G - T C CT + Excalibur_c51270_185 chr1A 8238652 A/G + G A AG + RAC875_c4805_330 chr1A 8251050 A/G + G A CT - Excalibur_c71158_54 chr1A 8296948 A/G + G A CT - BS00010128_51 chr1A 9105099 A/G + A G CT - RAC875_rep_c72805_651 chr1A 9105169 T/C - A G CT - RAC875_rep_c104335_293 chr1A 9107936 T/C - G A AG + Excalibur_c5139_198 chr1A 9110343 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c82557_201 chr1A 9122998 A/C + C A GT - BS00022943_51 chr1A 9579689 T/C - G A CT - Tdurum_contig68827_61 chr1A 9579689 A/G + G A CT - Kukri_c29655_239 chr1A 9579907 T/C - G A AG + RFL_Contig5637_1008 chr1A 9580120 T/C - G A CT - Kukri_c87556_380 chr1A 9643605 A/G + A G AG + GENE-4832_103 chr1A 9643692 A/G + A G CT - BS00108351_51 chr1A 9980771 A/G + G A CT - tplb0053o08_2004 chr1A 10048700 A/G + A G AG + IAAV8297 chr1A 10049764 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Kukri_c29150_143 chr1A 10052788 T/C - G A CT - Excalibur_c114401_105 chr1A 10054266 T/C - A G CT - RAC875_c18640_821 chr1A 10054563 T/C - A G CT - Excalibur_c49234_475 chr1A 10055658 T/C + T C CT + Tdurum_contig68637_256 chr1A 10068823 A/G - C T AG - Tdurum_contig43943_56 chr1A 10068932 A/G - C T AG - RAC875_c63624_1002 chr1A 10068933 A/G + A G AG + CAP11_c2581_302 chr1A 10069836 T/C + C T CT + CAP8_c2448_355 chr1A 10069891 A/C + A C AC + Tdurum_contig14847_354 chr1A 10070075 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c57939_78 chr1A 11571881 T/C + T C CT + Excalibur_c11848_919 chr1A 11664878 A/G + A G CT - CAP7_c3299_316 chr1A 11665248 A/G + A G CT - CAP7_c3299_342 chr1A 11665274 T/C + C T CT + Kukri_c5715_141 chr1A 11819683 T/C - A G AG + Excalibur_rep_c67198_530 chr1A 11940034 A/G - T C AG - BS00110709_51 chr1A 11950553 T/C - G A AG + BS00022270_51 chr1A 11950587 A/G - C T CT + RAC875_c25125_210 chr1A 12093324 A/G + A G CT - RAC875_c34888_65 chr1A 12093366 A/G - C T CT + BobWhite_c6558_234 chr1A 12098848 T/C + T C CT + Kukri_c45607_199 chr1A 12099004 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c33470_345 chr1A 12099909 T/C - A G CT - IACX11001 chr1A 12303846 A/G - C T CT + Kukri_c2121_1334 chr1A 12305206 T/C - G A AG + Ex_c4876_1221 chr1A 12305338 T/C - G A CT - Ex_c28368_426 chr1A 12313253 A/G - T C CT + BS00077351_51 chr1A 12364396 A/G + A G AG + tplb0061f07_961 chr1A 12368783 T/C - G A CT - BS00103478_51 chr1A 12369432 T/C - G A CT - Ku_c4823_673 chr1A 12411382 T/C - G A CT - Tdurum_contig42479_3110 chr1A 12506132 A/G + A G CT - Tdurum_contig42479_3800 chr1A 12506822 A/G + A G CT - IAAV4132 chr1A 13666918 A/G + G A CT - BS00079071_51 chr1A 13761856 T/C + T C AG - RAC875_c23587_548 chr1A 13767640 T/C - A G CT - RAC875_c23587_271 chr1A 13768014 A/G - C T CT + CAP7_c3847_204 chr1A 13861680 A/G - T C AG - Tdurum_contig75476_721 chr1A 13980147 A/G + A G CT - Tdurum_contig83113_134 chr1A 14056065 T/C - A G CT - Kukri_rep_c108031_378 chr1A 14143316 T/C + C T CT + BS00022977_51 chr1A 14163002 T/G + G T GT + Tdurum_contig50845_215 chr1A 14163002 A/C - G T GT + Tdurum_contig50845_82 chr1A 14163135 T/C - A G CT - BS00026453_51 chr1A 14253976 T/C - G A CT - BS00110358_51 chr1A 14361000 A/G + A G CT - GENE-3569_500 chr1A 15431071 T/C + T C CT + BobWhite_c1890_712 chr1A 15435210 T/C NA NA NA AG NA flanks do not match reference at this position Tdurum_contig61492_458 chr1A 15438673 T/C + C T CT + Tdurum_contig61492_684 chr1A 15438899 A/G + G A CT - BS00064536_51 chr1A 16389643 T/C - A G CT - BS00003761_51 chr1A 16390756 A/G + A G AG + IAAV1469 chr1A 18486532 T/C + T C AG - BobWhite_c46501_92 chr1A 20094363 T/C + T C CT + Excalibur_c24303_1145 chr1A 20094503 A/C + C A AC + Tdurum_contig11756_264 chr1A 20094659 A/G - T C CT + BS00039749_51 chr1A 20889641 A/C - G T AC - RAC875_c37934_225 chr1A 20977363 T/C + C T CT + RAC875_c37934_285 chr1A 20977423 T/C + C T AG - Kukri_c24144_1568 chr1A 21038166 A/G - T C AG - Excalibur_c110483_103 chr1A 21040602 T/C - A G AG + Kukri_rep_c72397_600 chr1A 21047359 T/C + T C CT + D_F1BEJMU01DOR77_203 chr1A 21331124 A/G + A G AG + IAAV3168 chr1A 21626816 T/C + T C CT + RAC875_c13012_174 chr1A 22287591 A/C + A C GT - Excalibur_c18694_273 chr1A 22288254 A/C + A C GT - Excalibur_rep_c92985_618 chr1A 22297261 A/G + A G CT - IAAV6888 chr1A 23130606 T/C - G A AG + Excalibur_c11941_612 chr1A 23966759 A/C NA NA NA GT NA flanks do not match reference at this position GENE-3956_91 chr1A 23966895 T/C + C T AG - BS00078982_51 chr1A 24247379 A/C + C A GT - IACX20627 chr1A 24320176 A/G - NA NA AG NA reference base A not among SNP alleles BS00105601_51 chr1A 24321355 T/C - G A CT - IAAV3527 chr1A 24944122 T/C + NA NA AG NA reference base G not among SNP alleles CAP7_c3250_98 chr1A 25544241 A/G + A G AG + Kukri_c16098_95 chr1A 25544603 T/C + T C CT + CAP7_c4833_141 chr1A 25545972 T/G - C A GT - Kukri_c7436_2259 chr1A 26958877 T/G - C A AC + Kukri_c7436_819 chr1A 26961112 A/G - T C AG - GENE-0074_370 chr1A 26961234 A/G + G A CT - Ku_c7436_656 chr1A 26961275 A/G - T C AG - RAC875_c8245_272 chr1A 26961620 T/C - G A AG + Kukri_c13136_1363 chr1A 28614097 T/C + C T CT + Excalibur_c7026_2635 chr1A 28620484 A/G + A G CT - RAC875_c14926_589 chr1A 28623752 T/C + C T CT + BS00011787_51 chr1A 28757527 A/G + G A AG + Kukri_c22508_119 chr1A 28757899 A/C - T G AC - Tdurum_contig13937_1782 chr1A 29191079 T/C + C T AG - BS00064263_51 chr1A 29611146 T/G - C A AC + BobWhite_c4499_153 chr1A 31779240 T/C + T C AG - BS00084022_51 chr1A 31781750 T/C + C T CT + GENE-0002_856 chr1A 32087536 T/C + C T CT + IAAV4318 chr1A 32454883 T/G NA NA NA AC NA flanks do not match reference at this position Excalibur_c14806_1091 chr1A 32532638 A/G + A G AG + Kukri_c46010_872 chr1A 32894232 T/G + G T GT + Tdurum_contig50355_269 chr1A 33020899 A/G + G A CT - BS00015528_51 chr1A 33020911 T/C + T C AG - Tdurum_contig13946_241 chr1A 33372421 T/C + T C CT + Tdurum_contig77289_179 chr1A 33373162 A/G - C T CT + Tdurum_contig29280_216 chr1A 33375555 T/G + G T AC - Kukri_c82555_88 chr1A 33375691 T/G + T G GT + RAC875_c10090_963 chr1A 35933865 A/C - T G AC - RAC875_rep_c111911_116 chr1A 35934711 T/C - A G CT - Excalibur_c1886_1232 chr1A 35939779 T/C - A G CT - Excalibur_c7237_1208 chr1A 36569350 A/G + G A CT - Tdurum_contig61515_259 chr1A 36569647 T/G - A C GT - Excalibur_c1263_901 chr1A 37467363 A/G + A G AG + BS00029346_51 chr1A 37501086 A/G + A G AG + IACX1592 chr1A 38729994 T/C + T C AG - Excalibur_c46833_204 chr1A 38731185 A/G + A G CT - RAC875_c89908_105 chr1A 38731840 A/G + A G AG + IAAV5652 chr1A 41709423 A/G + A G AG + RFL_Contig5444_1284 chr1A 41709697 T/C - G A CT - BobWhite_c48490_241 chr1A 41713076 T/C + T C AG - Tdurum_contig47183_205 chr1A 42256218 A/G - T C CT + Ku_c11769_252 chr1A 45794194 T/C + T C AG - Tdurum_contig9199_714 chr1A 45796984 A/G - T C CT + Excalibur_rep_c114535_55 chr1A 45797333 A/G - T C CT + Excalibur_c12215_352 chr1A 46239669 A/G - C T AG - BS00109971_51 chr1A 47213343 A/G - C T CT + Tdurum_contig5008_635 chr1A 47791170 A/G - T C AG - Tdurum_contig69753_513 chr1A 47822901 T/C + C T CT + Kukri_c26731_312 chr1A 48585209 T/C - A G CT - BS00022870_51 chr1A 48588559 A/G - T C CT + Kukri_c23985_229 chr1A 48978899 A/G + G A CT - BobWhite_rep_c66800_54 chr1A 48982512 T/C - A G AG + IACX5982 chr1A 49153543 A/C - T G AC - BobWhite_c4646_119 chr1A 49153584 T/C + T C AG - Excalibur_c77035_156 chr1A 49252857 T/C + T C CT + GENE-4777_297 chr1A 49287059 T/C + T C CT + RAC875_c5544_4156 chr1A 49287733 A/G + A G CT - Ra_c56967_900 chr1A 49530413 A/G + A G CT - BobWhite_rep_c61217_251 chr1A 52236195 T/C - G A CT - GENE-2541_51 chr1A 53909675 T/C + T C CT + CAP7_c7330_86 chr1A 54002300 A/G + A G AG + Tdurum_contig11824_281 chr1A 57306498 T/C - A G AG + RAC875_c46269_387 chr1A 57768535 T/C + C T CT + tplb0038o14_241 chr1A 58123918 T/G + T G GT + tplb0038o14_634 chr1A 58124311 T/C + T C AG - RAC875_rep_c69360_259 chr1A 58171968 A/G + A G CT - Excalibur_c39375_84 chr1A 58200776 A/C - T G AC - BS00062723_51 chr1A 58704168 A/G - C T AG - RAC875_c11899_366 chr1A 58704729 T/C + C T AG - Excalibur_c23341_117 chr1A 58712639 T/C + T C AG - BobWhite_c15153_337 chr1A 58748997 A/G - T C CT + Excalibur_c6213_689 chr1A 59131276 T/C - G A AG + BobWhite_c13378_662 chr1A 59615202 A/G + A G CT - Tdurum_contig14418_753 chr1A 62615609 T/C + T C AG - BS00067444_51 chr1A 63052201 T/C + T C CT + RAC875_rep_c110946_140 chr1A 63477003 A/G + A G AG + Excalibur_c2181_542 chr1A 64597565 T/C + T C CT + BobWhite_c15522_250 chr1A 64693405 T/C + T C CT + IAAV4349 chr1A 64713337 A/G - T C AG - Kukri_c32899_95 chr1A 64714162 T/G + T G AC - RAC875_c37183_331 chr1A 66893642 A/G + A G AG + GENE-0025_338 chr1A 69189236 T/G - C A AC + RAC875_c81146_179 chr1A 73300270 T/C + T C AG - Kukri_c20698_396 chr1A 73326650 T/C + T C CT + Tdurum_contig12173_180 chr1A 73355490 A/C - T G GT + Ex_c29914_480 chr1A 76031032 A/C NA NA NA GT NA flanks do not match reference at this position IACX7053 chr1A 77070587 A/G + NA NA CT NA reference base C not among SNP alleles Kukri_c10700_443 chr1A 80308757 T/C + T C AG - BS00110181_51 chr1A 82531597 A/G - C T AG - BS00064406_51 chr1A 83833186 T/C + T C CT + Excalibur_rep_c108957_455 chr1A 84014214 T/C + T C AG - Excalibur_c34970_131 chr1A 85034073 T/C + T C CT + Kukri_rep_c68217_1456 chr1A 86645141 A/G - C T AG - Excalibur_c14541_350 chr1A 91058593 A/G - C T AG - IAAV2375 chr1A 91058688 A/G - T C CT + GENE-0564_313 chr1A 91594145 A/G - T C CT + BobWhite_rep_c51917_234 chr1A 92565416 T/C + C T CT + IACX6344 chr1A 92567918 T/C + C T AG - IAAV1463 chr1A 92570693 A/G - T C CT + RAC875_c1668_1110 chr1A 92572247 A/G + G A CT - IAAV3128 chr1A 94113832 A/G + A G CT - CAP8_c2036_140 chr1A 94245262 A/G + A G AG + Excalibur_c52484_106 chr1A 95821231 T/C + T C CT + Kukri_c4099_321 chr1A 95852226 T/C - A G CT - GENE-0489_946 chr1A 95857404 A/G - T C CT + Tdurum_contig42247_2504 chr1A 96473450 T/G + T G GT + BobWhite_c48146_87 chr1A 97422339 A/G + A G CT - Kukri_c48434_88 chr1A 97800822 T/C - A G CT - JD_c4432_1913 chr1A 98242794 A/G - C T CT + IAAV7414 chr1A 100292729 T/C - G A AG + BobWhite_c24113_529 chr1A 100293004 T/C - A G CT - tplb0032d09_1393 chr1A 101377545 T/C - A G CT - Ku_c78471_263 chr1A 101378594 T/C + T C CT + BS00076668_51 chr1A 101670445 A/G + G A AG + RAC875_rep_c76047_63 chr1A 101763979 A/C + C A GT - CAP11_c2984_419 chr1A 102370423 A/G - T C CT + BS00067277_51 chr1A 103316377 T/C + C T CT + Excalibur_c102338_617 chr1A 104214285 T/C - A G CT - Excalibur_c13438_542 chr1A 105904252 T/C + T C CT + Excalibur_c5775_228 chr1A 105906068 A/G - T C AG - BobWhite_c18618_677 chr1A 106228780 T/C - A G CT - RAC875_c12670_158 chr1A 107102268 T/C + C T AG - Ex_c9201_714 chr1A 107648269 T/C + T C CT + BS00064029_51 chr1A 107777283 A/C + C A AC + GENE-0084_248 chr1A 108078413 A/C - T G AC - GENE-0041_182 chr1A 108689992 A/G NA NA NA AG NA flanks do not match reference at this position GENE-0041_486 chr1A 108690081 T/G - A C AC + GENE-0041_415 chr1A 108690144 T/C - A G CT - Kukri_rep_c101218_200 chr1A 108760708 T/C + T C AG - IAAV3583 chr1A 109982594 T/C + C T AG - RFL_Contig388_958 chr1A 111125690 T/G + T G GT + GENE-0032_895 chr1A 111131551 A/G + A G AG + GENE-0032_951 chr1A 111131603 T/C + C T CT + BS00087437_51 chr1A 113860349 T/C - G A CT - Kukri_c8943_1381 chr1A 113878583 A/G - T C AG - Tdurum_contig21489_536 chr1A 119150121 T/C - G A CT - GENE-0163_949 chr1A 120010272 T/G - A C GT - IAAV8824 chr1A 121046541 A/G - T C AG - Kukri_c26936_1370 chr1A 121046892 T/G - A C AC + Kukri_c26936_1090 chr1A 121047172 T/G - A C AC + Kukri_rep_c101022_1595 chr1A 121740753 T/C - A G AG + Kukri_c19224_182 chr1A 126857830 T/C - A G CT - Kukri_c26669_515 chr1A 127075701 A/C - T G AC - BS00063964_51 chr1A 127076716 T/G - A C GT - BS00004637_51 chr1A 127758757 T/C - A G AG + Tdurum_contig13709_317 chr1A 132414837 A/C + C A GT - RAC875_c21620_1359 chr1A 132784415 A/G - T C AG - RAC875_rep_c70404_755 chr1A 132785570 T/C - A G AG + RAC875_c30367_736 chr1A 134946334 T/G - A C AC + Excalibur_c15060_507 chr1A 134957145 T/C + T C CT + RAC875_c14902_1370 chr1A 136956695 A/G + A G AG + RAC875_c14902_1667 chr1A 136957387 T/C NA NA NA CT NA flanks do not match reference at this position GENE-0561_311 chr1A 145371716 T/C - G A AG + Excalibur_c22621_160 chr1A 146630542 A/C - T G AC - GENE-0553_173 chr1A 147355017 T/G + T G GT + BS00066308_51 chr1A 147908275 A/G - C T AG - Kukri_c66773_111 chr1A 148610726 A/C - G T GT + IAAV4362 chr1A 150450671 A/T - A T AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Excalibur_c52805_134 chr1A 150894872 T/C + T C AG - BS00003813_51 chr1A 150894884 T/C + C T AG - RAC875_c46062_63 chr1A 153586222 T/C + T C CT + BobWhite_c10399_401 chr1A 154011971 T/C + T C AG - RAC875_c21367_209 chr1A 154576016 A/G + A G AG + Excalibur_c7668_797 chr1A 155080314 A/G - T C AG - Excalibur_c2389_334 chr1A 155082240 A/C - T G AC - Excalibur_c14494_854 chr1A 155697423 A/C + A C GT - IAAV2777 chr1A 157829690 A/G - T C AG - BS00033760_51 chr1A 157831768 A/G - C T AG - Excalibur_c16256_551 chr1A 159517161 A/G - T C CT + BobWhite_c13654_447 chr1A 163393248 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c14968_674 chr1A 164461123 T/C - A G CT - IACX3433 chr1A 165173894 T/C - A G CT - GENE-0256_368 chr1A 165175647 T/C - G A AG + RAC875_c2021_1417 chr1A 166322397 T/C + C T CT + RAC875_c75854_126 chr1A 168569644 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c44553_550 chr1A 171453910 T/C - A G CT - RAC875_c15646_2033 chr1A 171454858 T/C - A G CT - Kukri_c23382_1431 chr1A 176457991 A/G - T C CT + BS00076538_51 chr1A 180412546 A/G - C T AG - BobWhite_c20703_141 chr1A 180413284 T/C + T C AG - Ex_c3799_2429 chr1A 182176248 A/G + A G AG + Excalibur_rep_c68921_433 chr1A 186989004 T/C - A G AG + BobWhite_rep_c66520_103 chr1A 189715531 T/C - A G AG + RAC875_c31882_2517 chr1A 189965033 T/C + T C AG - Kukri_c22856_385 chr1A 204829348 T/C + T C CT + Kukri_rep_c81206_235 chr1A 208681974 A/G + A G CT - BobWhite_c35092_94 chr1A 208910432 T/G - A C GT - RAC875_c53095_51 chr1A 209353855 A/G + A G CT - Ra_c70224_314 chr1A 209355735 T/C - A G AG + RAC875_c19509_174 chr1A 212022218 A/G - T C AG - RAC875_c25442_231 chr1A 216415143 A/C + A C AC + BS00066135_51 chr1A 218215074 T/C - G A AG + BS00065700_51 chr1A 219365252 T/C - A G CT - Tdurum_contig42633_1483 chr1A 222369213 T/C + T C CT + Ra_c7062_430 chr1A 222917663 T/C - A G AG + IAAV9022 chr1A 222918217 T/C + C T CT + Ex_c3567_1048 chr1A 222918978 T/G + G T GT + RAC875_c7305_75 chr1A 232606183 A/C + A C AC + BS00067330_51 chr1A 233921831 T/C - A G AG + IAAV5236 chr1A 236720979 A/T + A T AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c40579_501 chr1A 238656648 T/C + T C AG - BobWhite_c44224_71 chr1A 238680789 T/C - A G CT - BS00063063_51 chr1A 240318280 T/C - A G AG + Excalibur_c63753_211 chr1A 244501324 T/C + T C CT + IAAV742 chr1A 246130045 A/G + A G AG + Ex_c14515_218 chr1A 251590766 T/C - A G CT - Excalibur_c7692_139 chr1A 252324284 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_c62832_446 chr1A 252624024 A/G - C T AG - Kukri_c46608_277 chr1A 252624591 A/G - C T AG - BS00022207_51 chr1A 264213803 T/G - C A GT - BS00021730_51 chr1A 272313241 A/G + A G AG + BS00048887_51 chr1A 274785621 T/C + C T CT + BS00062969_51 chr1A 276322736 T/C + T C AG - GENE-0287_28 chr1A 276971926 A/C - T G GT + BS00086680_51 chr1A 281657026 A/G - T C AG - RAC875_c7341_144 chr1A 282546814 T/C + T C CT + TA004365-0417 chr1A 291255616 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_c31155_350 chr1A 292078341 A/C - G T GT + Excalibur_c65280_322 chr1A 293319410 T/G + T G AC - Kukri_c4318_101 chr1A 294858466 A/C - T G AC - CAP8_c806_297 chr1A 297380842 T/C - G A CT - GENE-0227_217 chr1A 297697348 A/C - G T GT + Excalibur_c20133_87 chr1A 298037397 T/C - G A CT - Excalibur_rep_c88290_94 chr1A 298108877 T/C + T C CT + BS00022201_51 chr1A 298116028 T/C + C T CT + Kukri_c362_91 chr1A 298116701 A/G + G A AG + Kukri_c362_151 chr1A 298116904 T/C + T C AG - BS00011835_51 chr1A 298117391 A/C + A C AC + BS00063885_51 chr1A 298561709 A/G - T C AG - Excalibur_s107771_77 chr1A 300109749 T/C + T C CT + BS00022156_51 chr1A 301197484 A/C - G T AC - Tdurum_contig43360_1592 chr1A 301197487 A/G - C T AG - Tdurum_contig43360_1381 chr1A 301197698 A/C - T G GT + IAAV4916 chr1A 301776516 T/C - G A AG + IAAV2546 chr1A 301776822 A/G + G A AG + BS00031200_51 chr1A 301782334 T/C + C T CT + Ra_c2322_174 chr1A 301857714 A/G + G A CT - Ra_c2322_1067 chr1A 301864279 T/C + T C CT + IAAV3552 chr1A 304037345 A/G - C T CT + RAC875_c41581_176 chr1A 305003327 A/G - C T AG - Excalibur_c37474_179 chr1A 306983490 A/G - C T CT + BS00064548_51 chr1A 307482606 T/C + T C CT + Ra_c10580_1629 chr1A 307705711 T/C + T C AG - RAC875_c49760_107 chr1A 308210617 A/G + A G AG + BS00095100_51 chr1A 308572338 T/C - G A AG + Tdurum_contig81558_272 chr1A 308812861 A/G + G A CT - BS00085851_51 chr1A 309401684 A/G - C T AG - BS00064679_51 chr1A 311806352 T/C + C T CT + BS00072686_51 chr1A 313161496 A/G + G A CT - BS00101116_51 chr1A 313161810 A/C - T G GT + GENE-0572_334 chr1A 313740706 T/C - G A AG + IACX542 chr1A 313740706 A/G + G A AG + BS00090634_51 chr1A 320222948 A/G - C T CT + Kukri_c6622_763 chr1A 320223805 A/G - C T AG - IAAV2709 chr1A 333886554 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c60610_118 chr1A 335108302 A/G + G A AG + BobWhite_c3144_473 chr1A 336476699 A/G + G A CT - Excalibur_c11273_284 chr1A 341869554 T/C + C T CT + RAC875_c18539_1159 chr1A 344294441 T/C + C T CT + Ex_c5759_663 chr1A 345108227 A/G - C T AG - RAC875_c15998_53 chr1A 345308692 A/G + G A CT - Excalibur_c102582_360 chr1A 345786602 T/C - A G CT - RFL_Contig921_337 chr1A 345788875 T/C NA NA NA CT NA flanks do not match reference at this position GENE-1214_288 chr1A 347919022 T/C - G A CT - Tdurum_contig41931_480 chr1A 351882476 A/C - T G AC - Ex_c12763_662 chr1A 352013338 T/C - G A CT - RAC875_rep_c71967_180 chr1A 352016352 A/G - C T CT + GENE-0126_140 chr1A 353254815 A/G + G A CT - Kukri_c43730_841 chr1A 353255356 T/G - C A GT - Excalibur_rep_c68424_255 chr1A 353255462 T/C NA NA NA CT NA flanks do not match reference at this position RFL_Contig5001_1099 chr1A 353916338 T/C + C T CT + RAC875_c33300_141 chr1A 354303779 A/G + A G AG + CAP12_c6266_339 chr1A 354823472 T/G - C A AC + CAP12_c6266_298 chr1A 354823513 A/G - C T AG - CAP12_c6266_187 chr1A 354823624 T/C - G A AG + RAC875_c68797_400 chr1A 354934792 T/C - A G AG + BobWhite_c46349_402 chr1A 354938468 T/C + C T CT + Excalibur_rep_c86757_244 chr1A 354950322 T/C - A G CT - Excalibur_c33881_618 chr1A 355324299 A/C - T G AC - Excalibur_c17872_137 chr1A 355335999 T/G + T G GT + Excalibur_c59486_172 chr1A 355716682 A/G + A G AG + Kukri_rep_c103147_745 chr1A 356474547 A/G - T C CT + IACX2325 chr1A 356474568 C/G - C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c38417_246 chr1A 358761707 T/G - A C GT - RAC875_c8515_653 chr1A 362628680 T/C + C T CT + Ra_c11023_679 chr1A 362864281 T/C - G A AG + Excalibur_c49588_76 chr1A 368197802 T/C NA NA NA AG NA flanks do not match reference at this position CAP7_c3269_236 chr1A 368198287 A/G - T C AG - IAAV749 chr1A 369089146 A/G - T C AG - Tdurum_contig48416_335 chr1A 369502385 A/G - T C AG - GENE-0053_224 chr1A 370093299 A/C NA NA NA AC NA flanks do not match reference at this position Kukri_c67601_267 chr1A 370095271 A/G + A G AG + BS00081455_51 chr1A 370097196 T/G + G T AC - Tdurum_contig62552_256 chr1A 370097408 A/G - T C CT + RAC875_c3751_96 chr1A 370107590 T/C + C T CT + BS00110415_51 chr1A 372315822 A/C - G T AC - BS00094681_51 chr1A 374689384 T/C - A G AG + IACX293 chr1A 375468835 T/C - A G CT - BS00077199_51 chr1A 375474953 T/C - A G CT - Kukri_c54467_100 chr1A 376137575 T/C - G A AG + IAAV7929 chr1A 376670363 A/G - C T AG - BS00110766_51 chr1A 377614438 A/G - C T CT + Excalibur_c3565_2673 chr1A 380964667 T/C - A G AG + Kukri_c19389_97 chr1A 381274245 T/G + T G GT + RAC875_c25799_457 chr1A 381314821 T/C - G A AG + BS00041358_51 chr1A 381822406 A/G + G A CT - RAC875_c31168_238 chr1A 382229667 T/C - G A CT - BS00065146_51 chr1A 382738759 A/G + G A CT - GENE-0491_632 chr1A 390094537 A/G - T C CT + RAC875_c9899_510 chr1A 391847139 A/G - T C CT + Excalibur_rep_c84731_611 chr1A 392529388 T/C - A G AG + Kukri_rep_c96140_621 chr1A 394852932 T/G + T G GT + BS00012051_51 chr1A 402258367 T/C - G A CT - GENE-0549_18 chr1A 403026115 A/G NA NA NA CT NA flanks do not match reference at this position RFL_Contig530_2305 chr1A 424803886 T/C + C T CT + IACX219 chr1A 436431272 T/G - C A GT - JD_c63991_766 chr1A 438300798 T/C + T C AG - GENE-0505_443 chr1A 441765309 T/C + T C CT + CAP7_c9231_230 chr1A 442567461 A/G + G A AG + Excalibur_c42595_581 chr1A 445884014 A/C - G T AC - RAC875_c46646_549 chr1A 449937122 A/G - C T CT + Kukri_c20672_360 chr1A 454333708 A/G + G A AG + tplb0046g22_1351 chr1A 458397080 A/G + G A CT - Kukri_c22434_513 chr1A 462434503 A/G + G A CT - IAAV7203 chr1A 462435377 A/G + A G CT - Ra_c2895_591 chr1A 462435782 T/G - A C GT - RFL_Contig2270_2610 chr1A 462794171 T/G - A C GT - RFL_Contig2270_1560 chr1A 462795554 A/G - T C CT + TA003238-0490 chr1A 463220160 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c59894_97 chr1A 463813646 A/C + C A GT - Kukri_c32430_109 chr1A 463827966 A/G - T C AG - BobWhite_c37935_124 chr1A 464796383 T/C + C T CT + RAC875_c86680_391 chr1A 464810348 A/G - T C AG - Kukri_c88698_296 chr1A 464837153 A/G + G A CT - Ex_c28144_1843 chr1A 471320712 T/C - G A CT - IACX3496 chr1A 471488518 A/C - G T AC - RAC875_c3910_1425 chr1A 471490140 T/C - A G CT - Ku_c10453_365 chr1A 471696945 A/G + A G CT - IAAV213 chr1A 472143502 T/C + C T CT + BS00033469_51 chr1A 473034633 T/G - A C AC + Excalibur_c56097_168 chr1A 473633876 A/G - T C AG - Ra_c58315_265 chr1A 473637156 A/G + G A AG + Kukri_c3582_87 chr1A 474642192 A/G - C T CT + RAC875_c25507_551 chr1A 475312850 A/G NA NA NA CT NA flanks do not match reference at this position IAAV1225 chr1A 477046669 T/G + T G AC - Kukri_c10239_2186 chr1A 477654671 T/G - A C AC + BS00065676_51 chr1A 477701436 T/C - G A CT - Kukri_c27785_400 chr1A 479827769 T/C - A G AG + RAC875_c2734_135 chr1A 480598537 T/C NA NA NA CT NA flanks do not match reference at this position BS00023126_51 chr1A 480604446 A/G - C T CT + BS00040968_51 chr1A 480755283 A/C - T G AC - BS00067420_51 chr1A 480755631 T/C - G A CT - BS00067421_51 chr1A 480755651 A/C - T G GT + BS00023101_51 chr1A 480831000 A/G - T C CT + IACX662 chr1A 480832499 T/G - C A AC + Excalibur_rep_c112145_271 chr1A 481651371 A/G - T C CT + BS00087600_51 chr1A 481654987 T/C + C T AG - BS00087601_51 chr1A 481655155 A/G + G A CT - IAAV2072 chr1A 482278982 T/G + T G GT + BS00022698_51 chr1A 482329681 T/C + C T CT + BS00002216_51 chr1A 482335916 T/C - G A AG + IACX4378 chr1A 482335926 T/C - G A AG + IACX4386 chr1A 482337514 A/G - C T AG - CAP11_c1972_285 chr1A 482761756 T/C + C T CT + RAC875_c94534_75 chr1A 482771048 T/C + T C AG - Excalibur_c30591_637 chr1A 482780984 A/G - C T CT + BobWhite_c32653_369 chr1A 482966522 A/G - C T CT + RFL_Contig3203_1971 chr1A 482966563 T/G - A C AC + Excalibur_c21487_129 chr1A 482966598 T/C + C T AG - RAC875_c43643_176 chr1A 483033358 A/G - T C AG - IAAV3049 chr1A 484332077 T/C - A G AG + RAC875_c31276_1128 chr1A 484335332 A/G + A G AG + Ex_c5192_943 chr1A 485002334 A/G - T C CT + Excalibur_c32167_59 chr1A 485342363 T/C - A G AG + Tdurum_contig42062_651 chr1A 485354299 A/G + G A CT - BobWhite_c5356_1272 chr1A 485356417 A/G - C T AG - Kukri_rep_c69946_1228 chr1A 485357107 A/C + C A AC + CAP12_c2265_240 chr1A 486052683 T/C - G A AG + Excalibur_c49421_443 chr1A 487012029 T/C - G A CT - Kukri_c52952_315 chr1A 487017792 A/G - T C AG - Ra_c6701_1579 chr1A 487090993 A/G - C T CT + IAAV5406 chr1A 487311547 T/C + T C AG - Ku_c8351_2029 chr1A 487311547 A/G - T C AG - Ku_c8351_945 chr1A 487312631 T/C - G A CT - RAC875_c38916_66 chr1A 487563715 T/C + T C AG - Kukri_c39628_318 chr1A 487732513 T/C - A G AG + RFL_Contig4231_575 chr1A 488070209 T/C + T C CT + Excalibur_c20286_882 chr1A 488623179 A/G + A G AG + BS00022733_51 chr1A 490313586 T/C + C T AG - RAC875_c23081_141 chr1A 491130184 A/G - C T AG - BobWhite_c12568_900 chr1A 491149118 T/C - A G AG + IACX11338 chr1A 492807667 T/C - A G CT - IACX5821 chr1A 493737003 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c27693_551 chr1A 494446381 A/G NA NA NA CT NA flanks do not match reference at this position Ex_c16529_304 chr1A 494448164 T/C + C T AG - Kukri_c16913_422 chr1A 495706733 T/C - G A AG + IAAV5535 chr1A 496311634 A/C + C A AC + RAC875_c102223_220 chr1A 496439651 T/C - A G CT - IACX3047 chr1A 496478834 A/G + G A CT - BS00021864_51 chr1A 497506253 A/G - T C AG - Ra_c105707_788 chr1A 497520555 T/C - G A CT - BS00089894_51 chr1A 497522675 T/C - A G AG + Kukri_c24715_175 chr1A 498050008 T/G + T G AC - Kukri_c30322_414 chr1A 498536695 T/C + C T CT + RAC875_rep_c112044_340 chr1A 498811359 T/C + T C AG - GENE-0524_302 chr1A 499632705 A/C + C A AC + Tdurum_contig42490_1315 chr1A 499797539 T/C + T C CT + BS00100120_51 chr1A 499807792 T/G - C A AC + IACX5921 chr1A 499979623 A/C + A C GT - IACX5960 chr1A 500563539 T/C - G A CT - BS00094553_51 chr1A 500979327 A/G + A G AG + BobWhite_c29908_113 chr1A 500980908 T/C - G A AG + Kukri_rep_c117029_125 chr1A 500988741 T/C + T C AG - RFL_Contig3919_1348 chr1A 501030862 T/C + T C CT + CAP8_c599_185 chr1A 501708279 A/C - T G AC - Ra_c108912_519 chr1A 503312428 T/C + C T CT + Kukri_c53153_92 chr1A 503372673 T/G + G T AC - BS00065325_51 chr1A 503376300 T/C - G A AG + BS00065324_51 chr1A 503376333 T/C - G A AG + TA004265-0757 chr1A 503380013 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c29540_1109 chr1A 504242218 A/G - C T AG - RAC875_c29540_413 chr1A 504242909 T/G - C A GT - RAC875_c29540_391 chr1A 504242931 T/G - C A AC + BS00021728_51 chr1A 504246961 T/C + T C CT + tplb0045g22_418 chr1A 505270073 T/C - A G CT - BS00096721_51 chr1A 505270201 A/G + A G CT - BS00067652_51 chr1A 505338262 A/G - C T AG - BS00064638_51 chr1A 505524402 A/G + A G AG + Kukri_c29039_315 chr1A 505672046 T/C + T C CT + BS00065601_51 chr1A 506545044 A/G - C T AG - Kukri_c53935_265 chr1A 506546795 T/C + C T AG - Kukri_rep_c105589_73 chr1A 506547570 T/C - A G CT - IAAV332 chr1A 506854510 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles CAP7_c1083_283 chr1A 506854586 A/G + G A AG + Excalibur_c3475_113 chr1A 506855550 A/G - T C AG - RAC875_c49074_374 chr1A 507875914 A/C - T G AC - RAC875_c16391_426 chr1A 508555158 A/G + G A CT - BS00030036_51 chr1A 508638227 A/C + A C GT - Kukri_c31891_1355 chr1A 508640884 T/C - A G AG + BS00022173_51 chr1A 508724101 T/G - A C GT - BS00079538_51 chr1A 508925284 A/C - T G GT + GENE-0511_161 chr1A 511100305 A/G - T C CT + CAP11_c3464_68 chr1A 511502175 T/C + C T AG - BobWhite_c46007_582 chr1A 512656031 A/G - C T AG - Tdurum_contig29616_55 chr1A 512658603 A/G - T C AG - BobWhite_c7337_717 chr1A 512658658 T/C + T C AG - BS00088035_51 chr1A 512878278 A/G - T C AG - Kukri_c54678_88 chr1A 513625907 T/C + C T CT + Kukri_c1313_1158 chr1A 513661860 A/C + C A GT - RAC875_c36737_316 chr1A 513662051 A/C - G T AC - Ku_c1313_1673 chr1A 513662375 T/C + C T CT + IAAV6234 chr1A 513893348 T/C + T C CT + Ra_c64515_242 chr1A 513894012 A/C + A C GT - Jagger_c5280_407 chr1A 514138226 T/C + C T CT + Kukri_rep_c109473_80 chr1A 514138403 A/G + A G CT - Kukri_c12984_465 chr1A 515546052 T/C + C T AG - RAC875_c80876_67 chr1A 515553365 T/G + T G GT + BS00022158_51 chr1A 516373257 T/C + T C CT + CAP12_c1979_117 chr1A 516378298 A/G + A G CT - Excalibur_c44668_382 chr1A 516454526 A/G - C T AG - BS00088136_51 chr1A 516563922 T/C - A G CT - Excalibur_c52725_585 chr1A 517400195 T/C - A G CT - Kukri_c28695_269 chr1A 517487694 A/G + A G CT - IAAV1142 chr1A 517894854 A/G - C T AG - Excalibur_c5443_473 chr1A 518666221 A/G + G A AG + BobWhite_c104_89 chr1A 520412991 T/G + G T AC - IAAV2694 chr1A 520413077 A/C + C A GT - Excalibur_c29605_535 chr1A 520579865 T/C - G A CT - Excalibur_c49946_169 chr1A 521277130 T/C - G A AG + BS00039378_51 chr1A 522500993 T/C - A G AG + BS00065430_51 chr1A 524116723 A/G + G A AG + BS00011146_51 chr1A 527177787 T/C + C T CT + CAP12_c3602_91 chr1A 527178211 A/G + A G AG + Tdurum_contig11896_550 chr1A 527951876 T/C + C T CT + BobWhite_c27438_81 chr1A 527951929 A/C - T G AC - Tdurum_contig10222_68 chr1A 527974284 A/G + G A AG + GENE-0392_97 chr1A 529247883 T/C - A G CT - RAC875_c21565_1111 chr1A 529667765 A/G + A G AG + Excalibur_c8396_300 chr1A 529669094 T/G - A C GT - Excalibur_c64439_87 chr1A 529786659 A/G + A G AG + BS00034278_51 chr1A 530173432 T/G + T G GT + CAP7_c1891_230 chr1A 530177169 A/C - G T GT + BS00009808_51 chr1A 530232680 T/C + C T AG - RAC875_c21954_276 chr1A 530233225 A/G - T C AG - Excalibur_rep_c69456_172 chr1A 530594328 T/G + T G AC - Excalibur_c7370_179 chr1A 531051927 A/G + A G CT - GENE-0527_92 chr1A 531605234 A/G + G A AG + Ku_c12688_352 chr1A 531644393 A/G + A G AG + BobWhite_c96_170 chr1A 531682521 A/C + A C AC + CAP7_c11581_78 chr1A 532090234 A/G + A G CT - RAC875_rep_c95460_302 chr1A 532246897 T/G NA NA NA AC NA flanks do not match reference at this position IACX1873 chr1A 532251781 A/G + A G CT - BS00087588_51 chr1A 532253659 A/G + G A AG + Kukri_c84024_375 chr1A 532745534 A/G - T C AG - RAC875_c32848_578 chr1A 532920739 T/C NA NA NA AG NA flanks do not match reference at this position BobWhite_c26122_129 chr1A 533141060 T/C + T C CT + CAP7_c4879_249 chr1A 533254365 A/C + A C AC + BS00028146_51 chr1A 533445272 A/G + G A AG + BS00011934_51 chr1A 533447516 T/C - G A AG + Kukri_c45512_193 chr1A 533902154 T/C - A G CT - RAC875_c15975_1208 chr1A 533902931 A/G - T C AG - BS00012042_51 chr1A 534242444 T/C - G A CT - BS00009104_51 chr1A 534265561 T/C + C T CT + RAC875_c102343_204 chr1A 534271958 A/G + A G CT - BS00110130_51 chr1A 535027905 A/G + A G CT - BS00022239_51 chr1A 535027925 T/C + T C CT + BS00088350_51 chr1A 535314781 T/C + C T CT + RAC875_c25814_361 chr1A 535324125 A/G - C T CT + BS00022396_51 chr1A 535434598 T/C - A G AG + BS00081002_51 chr1A 535434774 T/C - G A AG + Ex_c4060_510 chr1A 536431376 T/C + T C AG - RAC875_c6798_467 chr1A 536431377 A/G + G A CT - BS00022261_51 chr1A 536439290 A/G - C T AG - BS00109991_51 chr1A 536439290 T/C + C T AG - Excalibur_c47013_1503 chr1A 536963507 T/G + T G AC - BS00073413_51 chr1A 537082527 T/G + T G GT + RAC875_c120509_133 chr1A 537355984 T/C + T C AG - RAC875_c23168_480 chr1A 537965047 T/C + T C CT + GENE-0069_468 chr1A 537974262 A/G - C T CT + Excalibur_c97157_65 chr1A 539702744 T/C - A G CT - Kukri_c24570_282 chr1A 539964528 T/G - A C GT - Kukri_c7119_392 chr1A 540051171 T/C NA NA NA AG NA flanks do not match reference at this position IACX5994 chr1A 540051810 T/C - G A AG + IAAV544 chr1A 540143911 T/C + T C CT + Ra_c110766_321 chr1A 540336630 A/G + A G CT - Ku_c8992_405 chr1A 540403832 A/G - C T AG - RAC875_rep_c105766_652 chr1A 541469213 A/G + G A CT - Tdurum_contig56158_60 chr1A 541631356 T/C + C T CT + RAC875_c12348_720 chr1A 541632726 A/G - C T AG - RFL_Contig5334_831 chr1A 541990759 A/G + A G AG + RFL_Contig5334_1969 chr1A 541991897 T/C + C T AG - GENE-0033_233 chr1A 542003136 T/C - A G AG + Tdurum_contig96086_74 chr1A 542825309 T/C - G A AG + BobWhite_c41272_159 chr1A 542825339 A/G - T C CT + Kukri_s117372_152 chr1A 543959973 A/G + G A AG + BS00095510_51 chr1A 543961441 T/C + T C AG - BS00023935_51 chr1A 544054745 A/G - C T CT + Ex_c2226_244 chr1A 544054925 T/C - A G CT - BS00078085_51 chr1A 544055675 T/C + T C CT + RAC875_c32379_216 chr1A 544160240 A/C - G T GT + BS00070580_51 chr1A 544170135 A/G - C T AG - BS00110877_51 chr1A 544367564 T/C - G A AG + tplb0059d21_1032 chr1A 544374255 T/C - G A CT - BS00023203_51 chr1A 544378391 T/C + T C CT + BS00037976_51 chr1A 544391456 T/C + T C AG - BS00066278_51 chr1A 544431360 A/G - C T AG - BS00064349_51 chr1A 544431362 T/C - A G CT - Tdurum_contig15015_883 chr1A 544604437 A/G + A G CT - IACX14 chr1A 544605146 T/G - A C AC + BobWhite_c24825_349 chr1A 545888499 A/G NA NA NA AG NA flanks do not match reference at this position BS00036104_51 chr1A 545891035 A/G + G A CT - RAC875_c60162_129 chr1A 545891327 A/G + A G AG + RAC875_c60162_206 chr1A 545891404 A/G + G A CT - IAAV3650 chr1A 546036276 T/C - G A AG + Tdurum_contig75762_406 chr1A 546037075 A/G - C T CT + Ra_c29200_300 chr1A 546044483 A/C + C A AC + Excalibur_c54842_340 chr1A 546212974 A/C + A C AC + Tdurum_contig5711_242 chr1A 546520061 A/G - T C CT + BS00067119_51 chr1A 547906982 A/G + A G CT - Ku_c3523_1959 chr1A 547964005 T/C - A G CT - Tdurum_contig15639_225 chr1A 547964538 A/G + A G CT - BS00034899_51 chr1A 548941327 A/G + A G AG + RAC875_c16824_202 chr1A 549313790 A/G - T C AG - Tdurum_contig81642_298 chr1A 549638226 T/C - G A CT - Ra_c8027_1021 chr1A 549704338 A/G + A G AG + RAC875_c49433_308 chr1A 549842398 T/C + T C AG - BobWhite_rep_c49755_131 chr1A 550342866 T/C + T C CT + Jagger_c468_53 chr1A 550344021 A/G + G A AG + BS00030043_51 chr1A 550441969 A/C + C A AC + IAAV3695 chr1A 551322194 A/G NA NA NA AG NA flanks do not match reference at this position Ra_c5683_1762 chr1A 551461696 T/C - A G CT - BS00063612_51 chr1A 551462727 T/C + C T AG - JD_c285_1438 chr1A 551484519 A/G - T C CT + Kukri_c47131_569 chr1A 551532529 T/G + T G AC - Kukri_c51735_79 chr1A 552166194 A/G + A G CT - Excalibur_rep_c68706_1084 chr1A 554531407 A/G + G A AG + Excalibur_s103715_85 chr1A 556299741 A/C - T G AC - Jagger_c4380_159 chr1A 556299761 T/G + G T GT + RAC875_c17188_1696 chr1A 556941882 T/C - A G CT - RAC875_c15593_1421 chr1A 556942196 A/G - T C AG - Tdurum_contig56662_54 chr1A 557932890 A/G + A G CT - BobWhite_c46857_82 chr1A 558185399 T/C + C T CT + Tdurum_contig80278_250 chr1A 558185399 A/G - C T AG - Kukri_c67703_174 chr1A 558261471 A/G + A G AG + RAC875_c21673_641 chr1A 558261773 A/G + G A CT - RAC875_rep_c69152_184 chr1A 558479792 T/C - A G AG + RAC875_rep_c108284_98 chr1A 558514317 A/G NA NA NA AG NA flanks do not match reference at this position BS00072408_51 chr1A 558536628 T/C + T C CT + BS00066659_51 chr1A 558540826 T/C - G A AG + Tdurum_contig78830_348 chr1A 558977996 A/G + A G CT - Tdurum_contig30664_181 chr1A 560178250 T/G + T G GT + BS00056547_51 chr1A 560463557 T/C + T C AG - Tdurum_contig13516_251 chr1A 563684557 T/C + T C AG - Jagger_c6772_80 chr1A 564392648 T/C - G A AG + Excalibur_c1936_1072 chr1A 564749321 A/C - T G AC - BobWhite_c19182_280 chr1A 566480170 A/G - T C AG - Tdurum_contig18174_283 chr1A 566484733 T/C + C T CT + Excalibur_c23598_1502 chr1A 567976450 A/G - T C AG - Kukri_rep_c102102_273 chr1A 567977890 T/C - A G AG + RAC875_rep_c71093_1070 chr1A 568012820 A/G + A G AG + tplb0021i12_383 chr1A 568025609 A/G + A G CT - GENE-0208_1096 chr1A 568415991 T/G + G T AC - Kukri_c51781_199 chr1A 568547561 A/C - T G GT + tplb0030a05_2386 chr1A 569450170 A/G - T C AG - CAP12_c8163_118 chr1A 569466040 A/G + G A CT - Excalibur_c16947_114 chr1A 570449923 A/G - T C CT + Kukri_c2338_533 chr1A 570860046 A/G + G A AG + IAAV5567 chr1A 571269932 A/C - G T GT + Tdurum_contig8224_378 chr1A 571291310 T/C - G A CT - BobWhite_c37358_208 chr1A 571788143 T/C - G A CT - Tdurum_contig25612_195 chr1A 571788203 T/G - C A GT - BS00070560_51 chr1A 571789226 T/C + C T CT + CAP12_c3758_112 chr1A 571789641 A/C - G T AC - Excalibur_c66_147 chr1A 572350838 A/G + A G CT - Tdurum_contig81011_244 chr1A 572350933 T/C + T C AG - BobWhite_c11692_148 chr1A 573060743 T/G - A C AC + IAAV5949 chr1A 573322123 T/C NA NA NA CT NA flanks do not match reference at this position RFL_Contig3683_1784 chr1A 574338192 T/G - A C AC + RFL_Contig3683_668 chr1A 574339988 A/G - C T CT + BobWhite_c6664_644 chr1A 574935671 T/C + T C CT + IAAV4820 chr1A 575215821 T/C + T C AG - BobWhite_c39668_143 chr1A 576637173 A/G + G A AG + BS00023114_51 chr1A 577079120 T/C + C T CT + BS00106641_51 chr1A 577079132 T/C + T C CT + BS00022824_51 chr1A 577474214 T/C - A G CT - Ex_c3201_1046 chr1A 579299146 A/G + G A CT - IACX11266 chr1A 579830285 T/G + T G AC - IAAV3040 chr1A 579830525 A/G - C T CT + BS00011521_51 chr1A 579830592 A/G + G A CT - GENE-0514_210 chr1A 579865401 T/G + NA NA GT NA reference base A not among SNP alleles BS00021990_51 chr1A 580422511 A/C + C A AC + Kukri_c310_1953 chr1A 580424851 T/C + T C CT + Tdurum_contig70803_475 chr1A 580445849 T/C + T C AG - RAC875_c52947_84 chr1A 580495866 T/C + C T AG - Kukri_c65610_572 chr1A 580496867 A/G + A G CT - Tdurum_contig84252_155 chr1A 580496867 T/C - A G CT - CAP11_c1500_171 chr1A 581543310 A/G - T C AG - Tdurum_contig29886_139 chr1A 581585512 A/G - T C AG - RAC875_c1295_1603 chr1A 581828955 T/C - G A CT - BS00107935_51 chr1A 581828997 A/C - G T AC - Ku_c23222_204 chr1A 581830231 T/C - G A AG + Ra_c1295_635 chr1A 581830231 T/C - G A AG + Excalibur_c85499_232 chr1A 582219377 A/G - T C CT + BS00065694_51 chr1A 582222910 T/C + T C AG - Excalibur_c5838_110 chr1A 582710343 A/G - T C CT + BS00065170_51 chr1A 582749075 T/C + T C CT + RAC875_rep_c71278_345 chr1A 582865100 A/C - T G GT + BS00011892_51 chr1A 582865993 A/G + G A AG + RAC875_rep_c117660_128 chr1A 582867001 A/G + A G CT - IAAV4238 chr1A 582867126 A/G - C T AG - RAC875_c24317_1015 chr1A 582870070 T/C - A G CT - Kukri_c44201_497 chr1A 583291151 A/G - C T CT + Kukri_c61874_273 chr1A 583363900 T/C + T C AG - Kukri_c17412_1249 chr1A 583660309 A/G - C T AG - RAC875_c62550_470 chr1A 583894984 T/C + C T CT + RAC875_c43002_382 chr1A 584469326 T/C - G A CT - BS00056823_51 chr1A 584478751 A/C - G T AC - BobWhite_c20073_382 chr1A 584674117 T/G + G T AC - BS00024107_51 chr1A 584674133 A/G - T C AG - BobWhite_c20073_443 chr1A 584674178 A/G + G A AG + Excalibur_c98273_114 chr1A 585984332 T/G - A C GT - BS00070991_51 chr1A 586913972 A/G + A G CT - BS00070695_51 chr1A 586914403 A/G - T C CT + BS00022514_51 chr1A 586951988 T/C - A G CT - Kukri_c44500_315 chr1A 586952125 T/C - A G AG + BS00011947_51 chr1A 586952934 A/C - T G AC - Excalibur_c27376_74 chr1A 586953792 T/C - A G CT - tplb0053c24_1496 chr1A 586953813 A/G + G A CT - BobWhite_c1027_1127 chr1A 586993772 A/G - C T CT + BS00035273_51 chr1A 587360579 T/C - A G CT - IAAV8446 chr1A 587839840 A/G - C T CT + Tdurum_contig13681_286 chr1A 588297283 A/G + G A AG + Excalibur_rep_c103373_763 chr1A 588298717 T/C - A G CT - BS00011508_51 chr1A 588301413 A/G + A G AG + Excalibur_c6476_521 chr1A 588767571 A/G - T C CT + RAC875_c57566_61 chr1A 588902936 T/C - A G AG + BobWhite_c33208_98 chr1A 588903530 T/G - A C GT - RAC875_rep_c105487_241 chr1A 589023798 A/G - T C AG - BobWhite_c44947_277 chr1A 589023953 T/C - G A CT - RAC875_c2258_1526 chr1A 589042651 T/G + G T GT + RAC875_rep_c120646_120 chr1A 589054783 T/C NA NA NA AG NA flanks do not match reference at this position IACX6022 chr1A 589055795 A/G - T C AG - BS00054271_51 chr1A 589445376 A/G - T C CT + BobWhite_rep_c63205_215 chr1A 589450985 T/C + C T AG - BS00023417_51 chr1A 589475303 A/G - C T CT + BobWhite_rep_c63205_143 chr1A 589476498 T/C + C T AG - BS00067458_51 chr1A 589871232 A/C + A C GT - IAAV1301 chr1A 589874499 T/G + T G AC - Excalibur_c1255_293 chr1A 590002741 T/C - A G CT - BS00067741_51 chr1A 590003251 T/C + C T CT + RAC875_c29059_648 chr1A 591090300 A/G + G A AG + RAC875_rep_c106093_670 chr1A 591091610 A/G - T C AG - RAC875_c50996_1179 chr1A 591093643 T/C - A G AG + RAC875_c43389_105 chr1A 591095673 T/C + T C AG - BS00096930_51 chr1A 591147317 A/G - C T AG - RAC875_c85550_52 chr1A 591147481 A/G + G A AG + RAC875_c85550_73 chr1A 591147502 T/C + C T AG - CAP7_c1295_62 chr1A 591147606 A/G - C T CT + RFL_Contig2961_1493 chr1A 591613619 T/C - A G CT - RFL_Contig2961_1117 chr1A 591613995 T/G - A C AC + BS00021780_51 chr1A 591950271 A/G + G A CT - RAC875_rep_c106094_766 chr1A 592313102 A/G - T C CT + BobWhite_c66315_505 chr1A 592313453 T/C NA NA NA AG NA flanks do not match reference at this position Ku_c72511_106 chr1A 593301298 A/G NA NA NA CT NA flanks do not match reference at this position tplb0059i08_441 chr1A 593549127 T/C - A G AG + BS00026180_51 chr1B 168820 T/G NA NA NA GT NA flanks do not match reference at this position BS00022180_51 chr1B 1203959 T/C - G A AG + BS00093078_51 chr1B 1204018 T/C - A G CT - Excalibur_c12376_569 chr1B 1251530 T/C + C T CT + Kukri_c44369_131 chr1B 1419786 T/G - A C AC + BS00071161_51 chr1B 1533524 T/C + C T AG - BS00071333_51 chr1B 4094809 A/G - C T AG - BS00022504_51 chr1B 4345605 A/G - T C AG - BS00022505_51 chr1B 4347120 T/G - A C AC + BS00030667_51 chr1B 4348407 T/C - A G AG + Kukri_rep_c106834_139 chr1B 4349202 T/C - G A CT - BS00083177_51 chr1B 4349558 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c24163_155 chr1B 4518651 A/G - T C CT + BS00082565_51 chr1B 5175904 T/C + C T AG - BS00022482_51 chr1B 5176140 T/C + C T AG - BS00111170_51 chr1B 5694748 T/C + C T CT + RAC875_c32874_1164 chr1B 7991143 T/G + G T AC - TA006040-0724 chr1B 7995246 A/G - T C CT + Excalibur_c43567_850 chr1B 7995547 T/C + C T AG - IAAV392 chr1B 8254504 A/C + C A GT - BS00065487_51 chr1B 8559397 A/G + A G CT - BS00022429_51 chr1B 8559748 A/G + G A CT - IAAV3430 chr1B 8676676 T/C + C T CT + BS00005004_51 chr1B 8676778 T/G + T G GT + CAP12_c1619_54 chr1B 9088713 A/G + A G CT - Kukri_c36151_170 chr1B 9555802 A/G + A G CT - Tdurum_contig47083_278 chr1B 10103946 A/G + A G CT - RAC875_c78751_587 chr1B 10204845 A/G - T C CT + BS00103677_51 chr1B 10359531 A/C - T G AC - BS00110900_51 chr1B 10361105 A/G - T C AG - BS00068429_51 chr1B 10367413 A/G + G A AG + BS00032266_51 chr1B 11181523 T/C - G A CT - BS00006820_51 chr1B 11634673 A/G + A G AG + Kukri_c1312_666 chr1B 11859136 T/G + T G AC - RAC875_c63624_753 chr1B 11859589 T/C + T C AG - Ku_c1312_1194 chr1B 11859756 T/C + T C AG - RAC875_c63624_1040 chr1B 11859970 A/G + G A CT - BS00064829_51 chr1B 12813274 T/C - G A CT - Kukri_c76307_259 chr1B 14099157 A/C + C A GT - Tdurum_contig58525_304 chr1B 14152715 T/G - C A GT - BS00025964_51 chr1B 14510779 A/G + A G AG + BS00025965_51 chr1B 14510793 T/C + C T AG - BS00064398_51 chr1B 14655682 T/C + T C AG - GENE-0387_81 chr1B 14845572 A/G + G A AG + GENE-0815_140 chr1B 15142230 T/C + T C AG - Tdurum_contig76266_134 chr1B 15166195 T/C + C T CT + Kukri_rep_c69476_479 chr1B 15167620 T/C - A G CT - Tdurum_contig44219_318 chr1B 15169636 T/G + T G AC - Excalibur_rep_c116725_184 chr1B 15170932 A/G + A G AG + BS00105846_51 chr1B 15284528 T/C + T C CT + BS00108057_51 chr1B 15439285 T/C - G A CT - BS00089524_51 chr1B 15448151 A/C - T G AC - Kukri_c38845_821 chr1B 15449308 T/C - G A AG + BS00074962_51 chr1B 15658684 T/C - A G AG + BS00011695_51 chr1B 15745304 A/G - C T CT + RAC875_c5243_479 chr1B 15745720 A/G - C T AG - RAC875_c5243_206 chr1B 15745993 T/C - A G AG + RFL_Contig5906_985 chr1B 16217521 A/G + G A AG + Excalibur_c11666_134 chr1B 16850238 T/C + T C AG - Ku_c31363_2165 chr1B 17356503 A/C + A C GT - Tdurum_contig75546_247 chr1B 17691709 T/C - G A AG + Excalibur_c48622_109 chr1B 17790154 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c15942_571 chr1B 17790722 T/C + T C CT + Excalibur_c38281_82 chr1B 17796931 A/G NA NA NA AG NA flanks do not match reference at this position IAAV8117 chr1B 17812440 T/C - A G CT - IAAV4194 chr1B 17891522 T/C - A G AG + Tdurum_contig78972_316 chr1B 18419737 A/G + G A AG + BS00090770_51 chr1B 20589199 T/C - A G AG + Tdurum_contig29484_628 chr1B 20589379 T/C - G A AG + RAC875_c50835_124 chr1B 20589384 T/C - G A AG + BS00012052_51 chr1B 20591237 T/C - A G CT - BS00037387_51 chr1B 21843255 T/C + C T CT + BS00096770_51 chr1B 22074227 A/G - T C AG - BS00096769_51 chr1B 22074391 A/G - C T AG - BobWhite_c3661_88 chr1B 26135275 A/G - T C AG - Tdurum_contig44861_581 chr1B 26185906 A/C + C A GT - IAAV1518 chr1B 26186266 A/C + C A AC + Tdurum_contig44861_1253 chr1B 26186660 A/C + A C AC + Kukri_c38587_263 chr1B 26784234 T/C + T C AG - Kukri_c19251_579 chr1B 26970730 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c9309_145 chr1B 26970730 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c30974_65 chr1B 26970762 A/G + G A CT - BS00110463_51 chr1B 28485961 T/G + T G AC - Tdurum_contig61410_467 chr1B 28561000 T/C - A G AG + IACX7219 chr1B 28561252 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BobWhite_rep_c55186_299 chr1B 28561331 T/C + T C CT + Tdurum_contig61324_305 chr1B 28562237 T/C - A G CT - Tdurum_contig56188_569 chr1B 28563830 T/C - A G AG + IAAV7541 chr1B 28563888 T/C - G A AG + BS00004789_51 chr1B 28763553 A/G - T C CT + RAC875_c140_872 chr1B 30730709 A/G - C T CT + RAC875_c140_650 chr1B 30730931 T/C - G A CT - RAC875_c65864_437 chr1B 30731012 T/C - G A CT - Tdurum_contig45142_240 chr1B 30736929 T/C + C T CT + Tdurum_contig62213_423 chr1B 31379174 T/G + T G AC - Tdurum_contig9874_547 chr1B 32766585 T/C - G A CT - BS00022320_51 chr1B 37727517 A/G + G A CT - BS00065053_51 chr1B 38833879 T/C + T C AG - IAAV6525 chr1B 38911363 A/G - T C AG - BS00022590_51 chr1B 38911422 A/G + G A CT - Kukri_c47342_73 chr1B 39382990 A/G + A G AG + BS00067003_51 chr1B 39545430 T/C - G A CT - BS00106306_51 chr1B 39579722 T/C + T C CT + Kukri_c5221_506 chr1B 39583766 A/G + G A CT - RAC875_c1825_188 chr1B 39849668 T/C + T C AG - CAP12_c2714_164 chr1B 39852685 T/C + T C CT + IAAV7611 chr1B 39853060 T/G + G T GT + Kukri_rep_c100936_449 chr1B 40199660 T/C NA NA NA CT NA flanks do not match reference at this position BS00097523_51 chr1B 41086904 T/C - A G AG + Tdurum_contig55639_241 chr1B 41642360 A/G + A G AG + IAAV2838 chr1B 41642534 T/C - G A CT - BS00012068_51 chr1B 41744136 A/G NA NA NA CT NA flanks do not match reference at this position BS00065005_51 chr1B 42014449 A/G - C T AG - BS00064929_51 chr1B 42014857 T/C + T C AG - IACX6800 chr1B 42349326 A/G + A G CT - Tdurum_contig11334_554 chr1B 43321931 T/C + C T CT + Excalibur_c95656_129 chr1B 44933639 T/C - G A CT - Kukri_rep_c102900_1715 chr1B 45737545 T/C - G A CT - IAAV7845 chr1B 45737800 T/C - A G AG + RAC875_c90169_393 chr1B 47509385 T/C - G A AG + GENE-3653_580 chr1B 47636135 T/C - A G CT - BS00059502_51 chr1B 48347108 A/G - C T AG - RAC875_rep_c107325_644 chr1B 49881688 A/G - T C AG - Tdurum_contig30113_214 chr1B 50183768 A/G + G A AG + BS00084021_51 chr1B 50184168 T/C - G A AG + IACX502 chr1B 50184440 T/C + T C CT + BS00031417_51 chr1B 50186234 T/C - G A CT - BS00087784_51 chr1B 50777978 T/C + C T AG - BS00087787_51 chr1B 50778599 T/C + C T CT + Excalibur_c26936_636 chr1B 50778634 T/C + C T CT + Ra_c16879_977 chr1B 52405029 T/G - C A AC + Ra_c11488_297 chr1B 52899823 A/G + G A CT - BS00087133_51 chr1B 52900668 A/G + G A CT - BS00022604_51 chr1B 52900698 T/C + C T AG - IACX14648 chr1B 53050976 T/C + C T AG - RFL_Contig1081_570 chr1B 53051649 T/G NA NA NA GT NA flanks do not match reference at this position Tdurum_contig26281_139 chr1B 53248119 A/C - G T GT + Tdurum_contig82187_189 chr1B 53248886 T/G - A C GT - Excalibur_c5065_566 chr1B 54877019 A/G + G A AG + Excalibur_c28016_132 chr1B 56312043 A/G - T C AG - Kukri_c7886_195 chr1B 56314696 T/C + T C AG - IAAV7704 chr1B 56317014 T/C + T C CT + Kukri_c23300_267 chr1B 56879637 A/G - T C CT + Tdurum_contig75938_1546 chr1B 57003478 A/G + A G CT - BS00110546_51 chr1B 57085453 A/G - C T CT + BS00022319_51 chr1B 57430608 T/C - G A CT - IACX18625 chr1B 57712563 A/C + A C AC + Kukri_c6300_347 chr1B 57713154 T/C + T C CT + RAC875_rep_c109416_191 chr1B 58324264 T/C - A G CT - CAP8_rep_c9642_82 chr1B 58324563 A/G + G A AG + Excalibur_c17202_1833 chr1B 58325006 A/G + G A AG + Kukri_rep_c108299_221 chr1B 58754108 A/G - T C CT + Kukri_c40439_366 chr1B 59196975 A/C - T G AC - BS00099829_51 chr1B 59601361 T/G + T G GT + RAC875_c79370_378 chr1B 61668401 A/G - T C CT + Tdurum_contig16351_389 chr1B 63052891 T/C - A G AG + RAC875_c47884_100 chr1B 63054112 T/C + T C CT + Kukri_c25654_382 chr1B 67015050 A/C - T G AC - Kukri_c53962_102 chr1B 67021731 T/C - A G AG + BS00022902_51 chr1B 67540776 A/G - T C AG - Kukri_c3414_114 chr1B 68083993 T/C - A G CT - Kukri_rep_c107771_588 chr1B 68250105 T/G - C A GT - BS00023056_51 chr1B 69542780 A/G - T C AG - Tdurum_contig25384_255 chr1B 69825054 A/G - T C AG - IACX13974 chr1B 69826657 T/C - G A CT - BS00083533_51 chr1B 69906201 T/C + C T CT + Kukri_c7129_227 chr1B 69907086 A/G - C T CT + Tdurum_contig25732_112 chr1B 70192635 T/C + T C CT + Kukri_c5861_360 chr1B 70327929 T/C + C T AG - GENE-4777_662 chr1B 70328484 A/C + C A AC + BS00022745_51 chr1B 70711155 A/G - C T CT + Kukri_c4587_3422 chr1B 74232758 A/G + G A AG + BS00057730_51 chr1B 82310867 T/C - A G CT - Excalibur_c20863_318 chr1B 84962212 A/G + A G CT - Excalibur_c45655_318 chr1B 86705875 A/G + G A AG + BS00093231_51 chr1B 86808418 A/G - C T CT + Tdurum_contig100344_184 chr1B 87188376 A/C - T G GT + Tdurum_contig100344_160 chr1B 87188400 T/G - A C GT - BS00022916_51 chr1B 87733219 T/C - A G AG + RAC875_c82888_83 chr1B 87971145 A/G + A G CT - BS00084305_51 chr1B 90992756 T/G - C A GT - BS00084304_51 chr1B 90992761 T/C - A G CT - TA001473-0980 chr1B 90993340 A/G - T C CT + IAAV2366 chr1B 91557574 A/G + A G CT - BS00004453_51 chr1B 91557706 T/C + T C CT + BS00094467_51 chr1B 92871733 T/C + T C CT + BS00094469_51 chr1B 92871752 T/C + C T CT + IAAV9176 chr1B 93914996 T/G + T G GT + Excalibur_c20610_149 chr1B 94226739 A/G + A G AG + BS00067800_51 chr1B 94467646 A/G + G A CT - Kukri_c7647_1122 chr1B 94831734 T/C + T C AG - RAC875_c10659_570 chr1B 94832206 A/G - T C AG - BS00023058_51 chr1B 95234832 A/G - T C CT + RAC875_c63067_283 chr1B 95655004 T/C - A G AG + IAAV3666 chr1B 95667992 A/C - T G GT + IAAV6464 chr1B 96593056 A/G - T C AG - Tdurum_contig26338_65 chr1B 97376605 A/G - T C AG - IAAV2324 chr1B 97378545 A/G - T C AG - GENE-1623_147 chr1B 98168686 A/C + C A GT - RAC875_rep_c108757_136 chr1B 98722133 T/C + C T AG - BS00022736_51 chr1B 98722333 T/C NA NA NA AG NA flanks do not match reference at this position BS00069316_51 chr1B 98904265 T/C - G A AG + Kukri_c5299_462 chr1B 99597976 A/G - T C AG - BS00098730_51 chr1B 101222401 T/C + C T AG - Excalibur_c42346_236 chr1B 101223048 A/G + G A CT - JD_c6297_810 chr1B 104465437 A/C - G T AC - IAAV7575 chr1B 104468910 T/C - A G CT - Tdurum_contig14418_1242 chr1B 104469643 T/C + T C CT + IACX6397 chr1B 104721285 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Ku_c2189_853 chr1B 104772277 T/C - G A AG + BS00040513_51 chr1B 105697340 A/G + A G CT - RAC875_c5052_211 chr1B 106681724 A/G - T C AG - BobWhite_c27577_234 chr1B 106765393 T/G - A C AC + BS00001364_51 chr1B 106765881 A/C + C A AC + BS00095478_51 chr1B 106790959 T/C - A G AG + BS00095477_51 chr1B 106791021 A/G - C T AG - Excalibur_c24105_135 chr1B 106791066 A/C - T G AC - Kukri_c26973_189 chr1B 107133489 A/G + A G AG + RAC875_c46581_420 chr1B 107133549 T/C + T C CT + RAC875_rep_c69176_194 chr1B 107134223 A/G + A G AG + BobWhite_rep_c49610_521 chr1B 107135640 A/C - G T AC - BobWhite_rep_c50112_99 chr1B 107136537 T/C + C T AG - BS00049927_51 chr1B 108837080 T/G + G T GT + GENE-0403_266 chr1B 109728590 T/C + T C CT + GENE-0403_110 chr1B 109728703 A/C - G T AC - IAAV798 chr1B 109729114 T/C + C T AG - Kukri_rep_c108883_577 chr1B 109729544 A/G + A G AG + GENE-0025_120 chr1B 111260808 A/G - T C AG - IACX20130 chr1B 111368261 T/C - A G CT - IAAV2848 chr1B 111368318 T/C - G A AG + Ku_c5960_496 chr1B 112203158 T/C - A G CT - Tdurum_contig19251_352 chr1B 112864468 A/C + C A GT - Tdurum_contig20702_229 chr1B 113821034 T/G + G T GT + Kukri_c17540_394 chr1B 115278874 A/G + A G AG + Tdurum_contig30966_336 chr1B 115278877 A/G + A G CT - BS00069054_51 chr1B 115285439 A/G - T C AG - BS00088767_51 chr1B 115958139 T/C + T C AG - BS00081969_51 chr1B 117170205 A/C - T G AC - Excalibur_c7954_672 chr1B 117170355 A/G - C T AG - Tdurum_contig11065_1593 chr1B 117181118 A/G - T C CT + Tdurum_contig11065_1551 chr1B 117181256 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig11065_1319 chr1B 117182969 A/G - T C AG - Ku_c3695_1696 chr1B 117188767 A/G + G A AG + tplb0026b15_350 chr1B 117386221 A/C + A C GT - Tdurum_contig12173_284 chr1B 117392227 A/C - T G GT + Ex_c40520_1484 chr1B 119048438 T/C + C T CT + Ku_c11706_149 chr1B 119049270 A/G - C T CT + IAAV4559 chr1B 119099271 A/C + A C AC + Excalibur_c89515_95 chr1B 119683299 A/C - T G GT + BS00004981_51 chr1B 119766088 A/G + A G AG + BS00093945_51 chr1B 119767741 A/G + G A AG + BS00093946_51 chr1B 119767769 A/G + A G CT - BS00084722_51 chr1B 119885986 A/G + A G CT - IAAV7043 chr1B 120405775 T/C - A G CT - BS00093740_51 chr1B 120884051 A/G - C T CT + BS00093736_51 chr1B 120884188 T/G - C A GT - BS00010992_51 chr1B 122356281 T/C + T C CT + BS00107597_51 chr1B 123343351 A/G - T C CT + RAC875_c8849_134 chr1B 123965328 T/C - A G CT - BS00064498_51 chr1B 129999130 A/G - T C CT + Kukri_c34902_520 chr1B 130010868 T/C - A G AG + Kukri_c6135_150 chr1B 130017054 A/G - T C CT + RAC875_c47137_112 chr1B 130347891 A/G + A G AG + BS00005034_51 chr1B 130361313 A/G + A G AG + BS00038368_51 chr1B 130636853 T/G - A C GT - RFL_Contig1952_781 chr1B 132062167 T/C + T C AG - BS00087988_51 chr1B 132937686 T/C + T C CT + BS00073034_51 chr1B 136645760 T/C + C T AG - GENE-4436_150 chr1B 136649960 T/C - A G CT - RFL_Contig1567_2182 chr1B 137633486 T/C - A G CT - BS00083306_51 chr1B 137634367 T/C - A G CT - JD_c1532_462 chr1B 137645821 A/G + G A AG + BS00040342_51 chr1B 139671172 A/G - T C CT + BS00098306_51 chr1B 140295811 A/C - T G AC - Excalibur_rep_c101400_111 chr1B 140296571 T/G - A C AC + GENE-0121_95 chr1B 140296980 T/C NA NA NA CT NA flanks do not match reference at this position CAP11_c3367_77 chr1B 142298888 T/G - C A GT - RFL_Contig2670_718 chr1B 142522964 T/C - A G CT - Kukri_c42522_155 chr1B 144122247 A/G - T C AG - GENE-4608_406 chr1B 144274391 A/C + C A GT - BS00035690_51 chr1B 144931518 A/G + G A CT - BobWhite_c5757_260 chr1B 145453121 A/G + G A AG + BS00022507_51 chr1B 145456159 A/C - T G AC - BS00083237_51 chr1B 145456214 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_c42764_741 chr1B 145720288 T/G - A C GT - Kukri_c9105_1184 chr1B 146616088 A/G - C T CT + IACX5712 chr1B 148898293 A/G - T C CT + IAAV268 chr1B 148898320 A/C - T G GT + Kukri_rep_c68615_94 chr1B 149601483 A/G + A G AG + GENE-0189_45 chr1B 150367827 T/C + T C AG - BS00033738_51 chr1B 151468637 T/C - A G AG + GENE-0489_91 chr1B 151470333 T/C + C T CT + Excalibur_c10528_347 chr1B 153594557 T/C + T C CT + BobWhite_c29659_339 chr1B 154598791 T/C + C T CT + BS00093102_51 chr1B 155407575 A/G - C T AG - BS00093096_51 chr1B 155410966 T/C - G A CT - Kukri_c15901_1064 chr1B 156584811 T/C NA NA NA CT NA flanks do not match reference at this position BS00022593_51 chr1B 156595462 T/C - G A CT - BS00066165_51 chr1B 157901588 A/G - C T CT + IACX6356 chr1B 157902077 T/C - G A AG + tplb0053b16_1030 chr1B 157925597 T/C - A G CT - Tdurum_contig42092_1244 chr1B 159184541 T/G + T G AC - RAC875_c21598_248 chr1B 159388580 A/G - C T AG - GENE-0366_124 chr1B 159917045 T/G - C A AC + GENE-0466_416 chr1B 160322679 T/C - A G AG + BobWhite_c12695_394 chr1B 161212085 T/C + T C CT + Tdurum_contig10663_267 chr1B 161985094 T/C NA NA NA CT NA flanks do not match reference at this position BS00087939_51 chr1B 162781464 A/G + A G CT - GENE-0456_190 chr1B 162811359 T/G - A C AC + GENE-0456_163 chr1B 162811378 A/G - T C AG - BS00022625_51 chr1B 163096591 A/G - T C CT + BobWhite_s63351_73 chr1B 165818096 A/G + A G CT - BS00106579_51 chr1B 166078375 A/G - C T AG - BS00092426_51 chr1B 166590988 A/G + A G CT - BS00087444_51 chr1B 166593040 T/C - A G CT - BS00087441_51 chr1B 166593762 A/G - T C CT + RAC875_rep_c109118_164 chr1B 166657399 T/C - A G CT - Excalibur_c25624_679 chr1B 166658846 A/G + A G AG + BS00109001_51 chr1B 167108654 A/G - T C CT + BS00023185_51 chr1B 167108667 T/C - A G AG + BobWhite_rep_c53595_274 chr1B 167713691 T/C + T C CT + BS00063080_51 chr1B 169531788 T/C + T C CT + BS00081963_51 chr1B 169662016 A/G - T C AG - Kukri_rep_c115647_349 chr1B 171045019 A/C + A C GT - GENE-2762_144 chr1B 173975504 T/C - A G AG + BS00066990_51 chr1B 178027669 T/C + C T CT + BobWhite_c25389_615 chr1B 182198796 T/C + T C CT + D_GBF1XID01AROUO_311 chr1B 183267574 A/G - T C AG - Tdurum_contig13709_252 chr1B 183452129 A/C + A C AC + BS00091632_51 chr1B 186802399 T/C + T C AG - GENE-0040_121 chr1B 187210003 T/C + T C CT + Excalibur_rep_c112996_167 chr1B 187210342 T/C + T C AG - TA005710-0827 chr1B 187210692 T/C NA NA NA AG NA flanks do not match reference at this position BS00095751_51 chr1B 188262383 T/C + C T CT + RAC875_c14902_256 chr1B 188457502 A/G + A G CT - BS00015169_51 chr1B 189715536 T/G - A C GT - TA003235-0794 chr1B 189716006 T/C + T C CT + Kukri_c18305_873 chr1B 191666683 A/C - T G GT + Kukri_c29541_416 chr1B 191667162 A/C - T G AC - Kukri_c19709_383 chr1B 191706988 T/C - A G CT - RAC875_c1276_717 chr1B 192278871 T/C - A G AG + BS00027514_51 chr1B 193630173 A/G + A G AG + RAC875_c82649_146 chr1B 195558040 A/G - T C CT + Tdurum_contig13095_97 chr1B 195560078 T/G - A C GT - GENE-0181_607 chr1B 195593744 A/G + G A AG + BobWhite_c3771_441 chr1B 196462209 A/G + A G AG + BS00066398_51 chr1B 197291973 A/G - T C CT + BS00035794_51 chr1B 198644405 A/G - C T AG - Kukri_c17055_189 chr1B 199010877 T/G + T G GT + GENE-0433_66 chr1B 199574935 T/C - A G CT - RAC875_c25100_89 chr1B 199575738 T/C - A G CT - IAAV3801 chr1B 200300152 A/G + G A CT - BS00003758_51 chr1B 201757079 A/C + A C AC + Excalibur_c24859_517 chr1B 201924460 A/G + A G CT - Kukri_c51925_654 chr1B 203692704 A/G NA NA NA CT NA flanks do not match reference at this position BS00091993_51 chr1B 207272492 A/G + A G AG + Kukri_rep_c111568_656 chr1B 213911987 T/C + C T CT + Excalibur_c18009_66 chr1B 218421464 T/C - A G CT - GENE-2766_500 chr1B 223800576 T/C + C T CT + GENE-2795_120 chr1B 228171316 A/C - T G AC - Kukri_rep_c105316_262 chr1B 230943785 T/G - A C AC + GENE-0431_601 chr1B 234251783 T/C + C T AG - BS00109910_51 chr1B 234251835 T/C - G A AG + BS00019225_51 chr1B 234252086 T/C - G A AG + RFL_Contig4059_310 chr1B 249236238 A/G + G A AG + Kukri_c13598_1552 chr1B 252970726 T/C - A G CT - D_F5XZDLF01D3SI3_114 chr1B 254472937 T/G - C A AC + tplb0029e19_1870 chr1B 256212312 T/C - A G CT - RAC875_c29054_192 chr1B 260838900 A/C - T G GT + RAC875_c2341_1450 chr1B 263561008 A/G + G A AG + Kukri_c27690_411 chr1B 275457423 T/C - A G AG + Ex_c19477_336 chr1B 277765153 A/G - T C CT + IACX8452 chr1B 278092397 T/C - A G CT - Excalibur_c6497_535 chr1B 278473846 A/G + G A AG + BS00066443_51 chr1B 278687062 T/C - G A CT - BS00088264_51 chr1B 280167375 T/G + T G GT + tplb0059c20_2221 chr1B 281033084 A/G - C T AG - BS00023302_51 chr1B 281037224 A/G + G A AG + BS00066309_51 chr1B 282051713 A/G + A G AG + BS00066040_51 chr1B 282134142 T/C - G A CT - BS00077353_51 chr1B 282277101 T/C - G A CT - BS00073373_51 chr1B 282277219 A/G - C T AG - BS00065139_51 chr1B 282427911 T/C - A G AG + CAP8_c4506_82 chr1B 283904572 A/G + A G AG + BS00062770_51 chr1B 285336384 A/G - T C CT + BS00050126_51 chr1B 285345287 T/C - G A AG + GENE-0379_108 chr1B 286611959 T/C - G A AG + Excalibur_c41211_311 chr1B 286710182 T/C - A G CT - BS00050457_51 chr1B 288395934 T/C - A G CT - Kukri_c13537_2069 chr1B 288548176 A/C - T G GT + Excalibur_c56657_282 chr1B 290814000 A/G + G A CT - BobWhite_rep_c66146_237 chr1B 297114998 T/G + T G AC - Tdurum_contig31624_230 chr1B 297728896 A/C - G T GT + IACX7921 chr1B 299974461 A/G - T C AG - GENE-0173_309 chr1B 300575266 A/G - T C CT + GENE-0173_290 chr1B 300575281 T/C - A G CT - GENE-0173_168 chr1B 300575398 A/G - T C CT + Tdurum_contig60547_330 chr1B 300576796 T/C - A G AG + Tdurum_contig60547_129 chr1B 300576997 T/C - G A CT - Kukri_c31093_387 chr1B 304510265 T/C - A G CT - Ku_c11813_215 chr1B 307428422 T/G - C A GT - BobWhite_c13761_242 chr1B 313275636 A/G + G A AG + RAC875_c36859_235 chr1B 321682250 T/C NA NA NA CT NA flanks do not match reference at this position TA003382-0407 chr1B 324790716 T/C + T C CT + Tdurum_contig45715_549 chr1B 325286251 A/G + G A CT - Tdurum_contig45715_1246 chr1B 325286948 A/G + G A AG + Excalibur_c18876_334 chr1B 325286967 T/C - G A CT - RAC875_c8662_762 chr1B 327023404 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c51643_145 chr1B 327024193 A/G + A G CT - Excalibur_c27675_912 chr1B 327577718 T/C - A G AG + BS00022104_51 chr1B 327958039 A/G + G A AG + CAP7_c1241_128 chr1B 328439865 T/C - A G AG + tplb0029b01_123 chr1B 328642115 A/C + A C AC + BobWhite_c1456_615 chr1B 328642344 T/C - A G CT - tplb0029b01_1022 chr1B 328645331 T/C + T C AG - Ex_c24969_223 chr1B 328820781 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c9495_322 chr1B 329487285 T/C + T C AG - BobWhite_c22266_315 chr1B 329489647 T/C - G A CT - Ku_c28949_178 chr1B 332081835 T/G + T G AC - BS00073603_51 chr1B 333208165 A/G - C T AG - BobWhite_c15603_69 chr1B 333491504 T/C + T C AG - IAAV7757 chr1B 333491504 A/G - T C CT + BobWhite_c4126_442 chr1B 333602776 A/G + G A CT - BS00022670_51 chr1B 334549394 A/C - T G AC - RAC875_c44575_561 chr1B 336070019 T/C - A G AG + RAC875_c44575_396 chr1B 336070184 A/G - T C CT + Kukri_c30982_1173 chr1B 336210260 A/G + A G CT - RAC875_rep_c95069_54 chr1B 336647904 T/C - A G CT - BS00022632_51 chr1B 336648686 T/C + T C AG - RAC875_rep_c70803_1442 chr1B 340372963 A/G + A G AG + IACX8300 chr1B 341931499 T/C - A G AG + GENE-0405_237 chr1B 342647516 T/C + T C CT + CAP8_rep_c7560_159 chr1B 388011591 T/C - G A AG + Kukri_rep_c69674_605 chr1B 388757276 A/G + A G CT - IAAV3905 chr1B 396531147 A/G + A G CT - Kukri_c61766_907 chr1B 409627975 T/G - C A AC + BS00078228_51 chr1B 430168568 A/C - T G AC - BS00022089_51 chr1B 431457603 A/G - C T CT + BS00033681_51 chr1B 432116737 T/C + C T CT + JD_c6360_288 chr1B 432821849 T/C + T C AG - GENE-0136_82 chr1B 434564647 T/G - C A GT - Tdurum_contig48171_189 chr1B 437551468 A/G + G A AG + TA003801-1144 chr1B 442171115 T/G NA NA NA GT NA flanks do not match reference at this position Tdurum_contig28668_124 chr1B 442204884 A/G - C T CT + BS00022133_51 chr1B 443997720 A/C + C A AC + Ra_c71973_691 chr1B 443998525 A/C + C A AC + tplb0023b14_704 chr1B 445180564 T/G - A C GT - BS00073132_51 chr1B 447165536 A/G - T C CT + BS00032364_51 chr1B 447166794 A/G + A G CT - Tdurum_contig70304_781 chr1B 447323307 A/G - C T CT + Kukri_c4951_503 chr1B 449131796 A/G + G A AG + Kukri_rep_c106158_230 chr1B 449706111 A/G + A G CT - Ku_c6201_2890 chr1B 452316860 A/G + G A AG + RAC875_rep_c74070_518 chr1B 453343908 A/G NA NA NA CT NA flanks do not match reference at this position CAP12_c1981_78 chr1B 456185328 A/G - C T CT + BS00069723_51 chr1B 456253786 T/G + T G GT + RAC875_s105188_92 chr1B 456975829 T/G + G T AC - Ra_c3083_982 chr1B 457320821 A/G + A G AG + IAAV5704 chr1B 457460601 T/C - G A AG + Kukri_c75097_56 chr1B 458265142 T/C - A G CT - BobWhite_c346_253 chr1B 458385723 T/C + C T AG - RAC875_c51240_89 chr1B 459814868 A/G + A G AG + Kukri_c34894_112 chr1B 459925099 A/G + G A AG + IAAV2287 chr1B 460146752 T/G + G T AC - Kukri_c38105_452 chr1B 461298765 A/G - T C CT + Ra_c45721_2630 chr1B 461299197 T/C - A G AG + GENE-1150_214 chr1B 462795886 T/C + C T AG - BobWhite_c28635_896 chr1B 465589388 A/G + A G CT - IAAV8763 chr1B 466092832 T/C + T C AG - Tdurum_contig76481_798 chr1B 469974997 T/C + T C CT + Kukri_rep_c69810_502 chr1B 469976477 T/C NA NA NA CT NA flanks do not match reference at this position IACX15424 chr1B 469978497 A/C - T G GT + BobWhite_c1967_175 chr1B 470000713 T/C + T C CT + Tdurum_contig57183_581 chr1B 470000713 A/G - T C CT + BS00095568_51 chr1B 470000745 T/C + C T CT + BobWhite_c1967_388 chr1B 470002812 A/G + A G CT - Tdurum_contig57183_368 chr1B 470002812 T/C - A G CT - BobWhite_rep_c64920_402 chr1B 471193698 T/G + G T GT + Tdurum_contig56874_562 chr1B 471194010 T/C + T C CT + Tdurum_contig60052_184 chr1B 473529137 T/C - A G CT - Ra_c26829_375 chr1B 474259775 A/G + G A AG + Excalibur_s102212_259 chr1B 474448016 A/G + A G CT - CAP7_s12849_67 chr1B 474449437 A/G + A G AG + CAP8_c9553_109 chr1B 474449502 T/C + T C AG - Kukri_c67707_114 chr1B 474451762 A/C - T G GT + Tdurum_contig44255_814 chr1B 476019795 T/C + C T CT + RFL_Contig1601_750 chr1B 476033847 A/G + A G CT - GENE-0142_178 chr1B 476034083 A/G - C T AG - CAP7_c3456_113 chr1B 476034836 T/C - A G AG + Excalibur_rep_c105376_485 chr1B 476877866 T/C NA NA NA CT NA flanks do not match reference at this position BS00023142_51 chr1B 476880006 T/C - G A AG + Tdurum_contig15593_407 chr1B 476881818 A/G - T C AG - Tdurum_contig28316_243 chr1B 477394125 T/C - A G AG + Tdurum_contig28316_228 chr1B 477394140 T/G - A C GT - RAC875_c56417_377 chr1B 477403703 T/C + T C CT + Excalibur_c16154_246 chr1B 478566749 A/G + A G AG + BS00067146_51 chr1B 480821449 T/C + T C CT + Ra_c68984_1882 chr1B 480974301 A/G + G A AG + IAAV9039 chr1B 481709170 T/C - G A CT - RFL_Contig3343_2115 chr1B 481864554 A/G NA NA NA AG NA flanks do not match reference at this position IAAV7936 chr1B 483115229 T/G - A C AC + GENE-0165_389 chr1B 483292127 T/C - G A CT - Excalibur_c49906_242 chr1B 484360928 T/G - C A GT - IACX2578 chr1B 484366301 A/G + A G AG + BS00083072_51 chr1B 484376941 T/C + T C AG - BS00089313_51 chr1B 484889867 T/C - A G CT - Tdurum_contig98080_171 chr1B 486846450 T/C - A G CT - Tdurum_contig59449_400 chr1B 487407412 T/G - A C AC + Tdurum_contig59449_249 chr1B 487407563 T/C - A G CT - Excalibur_c90096_77 chr1B 487489153 A/C - G T GT + GENE-0107_807 chr1B 488217103 T/C + C T AG - BS00023001_51 chr1B 488658936 T/C - A G AG + IACX3408 chr1B 489134006 T/G + G T AC - BS00041355_51 chr1B 489994213 T/C + C T AG - Ku_c20478_390 chr1B 490452820 A/C - T G AC - tplb0024i15_1754 chr1B 491087439 T/C + T C CT + BS00022920_51 chr1B 492787435 T/C - A G AG + RAC875_c31261_367 chr1B 492861427 T/C - G A AG + IAAV6731 chr1B 493868052 A/C + C A AC + BS00022619_51 chr1B 494159127 T/C + T C AG - Ra_c37969_549 chr1B 494159220 T/C + T C AG - IAAV2125 chr1B 494160056 T/G - C A AC + RAC875_rep_c112555_200 chr1B 494160056 A/C + C A AC + TA003725-0553 chr1B 496095847 A/G + A G AG + RAC875_rep_c119728_146 chr1B 497781369 A/G + A G AG + Tdurum_contig81102_102 chr1B 497781690 A/G + A G CT - Excalibur_c5218_75 chr1B 497799279 T/C + C T AG - IAAV9005 chr1B 497821096 A/G NA NA NA CT NA flanks do not match reference at this position CAP11_c2974_53 chr1B 505068590 A/G - T C CT + BS00039583_51 chr1B 505072938 T/G - C A AC + Excalibur_c34625_281 chr1B 508554009 A/G + A G CT - Ku_c1571_1457 chr1B 510980080 T/C - A G CT - Tdurum_contig60509_232 chr1B 510980575 T/C - A G CT - Kukri_c13188_256 chr1B 511213188 T/C - G A CT - CAP12_c2759_111 chr1B 512631396 A/C - T G AC - BS00103166_51 chr1B 512631564 T/C NA NA NA AG NA flanks do not match reference at this position BobWhite_c20015_225 chr1B 512633667 A/G + A G CT - BS00022842_51 chr1B 513483315 T/C - A G AG + Tdurum_contig56276_226 chr1B 513483315 A/G + A G CT - BobWhite_c15312_405 chr1B 513545212 A/G + G A AG + GENE-0004_635 chr1B 515450328 A/G NA NA NA AG NA flanks do not match reference at this position BS00022124_51 chr1B 516951346 A/G + G A CT - Tdurum_contig58301_336 chr1B 518182733 A/C + C A GT - Tdurum_contig63834_340 chr1B 518914698 T/G - C A GT - Kukri_c4376_388 chr1B 520684201 A/G + G A AG + RAC875_c6701_291 chr1B 520785574 A/G - T C AG - BS00072982_51 chr1B 520810802 A/C + A C AC + Kukri_c22155_1010 chr1B 520926006 T/C - G A AG + CAP7_c12162_251 chr1B 521218985 A/G + G A AG + Tdurum_contig50473_889 chr1B 521225061 A/G + G A AG + Ex_c5858_1681 chr1B 526263978 A/G + A G AG + Ra_c25590_1406 chr1B 527001435 T/C + T C AG - CAP12_c424_402 chr1B 529855126 T/C + C T CT + BS00022742_51 chr1B 530061223 A/G - T C AG - GENE-0410_71 chr1B 530472849 A/C + NA NA GT NA reference base T not among SNP alleles Tdurum_contig31102_299 chr1B 530478729 A/G + A G AG + BS00000066_51 chr1B 530480819 T/C + T C AG - Kukri_c559_193 chr1B 530668798 A/G - C T CT + IACX9622 chr1B 530959358 C/G - C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00010130_51 chr1B 530959475 A/G - T C AG - IACX11291 chr1B 530959658 T/C - G A AG + BS00106626_51 chr1B 531166995 A/G + A G CT - BobWhite_c11338_605 chr1B 531211554 A/G - T C AG - BS00012250_51 chr1B 532163387 A/G + A G AG + IACX11029 chr1B 532163387 T/C - A G AG + BS00010399_51 chr1B 532163685 A/C + A C AC + Excalibur_c48379_461 chr1B 532166911 T/C - A G AG + Excalibur_c23992_436 chr1B 532169159 T/C - G A AG + Kukri_rep_c104054_174 chr1B 532170382 A/G NA NA NA CT NA flanks do not match reference at this position Ex_c102909_778 chr1B 532173004 T/C + T C AG - Excalibur_rep_c82767_175 chr1B 534669727 T/C - A G CT - RFL_Contig4977_2333 chr1B 535546089 A/G - T C CT + CAP12_c1129_220 chr1B 535797784 A/G - C T CT + Kukri_c73734_175 chr1B 540720886 T/C + C T AG - Excalibur_c40993_1129 chr1B 540730073 T/C + T C AG - Excalibur_c11333_1192 chr1B 541002882 T/C + T C CT + CAP8_c4452_431 chr1B 542431974 A/G + A G AG + BS00038643_51 chr1B 542927171 T/C - G A AG + GENE-0480_265 chr1B 543015744 A/G + A G CT - Tdurum_contig83770_218 chr1B 543473932 T/C + T C CT + RAC875_c32077_284 chr1B 544130232 T/C + T C CT + Excalibur_c52120_132 chr1B 544132366 T/C + T C AG - IAAV3567 chr1B 545207215 A/G - T C CT + Ku_c3647_2429 chr1B 545208141 T/C - A G CT - Tdurum_contig25457_175 chr1B 545644664 T/C - A G AG + Kukri_rep_c111676_103 chr1B 545800733 A/C - G T GT + BS00068083_51 chr1B 546273043 T/C - G A AG + Tdurum_contig892_633 chr1B 547584013 A/G + A G AG + Tdurum_contig64811_332 chr1B 547975222 A/G - C T CT + Tdurum_contig64811_273 chr1B 547975281 T/C - G A AG + IAAV4729 chr1B 548197511 T/C + C T CT + RAC875_c3835_782 chr1B 548536104 T/C - A G CT - IAAV6383 chr1B 548623129 T/C - G A CT - Ex_c402_1223 chr1B 548623161 T/G - A C GT - Tdurum_contig42797_1576 chr1B 548623161 A/C + A C GT - RAC875_c1045_445 chr1B 548623447 A/G + A G CT - Ku_c892_425 chr1B 548624113 T/C - G A CT - Tdurum_contig42797_2922 chr1B 548624512 A/G + G A CT - IAAV8432 chr1B 548625682 T/C - A G CT - Tdurum_contig42797_4145 chr1B 548625682 A/G + A G CT - JD_c13631_863 chr1B 548626063 T/C - G A AG + Excalibur_c17977_71 chr1B 548626629 T/C + C T CT + Ku_c4348_862 chr1B 548674813 T/C - A G CT - Tdurum_contig42749_3287 chr1B 548675711 A/G - C T CT + Tdurum_contig44540_510 chr1B 548679433 A/G + G A AG + Kukri_c66451_128 chr1B 548902916 A/C + C A AC + Excalibur_c4459_1867 chr1B 548967662 A/G - T C AG - Kukri_c1918_1074 chr1B 548968557 A/G + A G AG + Excalibur_rep_c66322_448 chr1B 548970158 A/C + A C AC + BS00096719_51 chr1B 551010161 T/C + C T AG - GENE-0120_431 chr1B 551013025 T/C - G A AG + RAC875_c95548_156 chr1B 551033002 T/C + C T CT + Kukri_rep_c111991_498 chr1B 553019391 T/C - A G CT - Excalibur_c8188_693 chr1B 553020410 T/C - A G AG + BS00093475_51 chr1B 553143367 T/C + T C CT + BobWhite_c48550_198 chr1B 553143807 T/C - A G CT - Tdurum_contig42755_1086 chr1B 553143807 A/G + A G CT - BS00067769_51 chr1B 554137239 T/C + T C CT + BobWhite_c35484_282 chr1B 554746320 T/G + T G AC - Excalibur_c6892_274 chr1B 555638068 T/G - A C GT - IACX4461 chr1B 555639681 T/C - G A AG + BobWhite_rep_c57575_65 chr1B 555641132 T/C - A G CT - BS00081396_51 chr1B 555933420 T/G - C A GT - BS00107749_51 chr1B 555939466 A/G + G A CT - CAP8_c818_370 chr1B 557943819 T/G + T G GT + tplb0048b10_1365 chr1B 559966736 A/G - T C AG - BS00089563_51 chr1B 560252498 A/C NA NA NA AC NA flanks do not match reference at this position BS00082071_51 chr1B 560494580 A/G + G A CT - Tdurum_contig48523_1838 chr1B 560504455 T/C + C T AG - Tdurum_contig64955_285 chr1B 561505842 T/C + C T AG - GENE-0315_356 chr1B 561506328 A/G NA NA NA AG NA flanks do not match reference at this position GENE-0315_211 chr1B 561506470 T/C - G A AG + RAC875_c24895_311 chr1B 561507333 A/C - G T AC - Kukri_rep_c113407_250 chr1B 561507702 T/G + G T AC - Kukri_c45852_78 chr1B 562375738 T/C - G A AG + Kukri_c25138_1155 chr1B 562458248 A/G - C T AG - BS00021710_51 chr1B 562893037 A/G - T C AG - BS00001835_51 chr1B 563028672 T/C NA NA NA AG NA flanks do not match reference at this position BS00101437_51 chr1B 563030044 T/C - G A AG + Excalibur_c60931_1260 chr1B 563030530 T/C + C T CT + Ku_c207_1431 chr1B 563304282 T/G NA NA NA AC NA flanks do not match reference at this position BS00063092_51 chr1B 563307053 A/C - G T AC - BS00076405_51 chr1B 563537174 T/G + G T GT + Ku_c106533_550 chr1B 563675235 A/G - T C AG - JD_c107_683 chr1B 563675946 T/C - A G AG + Tdurum_contig8158_269 chr1B 564162746 A/G + G A AG + BS00003934_51 chr1B 564909041 A/G + G A CT - RAC875_c55891_659 chr1B 564909233 A/G + A G CT - RAC875_c55891_712 chr1B 564909286 T/C + T C AG - Tdurum_contig57101_1616 chr1B 565334980 T/C - G A AG + Excalibur_c14911_466 chr1B 565669407 T/C + T C AG - Excalibur_c14911_976 chr1B 565669914 T/C + T C CT + Tdurum_contig42852_667 chr1B 565672749 A/G - C T CT + Kukri_c7770_176 chr1B 566603733 A/G + G A CT - Tdurum_contig47550_699 chr1B 566603733 T/C - G A CT - BobWhite_c11044_322 chr1B 566687552 T/C + C T AG - Tdurum_contig85620_467 chr1B 566687552 A/G - C T AG - Tdurum_contig85620_277 chr1B 566687742 T/C - A G AG + Tdurum_contig604_71 chr1B 566762497 A/C + C A AC + Tdurum_contig604_356 chr1B 566762782 T/C + C T AG - BS00075248_51 chr1B 566827314 T/C - G A AG + BS00075247_51 chr1B 566827320 A/G - T C CT + IACX11320 chr1B 566831296 T/C + T C AG - Kukri_c15391_468 chr1B 566831512 A/G + A G AG + Tdurum_contig52782_382 chr1B 566837536 A/G + G A CT - Tdurum_contig30517_578 chr1B 566838457 T/C - A G CT - Tdurum_contig30517_310 chr1B 566838725 T/C - A G AG + Excalibur_c112015_118 chr1B 566838895 T/C - G A CT - Kukri_rep_c103359_233 chr1B 568522753 T/C + T C CT + Kukri_c39698_228 chr1B 568522799 A/G + G A AG + Excalibur_c10496_651 chr1B 568965187 A/C NA NA NA AC NA flanks do not match reference at this position BobWhite_c43917_288 chr1B 568965779 A/G - T C AG - BobWhite_c5812_440 chr1B 568968795 T/C - A G CT - Excalibur_rep_c114983_53 chr1B 570276455 A/G - T C AG - BS00031596_51 chr1B 570483855 T/C + T C CT + Excalibur_c45119_251 chr1B 570484704 T/C - G A CT - Kukri_c9133_534 chr1B 570841018 A/G + G A AG + Kukri_c9133_2211 chr1B 570842695 A/G + G A CT - Kukri_c13043_1084 chr1B 571060292 A/G - C T CT + BS00086083_51 chr1B 571060426 A/G + G A AG + Kukri_c13043_832 chr1B 571060544 A/G - C T AG - Ex_c11930_509 chr1B 571176061 T/C - G A AG + RAC875_c275_229 chr1B 571437111 T/C + T C CT + Ku_c956_1797 chr1B 571439522 A/G + A G AG + BS00050882_51 chr1B 571707456 T/C - G A CT - RFL_Contig2686_571 chr1B 572288338 A/C - T G GT + CAP12_c2858_94 chr1B 572288558 T/C - G A CT - RFL_Contig2686_285 chr1B 572288624 T/G - C A GT - RAC875_c28041_460 chr1B 572296693 T/C + C T CT + RAC875_c36559_1994 chr1B 572296980 A/G - C T AG - IAAV2757 chr1B 572642654 T/G + T G GT + Excalibur_c51898_470 chr1B 572674875 A/G - T C CT + Tdurum_contig13117_1316 chr1B 573571920 T/C - A G AG + IAAV4569 chr1B 575726204 A/G + A G AG + Kukri_c25961_108 chr1B 575863850 A/G + A G CT - Kukri_c25961_166 chr1B 575863908 A/G + G A AG + IAAV2683 chr1B 575867598 T/C NA NA NA AG NA flanks do not match reference at this position IACX6346 chr1B 575867949 C/G - C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c87950_333 chr1B 577178630 T/C - A G AG + BS00063973_51 chr1B 577970537 A/G + A G AG + BS00067627_51 chr1B 580538027 A/G - C T AG - Kukri_c8143_355 chr1B 581201928 T/C + T C CT + Kukri_c9752_793 chr1B 581205643 A/G + G A AG + Tdurum_contig69792_167 chr1B 581205643 T/C - G A AG + Jagger_c7242_85 chr1B 581413100 T/C - G A CT - TA004264-0825 chr1B 581691835 A/G + A G AG + Excalibur_c27915_560 chr1B 581698067 T/C - G A AG + RAC875_rep_c105168_114 chr1B 582547580 A/G + A G AG + Kukri_c20486_255 chr1B 582715231 A/G + G A CT - Kukri_c51864_225 chr1B 582906917 T/C + C T AG - BS00076394_51 chr1B 583091745 A/G - C T CT + Kukri_c7657_986 chr1B 583147130 T/C - A G AG + Kukri_c7657_651 chr1B 583147550 A/G NA NA NA CT NA flanks do not match reference at this position BS00022551_51 chr1B 583446335 T/C + T C CT + Kukri_c5336_365 chr1B 584109033 T/C + C T AG - Kukri_c1932_300 chr1B 584147579 T/C + C T CT + BS00022789_51 chr1B 584156338 A/G + A G CT - Kukri_c22635_562 chr1B 586306188 A/G - T C AG - BS00026338_51 chr1B 587525603 T/C + C T AG - BS00065750_51 chr1B 588484110 T/C + C T AG - BS00069125_51 chr1B 588484644 A/G + A G CT - BS00066855_51 chr1B 588487021 T/C + T C AG - BS00004328_51 chr1B 588503942 A/G + A G AG + IACX6404 chr1B 588503942 T/C - A G AG + RFL_Contig7_380 chr1B 588505669 T/C - G A CT - RAC875_c62171_386 chr1B 588627542 A/C - T G GT + Ku_c28580_432 chr1B 588627558 T/C + C T AG - Ex_c69066_186 chr1B 588629220 T/C + T C CT + Excalibur_rep_c69066_270 chr1B 588629807 T/C + C T CT + IAAV2855 chr1B 588632435 T/C - A G CT - BobWhite_c15152_341 chr1B 589061492 T/C + C T CT + Kukri_c42202_271 chr1B 589068764 A/G + G A AG + BobWhite_c17644_456 chr1B 589071333 T/G - C A GT - RAC875_rep_c99365_219 chr1B 589073509 A/G + G A AG + BS00107589_51 chr1B 589074146 T/G - C A AC + BS00023148_51 chr1B 589074170 T/C - G A CT - Excalibur_rep_c106078_822 chr1B 589133879 A/G - T C CT + BS00073257_51 chr1B 589489117 T/C + C T CT + CAP7_c1490_115 chr1B 589897282 A/G - C T CT + BobWhite_c39656_106 chr1B 589919596 A/C - G T AC - BS00010436_51 chr1B 591109944 A/G - C T AG - IACX9046 chr1B 591109944 T/C + C T AG - BS00010148_51 chr1B 591110060 T/C - G A AG + Ku_c9909_1766 chr1B 592028866 T/G - A C GT - Excalibur_rep_c103592_955 chr1B 594140446 T/C + T C CT + CAP7_c9506_174 chr1B 597152694 T/C + T C CT + BS00069341_51 chr1B 598879585 T/C + T C CT + RAC875_c39401_229 chr1B 599339511 A/G + G A CT - BS00023071_51 chr1B 599340399 A/G + A G AG + RAC875_c52957_154 chr1B 600890308 A/C - T G AC - Excalibur_c44818_109 chr1B 600890454 T/C + C T AG - Kukri_c13978_132 chr1B 600890863 A/G - C T CT + RFL_Contig2176_1163 chr1B 600891075 A/G - T C AG - RFL_Contig2176_1111 chr1B 600891127 T/C - A G AG + RFL_Contig2176_932 chr1B 600891306 T/C - G A AG + BS00064162_51 chr1B 601007240 T/C - A G CT - BobWhite_c16206_317 chr1B 603217960 T/C + T C CT + Excalibur_rep_c107047_93 chr1B 603301191 A/C + A C GT - Excalibur_rep_c107047_469 chr1B 603302106 T/C + T C AG - Excalibur_rep_c107047_605 chr1B 603302242 A/G + G A CT - Tdurum_contig96049_200 chr1B 603753358 T/G - A C AC + IACX886 chr1B 604551793 A/G - T C AG - Excalibur_rep_c107035_354 chr1B 608994780 A/C - T G GT + Excalibur_rep_c101787_89 chr1B 608996427 A/G - T C AG - BS00072289_51 chr1B 610041187 T/C - G A AG + Kukri_rep_c104113_252 chr1B 611928605 A/C + A C GT - BS00023940_51 chr1B 613421889 T/C - A G AG + Tdurum_contig10362_555 chr1B 614331697 T/C - A G AG + Tdurum_contig10362_328 chr1B 614331924 A/G - T C CT + IACX906 chr1B 614451966 T/G + G T GT + Kukri_c19247_53 chr1B 614452510 A/G + A G AG + TA003586-0637 chr1B 614455638 A/G + A G AG + Kukri_c19247_711 chr1B 614455731 A/G + G A AG + Kukri_c30461_857 chr1B 614791406 T/C - A G AG + RFL_Contig2736_827 chr1B 615112103 T/C - G A CT - BS00022577_51 chr1B 615125928 A/G - C T AG - GENE-0506_129 chr1B 615126043 A/G + A G AG + Excalibur_c28045_741 chr1B 619259268 A/G - C T AG - Kukri_c11389_232 chr1B 619683453 A/G - C T AG - Kukri_c11389_59 chr1B 619683626 T/C - G A CT - IAAV8459 chr1B 619686519 T/C - G A CT - BS00022851_51 chr1B 619687954 A/G - T C AG - BS00095088_51 chr1B 619687982 A/G - C T CT + Ku_c16636_347 chr1B 619690185 A/G - T C AG - BS00021680_51 chr1B 619691966 A/G - C T CT + RAC875_c64190_212 chr1B 619692239 A/G NA NA NA AG NA flanks do not match reference at this position Ku_c79340_308 chr1B 619694168 T/C - G A CT - Kukri_c14733_486 chr1B 620704925 A/G - C T AG - IACX8117 chr1B 621270398 A/T + T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00067024_51 chr1B 621634610 T/G - A C AC + BS00063928_51 chr1B 621636668 A/C + C A GT - BS00022530_51 chr1B 622313964 A/G - C T AG - RAC875_c4908_1539 chr1B 622466441 A/C - T G AC - RAC875_c43945_807 chr1B 622476334 A/C NA NA NA GT NA flanks do not match reference at this position RFL_Contig2826_548 chr1B 622571889 A/G - C T CT + Excalibur_rep_c96924_118 chr1B 623713032 T/C + C T CT + BobWhite_c8016_301 chr1B 623722595 T/C - A G CT - RAC875_c1785_366 chr1B 623729825 A/G - T C AG - RFL_Contig5937_1677 chr1B 623730562 A/G + A G CT - RFL_Contig5937_1699 chr1B 623730584 T/C + C T CT + RAC875_c47427_235 chr1B 623731465 T/C + T C CT + BS00083060_51 chr1B 623731578 T/C + C T CT + BS00081749_51 chr1B 623762444 A/C + C A GT - Excalibur_c40808_441 chr1B 623833230 T/C - A G CT - Excalibur_c66196_256 chr1B 625569841 T/C + C T AG - Tdurum_contig41945_748 chr1B 626070817 T/C - G A AG + BobWhite_c16543_993 chr1B 626085821 A/C + A C AC + Tdurum_contig57479_236 chr1B 626103927 A/G + G A AG + RAC875_c66649_186 chr1B 626707542 T/C + C T CT + BobWhite_c9881_1312 chr1B 626713829 T/C NA NA NA AG NA flanks do not match reference at this position BS00076330_51 chr1B 626724382 T/C NA NA NA AG NA flanks do not match reference at this position BS00074328_51 chr1B 626725810 T/C - G A CT - Tdurum_contig67368_157 chr1B 627926616 A/G - T C CT + Tdurum_contig65853_242 chr1B 628514341 A/G + A G AG + BS00034450_51 chr1B 628514633 A/G NA NA NA CT NA flanks do not match reference at this position Tdurum_contig65853_534 chr1B 628514633 T/C NA NA NA CT NA flanks do not match reference at this position BS00072791_51 chr1B 629262992 A/G - T C CT + BS00022249_51 chr1B 629486985 A/G + A G CT - BS00096498_51 chr1B 629942046 T/C - A G CT - RAC875_c15190_1089 chr1B 630063072 A/G - C T AG - BobWhite_c20621_683 chr1B 630831693 A/G - C T CT + IACX4411 chr1B 630831715 T/C - G A AG + BobWhite_rep_c54139_273 chr1B 630926745 T/C - A G AG + Ra_c17685_927 chr1B 631718534 T/C + C T CT + Excalibur_c56999_109 chr1B 631833543 T/C + T C CT + BobWhite_c13124_430 chr1B 632001831 T/C + T C CT + BS00067526_51 chr1B 632010298 T/C - G A CT - CAP12_c5744_162 chr1B 632010532 A/G + A G CT - RAC875_c839_352 chr1B 632421098 A/G - T C AG - Kukri_c66214_59 chr1B 632753937 T/G + T G GT + Excalibur_c37496_271 chr1B 633138250 T/C + T C CT + RAC875_c46093_492 chr1B 633333021 T/C + C T CT + Tdurum_contig16606_648 chr1B 633333228 T/C + T C CT + BS00068327_51 chr1B 634415717 T/C + T C AG - RAC875_c27001_579 chr1B 635138148 T/C + C T CT + Kukri_c18109_475 chr1B 636264023 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c18109_649 chr1B 636264197 A/G + G A AG + Kukri_c18109_682 chr1B 636264230 T/C + T C CT + RAC875_c7357_1107 chr1B 636264290 T/C + T C CT + RAC875_c13258_955 chr1B 636738140 A/G - T C AG - BS00039135_51 chr1B 636753103 A/C - G T AC - Kukri_c5357_323 chr1B 637621743 T/G - A C GT - tplb0043a07_1521 chr1B 637621986 T/G - A C GT - tplb0043a07_880 chr1B 637622627 T/C - G A AG + Ra_c7324_527 chr1B 637622965 T/C - A G CT - BS00084216_51 chr1B 637826066 T/C - A G CT - BS00022539_51 chr1B 637826131 T/C - G A CT - Excalibur_c10111_127 chr1B 637826164 T/C - G A AG + Excalibur_c10111_85 chr1B 637826206 T/C - G A CT - tplb0034e16_925 chr1B 637827898 T/C + T C CT + IAAV2619 chr1B 637944902 A/G + A G CT - BS00094237_51 chr1B 638015205 T/C + C T AG - CAP11_c6406_104 chr1B 638015592 T/C + T C AG - IAAV1683 chr1B 640156966 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig10036_1614 chr1B 640157750 T/C - G A CT - Tdurum_contig10036_1044 chr1B 640159543 A/C NA NA NA AC NA flanks do not match reference at this position Excalibur_c11980_619 chr1B 640555451 A/G - C T CT + BobWhite_c2027_84 chr1B 640555610 T/C - A G CT - Kukri_c39223_871 chr1B 640556048 T/G - C A AC + Kukri_c39223_831 chr1B 640556088 T/C - G A AG + Tdurum_contig93532_89 chr1B 640559444 A/G + A G AG + TA004946-0577 chr1B 640560322 T/C NA NA NA CT NA flanks do not match reference at this position BS00069044_51 chr1B 640612495 A/G - T C AG - Excalibur_c96904_336 chr1B 640640045 A/G + G A CT - GENE-0371_208 chr1B 640848925 A/C + A C GT - TA002362-0954 chr1B 640848925 T/G - A C AC + Tdurum_contig42491_750 chr1B 640849257 A/G + A G AG + JD_c954_2440 chr1B 640850028 A/G + G A AG + BobWhite_c19733_301 chr1B 641552717 A/G - C T AG - Kukri_c21276_1056 chr1B 641632290 A/G - T C AG - Kukri_c21276_816 chr1B 641632530 A/C - T G AC - Excalibur_c63885_115 chr1B 641632868 A/G + G A AG + IAAV5863 chr1B 642476653 A/G + G A AG + RAC875_c818_1185 chr1B 642677953 T/C + T C CT + IAAV7428 chr1B 642678709 A/G + A G AG + Ex_c25733_348 chr1B 642770705 A/C + C A AC + BS00021876_51 chr1B 643096075 A/G - T C AG - IACX6230 chr1B 643101623 C/G - C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00084895_51 chr1B 643101627 A/G - T C AG - Excalibur_c25597_508 chr1B 643102204 T/C - A G CT - Excalibur_c42301_54 chr1B 643257877 T/C + T C AG - Tdurum_contig50988_500 chr1B 645514214 A/G - C T CT + BS00109244_51 chr1B 645571197 A/G - T C CT + BobWhite_c23617_167 chr1B 645571377 A/C - T G GT + Excalibur_c8585_701 chr1B 645571418 T/C + T C CT + Jagger_c3757_131 chr1B 645571972 A/G - T C AG - Tdurum_contig11216_942 chr1B 645572033 A/G + A G AG + BS00099794_51 chr1B 645708079 A/G + A G CT - RFL_Contig1823_1044 chr1B 645708159 T/C + C T AG - RAC875_c15625_520 chr1B 646167476 T/C - A G CT - CAP7_c199_62 chr1B 646167658 A/G - C T CT + Kukri_c57725_146 chr1B 646167745 T/C - A G AG + BobWhite_c294_450 chr1B 646167801 A/G NA NA NA AG NA flanks do not match reference at this position BS00070285_51 chr1B 646171937 A/G + A G AG + BS00002484_51 chr1B 646172198 A/G - T C AG - Tdurum_contig28853_142 chr1B 647228147 T/C + C T AG - BS00022678_51 chr1B 651544458 T/G + G T AC - Excalibur_c49496_705 chr1B 652453983 T/C - G A CT - BS00068077_51 chr1B 652468844 A/G + A G AG + BS00035267_51 chr1B 652576198 T/C + C T CT + RFL_Contig2971_282 chr1B 653185450 A/C + A C GT - IACX2984 chr1B 653185853 A/C + A C GT - BobWhite_c40868_120 chr1B 653875439 T/C - G A AG + BobWhite_c14362_86 chr1B 653888017 A/G - T C CT + Tdurum_contig8840_575 chr1B 654027223 T/C - A G AG + Tdurum_contig8840_540 chr1B 654027258 T/C - G A CT - Tdurum_contig8840_237 chr1B 654028044 T/C - A G CT - BS00028476_51 chr1B 654809149 A/G - T C CT + BS00023173_51 chr1B 655781639 A/G - C T CT + BS00045568_51 chr1B 655798556 A/G - T C CT + tplb0034p10_1134 chr1B 656235242 T/C - A G AG + BS00077831_51 chr1B 656852347 A/G + G A AG + CAP11_c2892_176 chr1B 657272889 T/C - A G CT - Excalibur_c250_2008 chr1B 657418661 T/G + G T GT + RFL_Contig4352_926 chr1B 657422182 A/G + A G AG + BS00075130_51 chr1B 658482895 A/C + A C GT - RAC875_c49225_66 chr1B 658498380 T/C + T C CT + GENE-0129_214 chr1B 658530620 A/C + C A GT - RAC875_rep_c111494_195 chr1B 658531012 T/C + C T AG - BobWhite_c39901_338 chr1B 658531715 T/C + C T CT + Kukri_c36758_140 chr1B 658712549 A/G - T C AG - BS00071893_51 chr1B 658738539 A/C - T G GT + Tdurum_contig68980_317 chr1B 660012179 A/C + A C AC + Tdurum_contig68980_448 chr1B 660012310 T/C + T C AG - Tdurum_contig13250_137 chr1B 660106297 A/G - C T CT + BS00015519_51 chr1B 660528121 T/C + T C CT + Kukri_rep_c89128_138 chr1B 660528325 A/G - C T CT + BS00032039_51 chr1B 660528592 T/G + G T AC - BS00012012_51 chr1B 660529225 A/G + G A AG + Tdurum_contig57153_1356 chr1B 661517151 A/G + A G CT - CAP7_c1853_297 chr1B 662021312 T/G - C A GT - CAP12_c1085_283 chr1B 662021317 A/C - T G AC - GENE-3606_1331 chr1B 662549594 T/G - C A AC + IACX8074 chr1B 662556369 T/C - A G CT - RAC875_c20798_336 chr1B 662669034 A/G NA NA NA CT NA flanks do not match reference at this position BS00078413_51 chr1B 662718706 A/G + G A CT - BS00078414_51 chr1B 662718722 T/G + T G AC - tplb0034g09_1257 chr1B 662910485 T/C NA NA NA AG NA flanks do not match reference at this position RFL_Contig5022_2001 chr1B 663047786 A/G + A G AG + Tdurum_contig18557_228 chr1B 664285845 T/C + T C AG - IACX2234 chr1B 664302475 A/G + A G AG + Tdurum_contig55429_147 chr1B 664302475 T/C - A G AG + Tdurum_contig55429_116 chr1B 664302506 T/C - A G CT - Kukri_c18230_1633 chr1B 664787622 A/C - T G GT + RAC875_c11491_739 chr1B 665310362 T/C - A G CT - GENE-0568_419 chr1B 665311375 A/G - C T CT + Excalibur_c88792_93 chr1B 665312066 T/C + T C CT + BobWhite_c9963_51 chr1B 665314481 A/G - T C CT + Kukri_c11000_1769 chr1B 665398816 A/G - T C CT + RAC875_c4047_115 chr1B 666916705 A/C + C A GT - BS00028747_51 chr1B 666925126 T/C + T C AG - RAC875_c1599_342 chr1B 667225124 A/G + A G AG + Tdurum_contig61914_169 chr1B 667717050 T/G - A C AC + Kukri_rep_c103550_213 chr1B 667822354 A/G - T C AG - BobWhite_c8293_236 chr1B 667931359 T/C + T C CT + IAAV4844 chr1B 668123435 A/G + G A CT - Ex_c4436_1947 chr1B 668124333 A/G + G A AG + Tdurum_contig94450_255 chr1B 671199303 T/C + C T CT + IAAV1913 chr1B 671996028 A/T + T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00089959_51 chr1B 671996077 A/G - C T AG - BS00022398_51 chr1B 673161052 A/C - T G AC - Tdurum_contig93330_263 chr1B 673176320 A/G + A G CT - Kukri_c1259_864 chr1B 673176421 A/G - C T AG - GENE-0171_87 chr1B 673641143 T/G + T G GT + Tdurum_contig46647_623 chr1B 673641771 A/G - C T AG - IACX17310 chr1B 673743239 T/C + T C AG - BS00084990_51 chr1B 673745712 A/G + G A CT - Tdurum_contig10354_270 chr1B 673786315 A/G - T C AG - Tdurum_contig10354_170 chr1B 673786415 A/G - C T CT + Tdurum_contig84791_198 chr1B 674003022 T/C + C T AG - BobWhite_c14422_282 chr1B 674661296 A/G - C T AG - Tdurum_contig42558_134 chr1B 674662148 A/C - T G AC - Tdurum_contig30426_261 chr1B 674667822 A/C - G T AC - RAC875_c43846_79 chr1B 674668636 T/C - G A CT - Kukri_c875_126 chr1B 674669990 T/C - G A AG + BS00060686_51 chr1B 675320327 T/G - C A GT - Tdurum_contig8669_131 chr1B 675559614 A/G + G A AG + Tdurum_contig8669_296 chr1B 675559779 A/C NA NA NA AC NA flanks do not match reference at this position BobWhite_c2135_96 chr1B 675565836 T/C NA NA NA AG NA flanks do not match reference at this position Ra_c97840_496 chr1B 676077082 A/G - T C AG - Tdurum_contig63370_207 chr1B 676079688 T/C + C T AG - RAC875_c24317_1351 chr1B 676081799 T/C - A G CT - BS00066305_51 chr1B 676201156 A/G - C T CT + IAAV4884 chr1B 676262921 T/C + T C AG - BobWhite_c34125_183 chr1B 676271684 T/C - A G AG + BS00022784_51 chr1B 676776721 T/C - A G AG + BS00063302_51 chr1B 676813408 A/G + A G AG + Tdurum_contig52086_342 chr1B 678263128 T/C - G A CT - Tdurum_contig52086_264 chr1B 678263206 T/G - A C GT - tplb0049h18_765 chr1B 678266671 A/G - T C AG - RAC875_c33937_211 chr1B 678470981 A/G + A G CT - BS00067000_51 chr1B 678484884 A/G - T C CT + RAC875_c20475_474 chr1B 678784370 T/C + C T CT + BobWhite_c4482_73 chr1B 679030805 A/C + A C GT - BobWhite_c4482_125 chr1B 679030857 A/G + G A AG + BobWhite_c4482_159 chr1B 679030891 A/G + A G AG + IAAV2162 chr1B 679748218 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Excalibur_c5888_169 chr1B 679749200 T/C - A G AG + Tdurum_contig13879_919 chr1B 680163586 T/C + C T CT + Kukri_c43555_378 chr1B 680782667 T/G + T G AC - RAC875_c39312_272 chr1B 680862434 T/C + T C AG - BobWhite_c6981_181 chr1B 680862538 A/G + A G CT - Excalibur_c55186_351 chr1B 680862694 T/C + T C AG - BS00010807_51 chr1B 680862961 A/G - C T AG - RAC875_c19174_645 chr1B 680864507 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_rep_c104959_641 chr1B 680866376 A/G + A G AG + Tdurum_contig97527_141 chr1B 680866583 A/C - T G AC - Tdurum_contig10099_454 chr1B 680867667 T/C - A G CT - GENE-0543_594 chr1B 681690608 A/C - G T GT + Kukri_rep_c104078_655 chr1B 683460738 A/G - T C AG - RAC875_c1113_1577 chr1B 683461467 T/C + C T CT + Tdurum_contig44851_987 chr1B 683470838 T/C - G A CT - Tdurum_contig44851_927 chr1B 683470898 T/C - A G AG + Tdurum_contig44851_888 chr1B 683470937 T/C - A G CT - RAC875_c26801_179 chr1B 683471655 A/G - T C AG - RAC875_c26801_129 chr1B 683471705 A/G - T C AG - RAC875_c2258_345 chr1B 683474111 A/G + G A AG + RAC875_rep_c112737_766 chr1B 683475062 T/C - A G CT - BobWhite_rep_c63264_629 chr1B 683574047 A/G NA NA NA AG NA flanks do not match reference at this position CAP7_c2089_140 chr1B 685288402 A/G - T C AG - TA001722-0749 chr1B 685647892 A/G - T C CT + Tdurum_contig1631_240 chr1B 686840596 T/C + T C AG - BobWhite_rep_c49533_93 chr1B 686843555 T/G + T G GT + Tdurum_contig48103_1481 chr1B 687088585 T/C - G A CT - IAAV5991 chr1B 687401349 T/G + T G AC - RAC875_c37075_53 chr1B 687715077 T/C NA NA NA AG NA flanks do not match reference at this position Tdurum_contig9144_222 chr1B 687719733 T/G - A C GT - Tdurum_contig92835_177 chr1B 687720400 T/C + T C CT + BS00027006_51 chr1B 687720416 T/C - G A AG + Kukri_c44587_130 chr1B 687795616 A/G + A G AG + Kukri_c16608_791 chr1B 687795939 A/G - T C AG - RAC875_c9601_1680 chr1B 687797796 A/C + A C AC + Excalibur_c25640_110 chr1B 687802310 A/G - C T CT + BobWhite_c1897_440 chr1B 688230741 T/C + T C CT + RFL_Contig2550_679 chr1B 688231155 T/C NA NA NA AG NA flanks do not match reference at this position Tdurum_contig51922_676 chr1B 688231155 A/G NA NA NA AG NA flanks do not match reference at this position RFL_Contig2550_583 chr1B 688231700 T/C - A G AG + JG_c473_540 chr1B 688231754 A/C - T G AC - BS00104270_51 chr1B 688232268 A/G - C T AG - BobWhite_c38981_117 chr1B 688238992 T/C + C T AG - RAC875_c6537_584 chr1B 688282677 T/G + G T GT + RAC875_c6537_2298 chr1B 688284559 T/C + C T CT + Tdurum_contig42108_958 chr1B 688707535 T/C + C T CT + IAAV5516 chr1B 688710381 A/G + G A AG + BS00082577_51 chr1B 688767394 A/G - C T CT + Tdurum_contig4851_653 chr1B 688768651 A/G - C T CT + Ku_c11537_539 chr1B 688769254 T/G + T G GT + BS00000744_51 chr1D 216862 T/C + T C CT + CAP12_c8501_370 chr1D 216986 A/G + G A CT - RAC875_c2070_566 chr1D 417199 T/C + C T AG - BobWhite_c359_1026 chr1D 417667 T/G + T G GT + Kukri_rep_c108573_60 chr1D 2221023 A/G - C T CT + Excalibur_rep_c70751_58 chr1D 2221205 A/C NA NA NA GT NA flanks do not match reference at this position GENE-0412_338 chr1D 2228430 T/C - A G CT - Excalibur_c90130_313 chr1D 2229773 T/C + C T CT + GENE-1118_58 chr1D 5406761 A/G - T C AG - Kukri_c3181_2340 chr1D 5517514 T/G + G T GT + GENE-0411_350 chr1D 6769424 A/C - G T GT + BS00021748_51 chr1D 6789564 A/G + G A AG + RAC875_rep_c108940_113 chr1D 6900530 T/C + T C AG - Excalibur_c28255_430 chr1D 7039059 A/G + A G AG + RAC875_c56811_258 chr1D 7039601 A/G - C T AG - IAAV1117 chr1D 7472938 T/G + T G GT + Excalibur_c9676_163 chr1D 7510244 A/G + A G CT - CAP7_c3533_280 chr1D 7834117 T/C + C T CT + Excalibur_rep_c105429_528 chr1D 7870630 T/C + C T CT + BobWhite_rep_c49356_237 chr1D 7877632 T/C + C T CT + Kukri_c54157_392 chr1D 7897179 T/C - G A AG + RFL_Contig4140_1135 chr1D 7947902 A/G - T C AG - IAAV8085 chr1D 7948109 T/C - G A AG + Tdurum_contig46413_779 chr1D 8605931 A/G + G A CT - GENE-0019_1155 chr1D 8712851 A/G NA NA NA AG NA flanks do not match reference at this position GENE-0019_427 chr1D 8712977 A/G + A G AG + Ra_c69552_1419 chr1D 8721360 A/G NA NA NA CT NA flanks do not match reference at this position D_GB5Y7FA01BMOJY_241 chr1D 8721371 A/G - C T AG - RAC875_c102411_201 chr1D 9762262 A/G - C T AG - Kukri_c8211_159 chr1D 9875153 T/C - G A AG + BobWhite_c14032_133 chr1D 10257281 T/G + T G GT + BobWhite_c14032_277 chr1D 10257425 A/G + A G CT - Kukri_rep_c68693_86 chr1D 10259627 A/G - T C CT + BS00069301_51 chr1D 10294956 A/C + C A AC + BS00069300_51 chr1D 10295006 A/G + G A CT - BobWhite_c33756_74 chr1D 10383022 T/G - A C GT - Excalibur_c5892_1129 chr1D 10660829 T/C - G A AG + Excalibur_c4876_832 chr1D 10662667 T/C - A G AG + Excalibur_c58154_84 chr1D 10668191 T/C + T C CT + tplb0043h23_1346 chr1D 10808906 T/C + T C AG - Kukri_c5756_302 chr1D 11548857 A/G - T C AG - RFL_Contig1338_2062 chr1D 11623252 T/C + C T AG - BS00053605_51 chr1D 11664846 T/C + C T CT + CAP8_c2401_433 chr1D 11879726 A/G + A G AG + Excalibur_c55363_265 chr1D 11966902 A/G - C T CT + Ku_c12842_664 chr1D 12303425 A/G + A G CT - Kukri_c11756_1706 chr1D 12311887 A/G NA NA NA CT NA flanks do not match reference at this position IAAV6899 chr1D 12314151 T/C + T C AG - CAP7_c973_156 chr1D 12315198 T/C + C T CT + RAC875_c7752_2913 chr1D 12533292 A/G - C T AG - Ex_c6145_1877 chr1D 12534836 T/G - A C GT - RAC875_c7752_1223 chr1D 12535399 A/C - T G AC - Ex_c6145_833 chr1D 12535879 A/G - C T CT + RAC875_c7752_549 chr1D 12536156 A/G - T C AG - RAC875_c7752_145 chr1D 12536798 T/G - C A AC + CAP12_c46_333 chr1D 15322246 A/G + A G AG + BS00022178_51 chr1D 16612833 T/C + C T CT + BS00104199_51 chr1D 16788821 A/G - C T AG - BS00023049_51 chr1D 16788841 A/C - G T GT + RAC875_c2040_564 chr1D 16789272 A/G - T C AG - tplb0055p02_1074 chr1D 17168306 A/C - T G GT + Kukri_c46169_294 chr1D 17630458 A/C + C A AC + Excalibur_c48750_124 chr1D 18066335 A/G + G A CT - RAC875_c29598_336 chr1D 18067663 A/G - C T AG - IAAV7510 chr1D 19128281 A/G - C T AG - IACX9354 chr1D 19128309 T/C - G A CT - D_F5XZDLF01A85DT_301 chr1D 19129436 A/G + A G AG + D_contig13475_402 chr1D 20045166 A/G + A G AG + Kukri_c33670_261 chr1D 20056265 A/G + G A CT - Kukri_c33670_506 chr1D 20056510 A/C + A C AC + IAAV1624 chr1D 21888389 A/G + G A AG + Kukri_c7436_943 chr1D 25730987 A/G - T C AG - Kukri_c35521_117 chr1D 25731131 A/G - C T CT + Excalibur_c10689_254 chr1D 26296910 A/G - T C AG - Excalibur_c16452_624 chr1D 27897630 A/G - C T CT + Excalibur_c5881_398 chr1D 28199298 T/C + T C AG - BS00070085_51 chr1D 28224828 A/G - C T CT + IAAV3422 chr1D 28576158 T/C + T C AG - BS00065844_51 chr1D 32529946 T/C + C T CT + RAC875_c62_1514 chr1D 32543966 T/G - A C GT - RFL_Contig5594_873 chr1D 32544344 A/C - G T AC - BS00000721_51 chr1D 32544374 T/C - G A CT - IACX589 chr1D 32544853 A/G - C T CT + RAC875_c62_321 chr1D 32545481 T/C - G A CT - IACX11290 chr1D 33472487 T/C + C T AG - BS00002178_51 chr1D 33712312 A/G - C T CT + Kukri_c9693_1890 chr1D 33756223 T/C + C T CT + Excalibur_c3260_989 chr1D 33756455 A/C + C A GT - Excalibur_c12703_766 chr1D 34619639 A/G - C T AG - BS00087086_51 chr1D 34619771 T/C + T C CT + BS00012936_51 chr1D 34621416 T/C + T C CT + RAC875_c102059_75 chr1D 35649801 A/G - C T CT + RAC875_rep_c96733_369 chr1D 36536786 T/C + T C CT + Kukri_rep_c102887_300 chr1D 36537653 A/C + C A GT - Kukri_c14040_499 chr1D 36832424 T/C + T C CT + JD_c12243_360 chr1D 36832447 T/C - A G CT - Kukri_rep_c112035_340 chr1D 37221137 T/G + T G GT + Excalibur_c4058_1121 chr1D 38295067 T/C + T C CT + Kukri_c22870_91 chr1D 38295126 T/C + C T CT + CAP7_c1609_203 chr1D 38552368 T/C + C T CT + BS00065478_51 chr1D 38581053 A/G + A G CT - D_contig74531_32 chr1D 38657660 T/C - A G AG + BS00086679_51 chr1D 38781446 T/C + T C CT + BS00074824_51 chr1D 38908618 T/C - A G CT - D_GBUVHFX01ANH44_230 chr1D 39868806 T/G - C A GT - D_contig22896_682 chr1D 39946699 A/G + A G AG + BS00066847_51 chr1D 40579284 T/C - G A CT - BS00067709_51 chr1D 40579470 A/G - C T CT + RAC875_c42113_93 chr1D 40598402 T/C + T C CT + IAAV5936 chr1D 41598479 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles IAAV739 chr1D 41751289 A/T + T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles IAAV8987 chr1D 41823148 A/C + NA NA AC NA reference base G not among SNP alleles IACX11153 chr1D 41823675 T/C + T C AG - IAAV4760 chr1D 41869071 A/G - C T AG - BS00067620_51 chr1D 42095414 A/G - T C AG - BobWhite_c816_289 chr1D 43126682 A/G + A G AG + IAAV4794 chr1D 43127054 A/G - T C AG - Excalibur_c46695_219 chr1D 43281537 A/G + G A CT - Jagger_c6199_90 chr1D 45489306 T/C + T C AG - IACX12270 chr1D 46182667 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles IAAV7445 chr1D 46183519 A/C - G T AC - RAC875_rep_c69508_215 chr1D 46184739 T/C - G A CT - Kukri_c53398_200 chr1D 47713864 A/G + G A AG + RAC875_c18749_87 chr1D 47716028 T/C + T C AG - RAC875_c8932_740 chr1D 47846234 T/G - C A AC + BS00077237_51 chr1D 47849849 T/C + T C AG - Kukri_c5113_1082 chr1D 47878785 T/C + T C AG - RAC875_rep_c81479_191 chr1D 47879551 T/C + T C AG - tplb0055o07_1820 chr1D 48023245 A/C + A C AC + IAAV4861 chr1D 48399991 A/C - T G GT + BS00013227_51 chr1D 48401161 A/C - T G AC - BS00091317_51 chr1D 48862978 A/G + G A CT - tplb0052b04_1104 chr1D 48864141 A/G + A G CT - RAC875_c48997_1160 chr1D 49422605 T/C + C T AG - Kukri_c49577_630 chr1D 49586207 T/C - G A AG + BS00033405_51 chr1D 49586445 A/G - C T AG - Excalibur_c18184_132 chr1D 49586908 T/C - G A AG + BS00024262_51 chr1D 49596715 T/G + T G AC - Kukri_c6167_1271 chr1D 49604348 A/G + A G AG + Excalibur_c4030_1770 chr1D 49935492 A/C - T G AC - Kukri_rep_c104386_273 chr1D 49942282 T/C - A G AG + Kukri_c44738_477 chr1D 50194647 T/G + G T AC - RAC875_c35094_476 chr1D 50296821 T/C - A G CT - RAC875_c118477_79 chr1D 50297620 T/C + T C AG - BS00072193_51 chr1D 50706109 T/G + G T AC - Kukri_c20844_116 chr1D 50962292 A/C - T G AC - Kukri_c3008_329 chr1D 50967991 T/C + T C CT + Kukri_c9864_1220 chr1D 50969417 T/C - G A AG + Kukri_c9864_936 chr1D 50969701 A/G - T C AG - Ku_c9864_772 chr1D 50969865 A/G - T C AG - D_contig16934_681 chr1D 52342624 T/C - G A CT - BS00096547_51 chr1D 52358137 T/G - C A AC + CAP12_c2978_93 chr1D 52574776 A/G + G A AG + Kukri_c30371_173 chr1D 54912819 T/C - A G AG + BS00051826_51 chr1D 56751172 T/C + T C AG - RAC875_c17951_108 chr1D 56752039 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c5958_1270 chr1D 56753027 T/C + C T AG - BS00094471_51 chr1D 57477576 A/G + A G CT - IACX13378 chr1D 59524929 A/G + A G CT - GENE-0087_561 chr1D 63373865 A/G + A G AG + IAAV4825 chr1D 63374179 A/T + NA NA AT NA reference base C not among SNP alleles GENE-0285_336 chr1D 63633904 A/G + A G CT - BS00058711_51 chr1D 63637697 T/C - A G AG + BS00067706_51 chr1D 63949901 A/G NA NA NA AG NA flanks do not match reference at this position GENE-0459_370 chr1D 66095853 A/G + A G CT - GENE-0459_114 chr1D 66095870 A/G NA NA NA AG NA flanks do not match reference at this position CAP8_c2544_283 chr1D 66178702 T/C - A G CT - BobWhite_c15522_625 chr1D 66179458 T/C + T C AG - Excalibur_c66156_743 chr1D 66185685 T/C - A G CT - Kukri_rep_c108883_500 chr1D 68446986 T/C + T C CT + RAC875_c10050_620 chr1D 68446986 A/G - T C AG - BobWhite_c39153_131 chr1D 69097095 T/C - A G AG + IACX18186 chr1D 69105537 C/G - NA NA CG NA reference base T not among SNP alleles BS00065322_51 chr1D 69181759 A/G + A G CT - BS00065314_51 chr1D 69181804 T/C + C T CT + RAC875_c85881_200 chr1D 69788922 A/G - T C CT + GENE-0539_113 chr1D 72904421 A/C - T G GT + Kukri_rep_c112609_711 chr1D 73675671 T/G - C A AC + BS00036866_51 chr1D 73723350 T/G - C A AC + RAC875_c455_1400 chr1D 73730627 A/G + A G CT - IAAV1772 chr1D 77362696 A/C - T G AC - Ex_c3312_446 chr1D 77364028 A/G + A G AG + Kukri_c9606_882 chr1D 78971772 T/C + T C AG - Kukri_c9606_1479 chr1D 78973508 A/G + A G AG + TA001371-0399 chr1D 80445391 A/G NA NA NA CT NA flanks do not match reference at this position BobWhite_c3068_393 chr1D 80447511 T/C + T C AG - BS00071903_51 chr1D 81277215 T/C - A G AG + RFL_Contig4206_193 chr1D 81481975 T/C + T C CT + D_GB5Y7FA01AOONB_113 chr1D 83820522 T/C + T C CT + IAAV4677 chr1D 84507463 C/G - C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles IAAV7602 chr1D 85186660 T/G - A C AC + RAC875_rep_c75626_232 chr1D 85196862 T/C - A G CT - D_contig34214_149 chr1D 85645999 T/C - A G AG + D_contig22105_362 chr1D 85926386 T/C + C T CT + BS00094759_51 chr1D 86218499 A/G - T C CT + D_GBB4FNX02H5X2X_75 chr1D 86519251 T/C - G A CT - BobWhite_c18773_75 chr1D 86915136 A/G + A G CT - D_GBB4FNX01DIPZ2_261 chr1D 86919055 T/C + T C CT + JD_c3173_947 chr1D 86920761 T/C NA NA NA CT NA flanks do not match reference at this position BS00098308_51 chr1D 87091318 A/G - T C AG - GENE-0121_495 chr1D 87092578 T/C + C T CT + D_contig07129_107 chr1D 87093167 T/G + G T GT + D_GBQ4KXB02H2M14_141 chr1D 87674960 A/G + A G AG + IAAV4705 chr1D 89126932 A/G - T C CT + D_contig18874_367 chr1D 89240321 A/G + A G CT - JD_c5757_605 chr1D 90645768 A/G + A G CT - BS00030733_51 chr1D 90648913 T/C NA NA NA AG NA flanks do not match reference at this position BS00110545_51 chr1D 93103181 A/G - T C AG - IAAV3763 chr1D 95794285 T/C + T C CT + D_GBQ4KXB01ARYBZ_386 chr1D 98833963 A/G - T C CT + IAAV7799 chr1D 98844627 T/C NA NA NA CT NA flanks do not match reference at this position BobWhite_c16559_71 chr1D 99546198 A/C - G T GT + BobWhite_c45771_129 chr1D 99670155 T/C + T C CT + BS00064750_51 chr1D 101288808 T/C + T C CT + GENE-0400_330 chr1D 101935965 A/G + G A CT - GENE-0254_148 chr1D 103351014 T/C + T C AG - Kukri_rep_c71840_754 chr1D 103351393 T/C + T C CT + RFL_Contig1736_1393 chr1D 103351767 T/C + C T CT + Ku_c17401_361 chr1D 103410910 A/G + A G AG + Excalibur_c17801_165 chr1D 103483318 T/C - A G AG + Excalibur_c49018_325 chr1D 105776270 T/C - A G CT - BS00088256_51 chr1D 106838845 T/C + T C CT + BS00110120_51 chr1D 108109855 A/G + A G AG + D_F5XZDLF01EKOCH_269 chr1D 108817141 T/C + C T AG - Excalibur_c43347_322 chr1D 109942352 T/C - A G AG + GENE-1529_694 chr1D 109974729 A/C - G T AC - BS00024812_51 chr1D 109980428 T/C + T C CT + IAAV6922 chr1D 110008567 A/C + A C GT - RAC875_rep_c109118_284 chr1D 110008683 T/C - A G AG + D_GB5Y7FA02JHKYJ_72 chr1D 110053849 A/G - T C CT + D_GDS7LZN02FII0B_71 chr1D 111092920 T/C + C T AG - D_contig07994_167 chr1D 112214960 T/C - G A CT - D_GBQ4KXB01B66WE_115 chr1D 112351617 T/C + T C AG - GENE-0163_519 chr1D 112769522 T/G - C A GT - BS00077837_51 chr1D 114153833 A/G + A G AG + GENE-0336_224 chr1D 114356025 A/G - C T CT + Excalibur_c8180_489 chr1D 116456198 A/G - C T AG - Ku_c6694_1837 chr1D 119308231 A/G + A G AG + IAAV2773 chr1D 119403783 A/C - NA NA GT NA reference base C not among SNP alleles TA005370-0351 chr1D 120535275 A/C - T G GT + GENE-0158_358 chr1D 121142693 T/C + C T CT + BS00068380_51 chr1D 121312106 T/G - A C AC + IAAV8664 chr1D 122546582 A/G + A G CT - GENE-0040_194 chr1D 122835717 A/G - T C CT + GENE-0339_174 chr1D 123104858 A/C + A C GT - D_GB5Y7FA01BDG4D_227 chr1D 125830658 A/G - C T AG - BS00087248_51 chr1D 130308325 A/G + A G CT - GENE-0346_235 chr1D 130609056 T/C + T C CT + RAC875_rep_c115865_721 chr1D 132206857 T/G - A C GT - GENE-0217_123 chr1D 132856607 A/G - T C CT + GENE-0217_113 chr1D 132856613 T/G - A C GT - BS00065311_51 chr1D 136953948 T/C - A G CT - RAC875_c30593_633 chr1D 137065276 A/C - T G AC - RAC875_c30593_58 chr1D 137074424 T/C - A G AG + IAAV6025 chr1D 137074718 A/G - T C CT + Excalibur_c14494_483 chr1D 137437618 T/C - A G CT - GENE-0303_730 chr1D 137439025 T/G - C A AC + RFL_Contig5353_817 chr1D 141275187 A/G + A G AG + BobWhite_c8218_162 chr1D 141277165 T/C + C T CT + GENE-0181_271 chr1D 141708906 A/G - C T AG - BS00021899_51 chr1D 142660706 T/C + NA NA CT NA reference base G not among SNP alleles BS00049883_51 chr1D 143178326 T/C - A G CT - RAC875_c3656_1229 chr1D 143958285 T/C + C T CT + BS00067404_51 chr1D 144302732 A/G - C T AG - IAAV8003 chr1D 148681147 T/C - A G AG + RAC875_rep_c70319_1224 chr1D 153775815 A/G + A G AG + IAAV4676 chr1D 154021977 T/G - NA NA AC NA reference base T not among SNP alleles RAC875_c27161_152 chr1D 156285618 T/C - A G AG + RAC875_c42715_856 chr1D 158107441 T/C + T C CT + Kukri_c7476_415 chr1D 168484317 A/G - T C CT + Kukri_c18350_208 chr1D 170218724 T/G - A C GT - BobWhite_rep_c65565_359 chr1D 170649310 T/C + T C CT + D_contig34866_267 chr1D 176352418 T/C + C T AG - Kukri_c54856_331 chr1D 180225109 T/C + T C AG - Excalibur_c1243_587 chr1D 182581435 A/G - T C AG - BS00068215_51 chr1D 190783799 A/G + A G AG + Excalibur_c27917_676 chr1D 194925419 A/G - T C AG - D_GA8KES402HPX2O_67 chr1D 196793544 T/G - A C AC + BS00068256_51 chr1D 197740356 A/G + A G CT - Excalibur_c21107_396 chr1D 199428161 A/G + G A CT - D_contig27734_63 chr1D 201490868 A/G - T C CT + D_GBB4FNX01DH2FL_308 chr1D 201593372 T/C + C T AG - BS00022962_51 chr1D 206101173 A/G + G A CT - BobWhite_c11895_332 chr1D 207658165 A/C - T G AC - Kukri_rep_c111517_289 chr1D 208087664 A/G + A G CT - RAC875_c762_120 chr1D 209512084 T/G + T G GT + BS00021895_51 chr1D 213341645 A/G - T C AG - Kukri_rep_c79491_139 chr1D 220921364 T/C + C T CT + IAAV3232 chr1D 224139493 A/C + C A AC + Excalibur_c10319_229 chr1D 229485404 T/C NA NA NA AG NA flanks do not match reference at this position BobWhite_c4236_410 chr1D 229880130 T/C - G A AG + BS00009866_51 chr1D 236438885 A/G + A G AG + Kukri_c27717_316 chr1D 238060333 A/G - C T CT + IACX10924 chr1D 238691538 T/C + C T AG - RFL_Contig5450_993 chr1D 246651234 T/C - G A AG + Excalibur_rep_c67757_264 chr1D 247510864 A/G + G A AG + Excalibur_s113941_196 chr1D 247518480 T/C + T C CT + RAC875_c7236_3265 chr1D 247533307 A/G + A G AG + BS00032149_51 chr1D 253209375 A/G + G A AG + Kukri_c22289_168 chr1D 256999410 A/G + A G CT - Excalibur_c81236_77 chr1D 257000278 T/G + T G GT + D_GBQ4KXB01BEQ1K_84 chr1D 257474669 A/G - C T CT + BS00066976_51 chr1D 258332419 T/C + C T CT + BS00064524_51 chr1D 258362463 T/C + C T AG - BS00066132_51 chr1D 258382711 A/G - C T AG - Kukri_c32885_145 chr1D 261741614 T/C - A G CT - Ex_c5759_628 chr1D 272541484 A/G - T C CT + BobWhite_c8428_346 chr1D 273814636 T/G + T G GT + Excalibur_rep_c107489_168 chr1D 283551866 T/C + T C CT + GENE-0071_115 chr1D 283576031 T/C - A G AG + CAP8_c2843_226 chr1D 285055153 A/G + A G CT - Kukri_c47825_138 chr1D 291087045 A/G - T C CT + BS00021878_51 chr1D 297535814 T/C - NA NA CT NA reference base C not among SNP alleles Excalibur_rep_c113303_500 chr1D 303336969 T/C NA NA NA AG NA flanks do not match reference at this position BS00068358_51 chr1D 303516810 A/G - T C AG - BobWhite_c4942_140 chr1D 308263063 T/G - A C AC + GENE-0446_243 chr1D 308269723 A/G + G A AG + Excalibur_c54055_694 chr1D 308455892 T/C - G A CT - D_contig52360_374 chr1D 309566246 T/G + G T AC - RAC875_c1491_2446 chr1D 319513021 A/G - T C AG - BS00052386_51 chr1D 322069316 A/G + G A AG + RAC875_rep_c105196_532 chr1D 325964513 A/G + A G AG + GENE-3626_308 chr1D 337902041 T/C - A G CT - BS00110052_51 chr1D 340557868 A/G - T C AG - RAC875_c33279_526 chr1D 351440063 A/G - C T CT + BS00071465_51 chr1D 354718015 T/C - A G CT - BS00038418_51 chr1D 356154031 A/G - T C AG - Excalibur_rep_c67541_1585 chr1D 362320696 A/G - T C CT + IAAV9050 chr1D 364384765 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles IACX18883 chr1D 365536293 A/G - T C CT + D_contig14507_369 chr1D 365846043 A/G - C T CT + BS00063068_51 chr1D 374047117 A/G - C T AG - RAC875_c41275_131 chr1D 374373434 A/G + A G CT - GENE-0112_64 chr1D 375955420 A/G - T C CT + Excalibur_c10167_1028 chr1D 376782672 A/G NA NA NA CT NA flanks do not match reference at this position BS00012283_51 chr1D 379795569 A/G - T C AG - IACX11070 chr1D 379795569 T/C + T C AG - BobWhite_rep_c63819_182 chr1D 382635686 T/C - G A CT - RAC875_rep_c98040_163 chr1D 382721260 A/G - C T AG - BobWhite_c18881_338 chr1D 387894895 T/G - C A GT - BobWhite_c16005_289 chr1D 391741516 T/C + T C CT + RAC875_c8888_802 chr1D 391741633 T/G + T G GT + BobWhite_c26850_78 chr1D 393440542 A/C + A C AC + Kukri_c25215_124 chr1D 393734731 T/C + T C CT + Excalibur_c34697_831 chr1D 394256505 A/C - G T AC - Ra_c62804_1641 chr1D 397074123 T/C - A G CT - Excalibur_c48379_413 chr1D 397074168 T/C - A G AG + Ex_c105443_895 chr1D 397079798 T/C - A G CT - Excalibur_c35821_61 chr1D 398979967 T/C + T C AG - Ku_c16913_363 chr1D 398980222 T/C - A G CT - RAC875_c25212_173 chr1D 399263572 A/G - C T AG - CAP12_c1906_217 chr1D 403235849 T/C - A G CT - TA003955-1138 chr1D 403946054 A/G + A G AG + GENE-1476_579 chr1D 405111303 A/G - T C AG - Ku_c3647_1443 chr1D 405369265 T/C - G A CT - D_GBF1XID01DNWRS_378 chr1D 407808792 A/G + A G CT - TA004358-0724 chr1D 407875162 A/G - T C CT + RFL_Contig3622_1217 chr1D 407875598 T/C + C T AG - RFL_Contig22_387 chr1D 407917252 T/G NA NA NA AC NA flanks do not match reference at this position IAAV7745 chr1D 408078390 T/C + T C CT + RAC875_c43831_91 chr1D 408078450 A/G + A G AG + RAC875_c54260_127 chr1D 408152539 T/C - A G CT - BS00079095_51 chr1D 408207062 T/G - C A GT - Excalibur_c19237_895 chr1D 408207733 A/C + C A AC + RAC875_c3604_1527 chr1D 408241941 T/C - A G CT - D_contig06122_208 chr1D 408408350 T/C - G A CT - Ku_c5560_2665 chr1D 408408350 A/G + G A CT - BS00014671_51 chr1D 408535181 A/G + G A CT - IAAV2840 chr1D 408535181 T/C - G A CT - IAAV868 chr1D 409500632 A/C + C A AC + Ra_c21676_178 chr1D 410464891 A/G - T C CT + Kukri_c29121_654 chr1D 410466892 T/G + G T AC - Excalibur_c8188_243 chr1D 410468003 T/C - A G AG + Kukri_c12758_2101 chr1D 410501086 T/C - G A CT - BS00058554_51 chr1D 410792212 T/C + T C AG - RAC875_c49612_102 chr1D 412023762 A/G - T C AG - D_GA8KES401EYUM8_190 chr1D 412081300 T/C - G A AG + Kukri_c6051_640 chr1D 412158918 T/C - A G CT - BS00082503_51 chr1D 412219244 A/G - T C AG - CAP12_c6939_216 chr1D 414280451 A/G - T C AG - GENE-0511_484 chr1D 414301748 T/G - A C AC + GENE-0511_403 chr1D 414301821 T/C - G A CT - BS00075001_51 chr1D 414303471 A/G + A G CT - BS00021702_51 chr1D 414565902 T/C + C T AG - Excalibur_c48317_242 chr1D 416099630 T/C - A G CT - RAC875_c87321_108 chr1D 416101167 T/C + T C AG - IAAV7473 chr1D 416128514 T/C - A G AG + Excalibur_c50856_63 chr1D 416458439 T/C NA NA NA AG NA flanks do not match reference at this position Ra_c1211_1656 chr1D 416619932 T/C + T C AG - RAC875_c1211_3475 chr1D 416624080 T/G + G T GT + Ra_c3045_2659 chr1D 419734307 A/G - T C CT + Ra_c3045_1739 chr1D 419735227 T/G - A C AC + Ra_c3045_1361 chr1D 419735605 T/C - A G CT - Excalibur_c9149_1326 chr1D 419737307 T/C - A G CT - Kukri_c12183_262 chr1D 420538002 T/C + T C CT + IAAV6648 chr1D 420553939 T/C - A G CT - RAC875_c46460_1128 chr1D 421882420 A/G + G A AG + IAAV3802 chr1D 422055820 T/C + T C AG - Kukri_c13043_1293 chr1D 422055820 A/G - T C AG - D_GA8KES401CVVAD_281 chr1D 422056077 T/C + T C CT + CAP7_c9557_164 chr1D 423035545 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c19857_549 chr1D 423044749 T/G - C A GT - Ex_c101469_91 chr1D 423264773 A/C NA NA NA GT NA flanks do not match reference at this position Kukri_c13363_675 chr1D 423264773 A/C NA NA NA GT NA flanks do not match reference at this position IAAV2396 chr1D 423267570 A/G + A G CT - Excalibur_rep_c69044_1105 chr1D 423269316 A/G + A G CT - Ra_c27073_507 chr1D 423270143 A/G + G A AG + Ra_c11906_1618 chr1D 423857774 A/G - T C AG - Ra_c11906_1480 chr1D 423858573 A/G - C T AG - Ra_c11906_1441 chr1D 423858612 A/G - C T CT + Ra_c11906_1417 chr1D 423858636 T/C NA NA NA AG NA flanks do not match reference at this position RFL_Contig5373_701 chr1D 423860637 A/G - C T CT + IAAV5588 chr1D 424736692 A/C + C A AC + BS00089031_51 chr1D 424736967 T/C - G A CT - RFL_Contig651_953 chr1D 424989213 T/C + T C CT + GENE-0487_644 chr1D 426416388 A/G - T C CT + tplb0036b21_694 chr1D 426652680 T/G + T G GT + IAAV149 chr1D 427331602 A/G + A G CT - Jagger_c5542_100 chr1D 427371980 A/G + G A CT - TA002789-1409 chr1D 430412982 A/G + A G AG + IAAV8839 chr1D 430416719 A/G - C T CT + Kukri_c7948_86 chr1D 430417053 T/G - A C GT - Ex_c68201_1182 chr1D 430565264 A/G - C T AG - Ex_c18035_840 chr1D 430568197 T/C - A G AG + Ex_c18035_602 chr1D 430568654 T/C - G A CT - Ra_c15730_3403 chr1D 431427774 A/G - T C CT + IACX1420 chr1D 431428150 T/C + T C CT + IACX1549 chr1D 431428430 T/C + C T CT + RAC875_rep_c106884_592 chr1D 431429511 T/C - A G CT - Excalibur_c16570_925 chr1D 431705988 T/C + C T AG - Kukri_c59519_352 chr1D 431706493 A/G + A G CT - Excalibur_c3258_402 chr1D 431821197 A/G - T C CT + Excalibur_c1236_278 chr1D 431823265 A/G - T C AG - RFL_Contig5449_1330 chr1D 431958571 T/C + C T CT + Excalibur_rep_c103577_181 chr1D 432707953 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c55026_311 chr1D 432708157 T/C - A G AG + D_contig20248_176 chr1D 432795777 T/C + T C AG - RAC875_c10083_800 chr1D 432795824 T/C + T C CT + RAC875_c35777_484 chr1D 432796411 A/G + A G CT - IAAV3490 chr1D 433213085 A/G NA NA NA CT NA flanks do not match reference at this position RFL_Contig4705_3207 chr1D 433213628 T/C - A G AG + IACX574 chr1D 433252851 T/C - A G CT - IAAV724 chr1D 433254100 A/G + A G CT - D_GDS7LZN02GSCOW_131 chr1D 433272939 T/G - A C AC + Excalibur_c8231_398 chr1D 433274521 T/G NA NA NA AC NA flanks do not match reference at this position IAAV9177 chr1D 433905045 T/C + C T AG - BS00003816_51 chr1D 435801553 T/C - A G CT - TA004690-1102 chr1D 435801709 T/C - A G AG + BS00093390_51 chr1D 436189752 T/C - A G CT - Excalibur_c23906_303 chr1D 436999704 T/C + T C CT + CAP8_c1338_137 chr1D 440399268 A/G + A G CT - Excalibur_c97157_137 chr1D 443747031 T/C - A G AG + Excalibur_rep_c107047_679 chr1D 443825374 T/C + T C AG - RAC875_c21411_162 chr1D 444335737 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c13463_728 chr1D 449471802 A/G + G A CT - BS00036103_51 chr1D 451129057 T/C + C T CT + RAC875_c291_2591 chr1D 454174445 T/G - C A AC + Kukri_rep_c86467_51 chr1D 454175048 A/G - T C CT + RAC875_c291_2201 chr1D 454175072 A/G - T C CT + IAAV8693 chr1D 454175360 A/G - T C AG - RAC875_c291_1860 chr1D 454175500 A/G - T C AG - RAC875_c291_696 chr1D 454177427 T/C - A G CT - RAC875_c291_647 chr1D 454177476 A/G - T C CT + Kukri_c82086_387 chr1D 455802422 T/G + T G GT + Excalibur_c11680_81 chr1D 457151509 A/G + A G AG + D_GBUVHFX01API9H_416 chr1D 458280906 A/G + A G CT - IACX2961 chr1D 458484152 A/G - T C CT + D_contig29383_280 chr1D 458681231 T/C + C T CT + Excalibur_c19640_270 chr1D 459049903 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c30203_57 chr1D 459050340 T/C - G A CT - tplb0030m20_410 chr1D 459052944 A/C - T G GT + BS00087544_51 chr1D 460743780 A/G + G A CT - Ra_c7324_1464 chr1D 462488015 T/C - A G CT - Kukri_c30159_573 chr1D 464145050 T/C - G A CT - IAAV1549 chr1D 464319712 T/C + T C AG - RAC875_c38646_985 chr1D 464597173 A/G - C T AG - TA004668-0687 chr1D 466366088 T/C NA NA NA CT NA flanks do not match reference at this position BobWhite_s64374_97 chr1D 467034395 T/C + T C CT + BS00021934_51 chr1D 467936120 T/C - G A AG + Kukri_c25512_53 chr1D 469801855 A/G + A G CT - BS00000226_51 chr1D 469890130 A/G + G A AG + BS00094562_51 chr1D 470729115 A/G - T C CT + IACX8359 chr1D 470729220 C/G NA NA NA CG NA flanks do not match reference at this position RAC875_c36980_161 chr1D 472520859 T/C + T C AG - BS00021917_51 chr1D 472527736 T/C - G A AG + GENE-0129_110 chr1D 473638228 T/C + T C CT + GENE-0208_279 chr1D 474013373 T/C + T C CT + GENE-0416_480 chr1D 476257353 T/G - A C GT - Ku_c15764_208 chr1D 479036067 T/C + T C CT + GENE-0439_61 chr1D 480891920 T/C + T C CT + RAC875_c3001_1236 chr1D 483514756 A/G + A G AG + Kukri_c65610_551 chr1D 483676178 T/C + C T CT + BS00009377_51 chr1D 484403613 A/G + A G AG + RAC875_c43846_154 chr1D 484416394 T/C - A G CT - RAC875_c40434_373 chr1D 485106032 A/G - T C AG - BS00063255_51 chr1D 485436610 T/G - A C AC + Kukri_c14292_157 chr1D 485506706 T/C - A G AG + Kukri_c67675_174 chr1D 485548284 T/C + T C CT + Excalibur_c41967_2009 chr1D 485560935 T/C + C T CT + Kukri_c20495_1745 chr1D 485563418 T/C + T C CT + RAC875_c24317_268 chr1D 485563418 A/G - T C CT + Excalibur_c33742_419 chr1D 485754269 T/C - A G AG + BS00011292_51 chr1D 486066733 A/G - C T AG - BobWhite_c8375_71 chr1D 486156766 A/C + A C AC + RFL_Contig3395_1575 chr1D 487168737 A/G - T C AG - BobWhite_c45204_251 chr1D 487171886 T/C - G A CT - tplb0049h18_1622 chr1D 487172298 T/C - A G CT - Tdurum_contig45965_563 chr1D 487838586 T/C + C T AG - RAC875_c48884_374 chr1D 487952328 A/C - T G AC - Excalibur_c5888_641 chr1D 487952728 T/C - G A AG + BS00022654_51 chr1D 487957118 T/C - G A AG + BobWhite_c1027_474 chr1D 487958867 A/G - T C AG - Excalibur_c46365_304 chr1D 488572879 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c4204_1946 chr1D 488573114 T/C - G A AG + Excalibur_c46365_463 chr1D 488573126 T/C + T C CT + GENE-0543_1074 chr1D 488573539 A/G - T C CT + Excalibur_c32722_690 chr1D 488577242 A/G - T C AG - BS00009375_51 chr1D 488577742 T/C - G A CT - Excalibur_rep_c104128_176 chr1D 488974122 T/C + T C AG - Kukri_rep_c110487_219 chr1D 489537873 T/C + T C AG - Excalibur_c41592_100 chr1D 490927371 A/G - T C AG - Excalibur_c981_294 chr1D 490930764 T/C - A G AG + RAC875_rep_c107383_166 chr1D 491043140 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c2258_1028 chr1D 491044471 T/C + T C AG - BS00011913_51 chr1D 491051266 A/G + A G AG + BS00036558_51 chr1D 492534009 A/G - C T AG - Kukri_c12190_1080 chr1D 492611112 A/G + A G CT - Ra_c50996_468 chr1D 492611715 A/G - C T CT + Excalibur_c500_279 chr1D 492891571 A/C + A C GT - RFL_Contig2961_2082 chr1D 493485192 A/G - T C AG - RFL_Contig2961_2046 chr1D 493485228 A/G - T C CT + RFL_Contig2961_1695 chr1D 493485579 A/G - T C CT + RAC875_rep_c71921_672 chr1D 493607565 A/G + G A AG + Kukri_c94613_637 chr1D 493621054 A/G + G A CT - Excalibur_c36269_513 chr1D 493621117 T/C - A G CT - BS00048032_51 chr1D 493702726 A/G + A G CT - Excalibur_c10063_189 chr1D 493935983 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c10063_93 chr1D 493936079 T/G - A C AC + BS00010851_51 chr1D 494063317 T/C - A G AG + Excalibur_c20532_785 chr1D 494471750 A/G + A G AG + Kukri_rep_c103800_479 chr1D 494554017 T/C + C T CT + BobWhite_c1897_1010 chr1D 495113025 T/C + T C CT + Excalibur_c92298_213 chr1D 495126551 T/C - G A CT - Tdurum_contig10208_283 chr2A 260389 T/C + T C AG - Kukri_c22599_114 chr2A 397615 A/G - T C CT + RFL_Contig6096_477 chr2A 398242 A/C NA NA NA AC NA flanks do not match reference at this position IACX11071 chr2A 528114 T/C + C T CT + IAAV5703 chr2A 528331 A/C + C A AC + tplb0041b11_529 chr2A 532065 T/C - A G CT - BS00111318_51 chr2A 2378524 A/G - T C CT + GENE-1019_498 chr2A 2478511 A/C + A C AC + Kukri_rep_c109912_394 chr2A 2486857 T/C + T C AG - Ex_c19516_3687 chr2A 2640560 A/C - G T AC - Kukri_c4698_3401 chr2A 2647481 T/G + T G AC - IACX10969 chr2A 3108184 A/G + G A AG + BS00023052_51 chr2A 3111177 A/G + G A CT - RFL_Contig174_406 chr2A 3114049 A/G + A G AG + Tdurum_contig56157_1595 chr2A 3335093 A/C + NA NA GT NA reference base G not among SNP alleles Excalibur_c15379_1305 chr2A 3445818 T/C + T C CT + RAC875_c34512_493 chr2A 3798071 A/G + A G CT - BobWhite_c22255_814 chr2A 3960514 T/C - A G CT - BS00003735_51 chr2A 3962554 T/C + C T AG - BS00022024_51 chr2A 3965150 T/C - G A CT - CAP8_c2783_336 chr2A 3965164 A/G - T C AG - RFL_Contig4030_493 chr2A 3966981 A/C - T G AC - BobWhite_c22714_132 chr2A 4168425 T/C - G A AG + BS00004221_51 chr2A 4171296 A/G - T C AG - Excalibur_c43068_142 chr2A 4212885 T/G - C A GT - BobWhite_c44229_425 chr2A 4213131 T/C + T C CT + Kukri_c22152_730 chr2A 4213410 T/C + C T AG - Kukri_c22152_901 chr2A 4213581 T/C + T C CT + Kukri_c22152_944 chr2A 4213624 A/C + A C AC + Kukri_c22152_1059 chr2A 4213821 T/C + C T CT + RAC875_rep_c107312_796 chr2A 4219741 T/C - A G CT - IACX11448 chr2A 4786944 C/G - NA NA CG NA reference base A not among SNP alleles Kukri_c33374_1048 chr2A 4790384 T/C + T C CT + TA002095-0637 chr2A 5526356 T/C NA NA NA CT NA flanks do not match reference at this position tplb0032i02_1388 chr2A 5677351 T/C + C T CT + tplb0032i02_1435 chr2A 5677398 A/G + A G AG + Ra_c510_171 chr2A 5912372 T/C - A G AG + BS00022393_51 chr2A 5929857 T/C + T C CT + Excalibur_c12980_2621 chr2A 7545148 A/G - T C CT + Tdurum_contig76595_208 chr2A 7545282 T/C - A G CT - Kukri_c31776_1621 chr2A 7550113 T/C + T C CT + RAC875_c42847_141 chr2A 7687523 T/C - G A AG + Excalibur_c10442_1743 chr2A 10599430 T/C - A G AG + Excalibur_c25445_978 chr2A 10599813 A/G - C T AG - GENE-1273_59 chr2A 10600255 T/C + T C CT + GENE-1273_438 chr2A 10600312 A/G - T C CT + BobWhite_c10673_330 chr2A 10993028 A/C - T G GT + Jagger_c8924_107 chr2A 10993145 T/C - G A AG + BobWhite_c10673_138 chr2A 10993220 T/C - A G AG + RAC875_c39634_370 chr2A 10993272 T/C - G A CT - RAC875_c609_362 chr2A 11547581 A/G + A G CT - BS00013534_51 chr2A 11909742 A/G + A G AG + Kukri_c23195_266 chr2A 12327554 T/G - A C AC + RAC875_c2300_1021 chr2A 12340138 A/G + A G CT - Excalibur_c4748_859 chr2A 12340658 T/C + T C AG - BS00109498_51 chr2A 12588147 A/G + A G CT - IACX10973 chr2A 13408994 T/C - G A CT - RAC875_c52554_258 chr2A 13847506 T/C + C T CT + BS00065192_51 chr2A 13914528 A/G + A G AG + BS00093111_51 chr2A 14811514 T/C + T C CT + BS00022760_51 chr2A 14812057 T/C + T C CT + Excalibur_c8436_386 chr2A 14815455 A/G + A G AG + IAAV4102 chr2A 14819129 A/C - T G AC - BS00071630_51 chr2A 14940140 A/G + A G CT - IACX6178 chr2A 15612817 T/C + T C CT + RAC875_c98844_403 chr2A 15623703 T/C + T C CT + CAP8_c1562_139 chr2A 15883378 A/C - T G AC - BS00080836_51 chr2A 15948204 A/G - C T AG - Excalibur_rep_c70913_93 chr2A 15949580 T/C - A G AG + RAC875_c75791_227 chr2A 15962992 A/G + A G AG + RAC875_c90426_151 chr2A 16259626 T/C - G A AG + Excalibur_rep_c112367_293 chr2A 16402442 T/C - G A AG + BS00067214_51 chr2A 16404735 A/G - C T CT + BS00107263_51 chr2A 16523342 T/C - G A CT - BS00027484_51 chr2A 16524182 A/C + A C GT - BS00004112_51 chr2A 16672502 T/C - A G AG + BS00004243_51 chr2A 16672508 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_rep_c106566_197 chr2A 16673159 T/G - A C AC + Kukri_c19434_936 chr2A 16721535 T/C - A G CT - BS00011466_51 chr2A 16899269 T/C - A G CT - IAAV3985 chr2A 16899279 A/G - T C CT + RAC875_c829_1143 chr2A 17000920 T/C - A G CT - RAC875_c829_355 chr2A 17001708 T/C - G A AG + BS00066686_51 chr2A 17225990 T/C - A G CT - BS00083974_51 chr2A 17658893 T/C - G A CT - IACX12079 chr2A 18017808 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles TA001766-2030 chr2A 18423481 A/G - T C CT + BS00080569_51 chr2A 18587345 T/C + C T AG - BS00080570_51 chr2A 18587379 T/G + G T GT + BS00039973_51 chr2A 18911939 T/C - G A AG + BS00039972_51 chr2A 18911953 T/G - A C GT - Excalibur_c35611_446 chr2A 19027516 A/G + A G CT - RAC875_s118883_99 chr2A 19650285 A/G + A G CT - IAAV165 chr2A 19652003 T/C - G A CT - IACX8278 chr2A 19652051 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00065667_51 chr2A 21207925 T/C + T C CT + BS00021706_51 chr2A 21261871 A/G - C T CT + BS00111069_51 chr2A 21261912 A/G - C T AG - Excalibur_c21663_145 chr2A 21534263 A/G - C T CT + GENE-1123_303 chr2A 24061798 T/C + C T CT + BS00067684_51 chr2A 24150449 A/G - C T AG - TA003766-0683 chr2A 24410121 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_rep_c111906_144 chr2A 27967266 A/G - T C CT + Tdurum_contig42153_3715 chr2A 28015766 A/G - T C AG - Kukri_c42095_196 chr2A 28803532 A/C + A C AC + RAC875_c14082_2606 chr2A 29102584 A/G + A G AG + Kukri_c31508_91 chr2A 29285455 T/C - A G AG + RAC875_c62936_139 chr2A 29285540 A/G - T C AG - GENE-3260_378 chr2A 29589509 T/C + C T CT + CAP11_rep_c9060_520 chr2A 30047950 T/C - A G AG + BobWhite_c58481_104 chr2A 30071860 T/C - A G AG + CAP8_rep_c8022_270 chr2A 30079452 T/C - G A CT - BS00011425_51 chr2A 30149107 A/G - T C AG - D_GA8KES402GRIFZ_148 chr2A 30156147 A/G + G A CT - GENE-1417_537 chr2A 30451752 A/G NA NA NA AG NA flanks do not match reference at this position GENE-1417_406 chr2A 30451879 T/C - G A CT - Kukri_c27040_1026 chr2A 30455490 A/G - T C AG - Kukri_c27040_309 chr2A 30456670 T/G - C A AC + CAP7_c3132_150 chr2A 30549733 A/G - T C CT + BobWhite_c19433_329 chr2A 30866076 A/G - T C AG - IACX8391 chr2A 31089755 T/C + C T CT + BS00004724_51 chr2A 31693325 A/G - C T AG - BS00079035_51 chr2A 31953310 A/C + C A AC + RAC875_c31045_882 chr2A 31957341 T/C + T C AG - Excalibur_c92241_336 chr2A 32139650 T/G + G T GT + BS00022982_51 chr2A 32139721 A/G - C T CT + D_F5MV3MU01EAJ4J_240 chr2A 32139938 T/C + T C CT + RAC875_rep_c78518_198 chr2A 32144183 T/C - G A AG + Excalibur_rep_c67994_169 chr2A 32144379 T/C - G A CT - Kukri_rep_c104307_905 chr2A 32144831 A/G - T C AG - Excalibur_c15740_1106 chr2A 32150710 T/G + T G GT + BS00073382_51 chr2A 32153183 A/G - C T AG - BS00070797_51 chr2A 32153336 T/C - A G AG + GENE-0749_215 chr2A 32269330 T/C - G A AG + Kukri_rep_c113542_254 chr2A 33044220 A/G + A G AG + BobWhite_c23790_98 chr2A 33044822 A/G - C T AG - Kukri_c59939_94 chr2A 33699460 T/C NA NA NA AG NA flanks do not match reference at this position Ku_c23118_149 chr2A 34499208 A/G + G A CT - Kukri_c37166_91 chr2A 34653783 T/C - A G CT - BS00076693_51 chr2A 34665317 T/C + C T CT + Tdurum_contig11803_935 chr2A 36039940 A/G - T C CT + Tdurum_contig11803_515 chr2A 36040924 T/C - A G AG + Tdurum_contig11803_475 chr2A 36040964 T/C - A G CT - BobWhite_c26374_339 chr2A 36138748 A/G NA NA NA AG NA flanks do not match reference at this position IAAV2585 chr2A 36631178 A/G + A G CT - Ku_c269_2643 chr2A 36632023 A/G + G A CT - Ra_c2798_261 chr2A 36632177 T/C - G A AG + Kukri_c5497_312 chr2A 38914290 A/G - C T CT + Ra_c58279_684 chr2A 41232546 A/G + A G AG + Ra_c58279_702 chr2A 41232564 T/C + C T CT + Ku_c972_560 chr2A 42392191 A/G - T C AG - Excalibur_c32875_78 chr2A 42402263 A/G + G A CT - BS00049937_51 chr2A 43299300 A/G - C T AG - Kukri_c35248_185 chr2A 43445962 A/G + A G CT - IACX8108 chr2A 44094660 A/G + A G AG + Kukri_c1728_1876 chr2A 44094979 T/G NA NA NA AC NA flanks do not match reference at this position IAAV2654 chr2A 44836111 A/G NA NA NA CT NA flanks do not match reference at this position Tdurum_contig46797_585 chr2A 44836509 A/G + G A CT - BobWhite_c18852_91 chr2A 45120215 T/G + G T GT + Ra_c10616_265 chr2A 46107321 A/G - C T AG - IAAV7468 chr2A 46108342 A/G - T C AG - BS00044274_51 chr2A 47826702 A/C - G T GT + BS00044272_51 chr2A 47826767 A/G - T C CT + Tdurum_contig30680_120 chr2A 47830474 T/C + T C AG - GENE-0647_106 chr2A 47832773 T/C - A G AG + RAC875_c62278_69 chr2A 47908337 A/G + G A AG + Kukri_c12368_82 chr2A 47910890 A/C - T G GT + Kukri_c22904_824 chr2A 48862984 A/G - T C CT + BS00091830_51 chr2A 48868261 T/C - A G CT - Kukri_c56203_965 chr2A 48868267 A/G - T C AG - RAC875_c10357_732 chr2A 48874233 T/C - G A AG + Excalibur_rep_c105284_131 chr2A 49451545 A/G - C T CT + Excalibur_rep_c105284_110 chr2A 49451566 A/G - T C AG - Excalibur_c25235_1178 chr2A 49453128 A/G + A G CT - BS00066186_51 chr2A 49848688 T/C + T C AG - BS00022013_51 chr2A 49851341 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c24614_194 chr2A 50151742 A/C - T G GT + Excalibur_c53027_323 chr2A 51564152 T/C - A G CT - TA005827-0874 chr2A 51567656 T/C + T C CT + Excalibur_c26918_75 chr2A 53921629 T/C + C T AG - Tdurum_contig66015_346 chr2A 58394953 A/G + G A AG + Excalibur_c28393_259 chr2A 58672258 A/G - T C CT + BS00045900_51 chr2A 59060148 A/G + G A CT - BS00083146_51 chr2A 59323160 A/G - T C AG - BS00085308_51 chr2A 59556598 A/G + A G AG + Tdurum_contig47258_1039 chr2A 59558265 T/C + C T CT + TA004602-1630 chr2A 61286607 A/G - T C CT + Kukri_c41248_179 chr2A 61384163 T/C - A G CT - Kukri_c20220_469 chr2A 62298915 A/G + G A AG + RFL_Contig1049_1473 chr2A 62299513 T/C - A G AG + BS00070693_51 chr2A 62302232 A/G - C T CT + Excalibur_c109119_126 chr2A 63136547 T/C + C T CT + Kukri_c10707_613 chr2A 63140459 A/G - T C CT + Kukri_c10707_203 chr2A 63148360 A/G - C T AG - IACX9380 chr2A 65184063 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Kukri_c5904_80 chr2A 66580923 T/C - G A CT - Excalibur_c18441_1160 chr2A 66804144 A/G + A G CT - BS00011740_51 chr2A 67521478 A/G + G A AG + RAC875_rep_c116200_396 chr2A 67521839 T/C NA NA NA CT NA flanks do not match reference at this position GENE-1246_417 chr2A 68254770 A/G - T C CT + Kukri_c13747_495 chr2A 69325109 A/G - T C CT + Tdurum_contig32621_437 chr2A 69325470 T/C + C T CT + Kukri_c4790_923 chr2A 69325626 T/C - A G AG + Tdurum_contig31599_351 chr2A 70871666 T/C + T C CT + RAC875_c34757_180 chr2A 70877074 T/C + C T CT + IACX5910 chr2A 70983415 C/G - C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Jagger_c2047_362 chr2A 70984364 A/G - C T AG - JG_c936_115 chr2A 71421166 T/C + T C AG - IACX5935 chr2A 74104534 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00036766_51 chr2A 74107904 T/C + T C AG - BS00036767_51 chr2A 74108007 A/G + G A AG + Kukri_rep_c83485_398 chr2A 74136348 T/C - A G AG + Kukri_rep_c101747_211 chr2A 74136793 T/C - A G CT - BS00066978_51 chr2A 74788549 T/C - G A CT - Tdurum_contig48302_539 chr2A 74788549 A/G + G A CT - Excalibur_c15733_252 chr2A 74789379 T/C - G A CT - RAC875_c20700_853 chr2A 74877864 A/G + A G CT - Excalibur_c3108_2958 chr2A 74963969 A/C + A C AC + Excalibur_c3108_5476 chr2A 74968096 A/G + G A AG + RAC875_c10344_864 chr2A 74968759 T/C + C T AG - Tdurum_contig5311_67 chr2A 75292133 A/G - C T AG - Tdurum_contig82812_213 chr2A 75316433 A/G + A G AG + RAC875_c7699_292 chr2A 76344553 T/G + T G AC - BS00055933_51 chr2A 77157995 T/C + C T AG - BS00039983_51 chr2A 77163127 T/C + C T AG - RAC875_rep_c111063_235 chr2A 77165842 A/C - T G GT + BS00062843_51 chr2A 77335085 A/G + G A CT - Kukri_s109348_329 chr2A 77528386 A/G - C T AG - Kukri_c15308_173 chr2A 77532354 A/G + G A AG + RAC875_c9959_417 chr2A 77752226 T/C + T C AG - Kukri_rep_c104727_91 chr2A 77756773 A/G + G A AG + IAAV733 chr2A 78328838 A/C - G T AC - BobWhite_c27165_244 chr2A 78330376 T/C + C T AG - RAC875_rep_c70093_1079 chr2A 78331311 A/G + A G AG + Kukri_c40035_258 chr2A 78564313 T/C + C T AG - Kukri_c24852_466 chr2A 78844411 T/C - G A AG + BS00021739_51 chr2A 79748588 A/G + G A CT - RAC875_rep_c73925_276 chr2A 79748611 T/G - A C GT - IACX2067 chr2A 81096149 A/G - C T CT + Excalibur_c6808_541 chr2A 81752187 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c6808_959 chr2A 81753399 A/G + G A CT - RAC875_c10347_1107 chr2A 81753713 A/G - C T CT + Excalibur_c5121_930 chr2A 81765640 T/C - A G CT - Excalibur_c7444_391 chr2A 81786966 T/C - A G CT - Ku_c33021_109 chr2A 82201267 A/G - T C CT + Excalibur_c44080_386 chr2A 82345253 A/C - G T AC - Excalibur_c12169_1088 chr2A 82350302 A/G - C T CT + GENE-0644_370 chr2A 83821314 T/C + T C CT + GENE-0644_421 chr2A 83821357 T/G + T G AC - BS00043082_51 chr2A 83827394 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c4847_631 chr2A 83927470 A/G + G A AG + BobWhite_c45336_321 chr2A 84940954 T/C NA NA NA AG NA flanks do not match reference at this position BobWhite_c12252_476 chr2A 85288961 A/G - T C AG - Excalibur_c50934_159 chr2A 85289098 A/G + A G CT - Ex_c721_2127 chr2A 85599635 A/G + A G AG + Ex_c721_2374 chr2A 85599882 T/C + C T AG - Kukri_rep_c105404_235 chr2A 86437050 A/G - T C AG - BS00074780_51 chr2A 86905776 A/G - T C AG - BS00107555_51 chr2A 87461823 T/C + C T CT + Kukri_c42616_467 chr2A 87855284 A/G + A G AG + Kukri_c10860_1283 chr2A 87857405 A/G - C T AG - Kukri_c29034_801 chr2A 87881599 T/C + C T CT + Kukri_c29034_867 chr2A 87881665 T/C + C T AG - Kukri_c67546_342 chr2A 87884564 A/G - T C AG - BobWhite_c3644_491 chr2A 87891249 A/C + C A AC + Kukri_c39968_221 chr2A 88011705 A/G + A G AG + Tdurum_contig64391_231 chr2A 88012443 T/C + T C CT + Tdurum_contig56511_144 chr2A 88732336 A/G - C T AG - RFL_Contig3604_484 chr2A 89119637 T/C + T C AG - IACX636 chr2A 89120396 T/C + T C CT + GENE-3867_1133 chr2A 89163997 T/C + C T CT + Excalibur_c28938_185 chr2A 89487233 T/C - G A CT - Tdurum_contig44062_733 chr2A 89768197 T/C + C T CT + BS00065418_51 chr2A 90576840 T/G + T G AC - GENE-1196_146 chr2A 92311801 A/G + G A AG + Excalibur_c1535_1115 chr2A 93405240 A/G + A G AG + Tdurum_contig45580_2786 chr2A 93882550 A/G - C T AG - Tdurum_contig45580_1717 chr2A 93885837 A/G NA NA NA AG NA flanks do not match reference at this position BS00028759_51 chr2A 93890653 T/C - G A AG + BobWhite_c5562_219 chr2A 93936249 T/C - G A AG + BobWhite_rep_c64680_305 chr2A 94003217 T/C NA NA NA CT NA flanks do not match reference at this position BS00090940_51 chr2A 97308160 A/G + G A AG + Tdurum_contig2818_118 chr2A 97841463 T/C + T C CT + IAAV539 chr2A 97842216 A/G + G A CT - Tdurum_contig93884_223 chr2A 98124074 A/G + A G CT - BS00104558_51 chr2A 99148612 T/C - A G CT - Tdurum_contig33435_131 chr2A 99167461 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_rep_c119471_174 chr2A 101994229 A/G + G A AG + Tdurum_contig62073_376 chr2A 101994229 T/C - G A AG + RAC875_c10448_718 chr2A 103099000 A/G - T C CT + BS00092273_51 chr2A 104874112 T/G + T G GT + Kukri_rep_c107604_76 chr2A 104971860 A/G + A G AG + TA003045-1227 chr2A 115120841 A/G + A G AG + BobWhite_c62913_316 chr2A 115421418 T/C + T C CT + BS00032820_51 chr2A 115999969 T/G - C A AC + RAC875_rep_c115874_98 chr2A 116160060 T/C - A G AG + Kukri_c45015_363 chr2A 117180659 T/G - A C GT - Kukri_c45015_145 chr2A 117180877 T/G - C A GT - Tdurum_contig31263_473 chr2A 117387766 T/C - A G AG + Excalibur_c11398_913 chr2A 118446604 T/C + C T CT + Kukri_c2803_1547 chr2A 121594990 A/G + A G AG + Kukri_c42244_175 chr2A 125957066 A/G - T C CT + Excalibur_c21990_102 chr2A 127008211 T/C + T C CT + RAC875_c50245_540 chr2A 127207073 A/G - C T AG - BobWhite_c10331_517 chr2A 128251479 T/C - G A CT - IAAV5331 chr2A 133985349 A/G + G A CT - Tdurum_contig11768_450 chr2A 133985760 A/C - T G AC - CAP12_rep_c4483_158 chr2A 136164859 A/C - G T AC - Kukri_c55420_355 chr2A 137128672 T/C + T C CT + RAC875_c1771_2604 chr2A 141166801 A/G + G A CT - Excalibur_c24033_860 chr2A 142717730 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c10538_429 chr2A 142718310 A/G NA NA NA AG NA flanks do not match reference at this position CAP8_c240_375 chr2A 143028807 T/G + T G GT + Kukri_rep_c104256_121 chr2A 144860119 A/G + G A AG + Excalibur_c18173_307 chr2A 145198269 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_c4630_314 chr2A 148157244 T/C + T C CT + Kukri_c100_424 chr2A 148858701 A/G + A G CT - Excalibur_rep_c113502_317 chr2A 148859447 T/C + T C CT + Excalibur_c8001_1753 chr2A 156368023 T/C - G A AG + BS00089457_51 chr2A 157933829 A/G + A G CT - BobWhite_c5096_156 chr2A 165838857 A/G + G A AG + Kukri_rep_c112814_700 chr2A 166255427 A/G - T C CT + Kukri_rep_c112814_587 chr2A 166255540 A/G - C T AG - Excalibur_rep_c107523_281 chr2A 166629550 A/C + A C AC + Excalibur_c99830_158 chr2A 167114241 T/C + C T CT + Kukri_rep_c101360_1058 chr2A 171952718 A/C - T G GT + RAC875_c6183_269 chr2A 173500907 T/C + T C CT + RFL_Contig5279_500 chr2A 176887936 A/G + G A CT - Tdurum_contig29662_110 chr2A 179669105 A/G - T C CT + RAC875_c2209_988 chr2A 187481472 A/G - T C AG - Ku_c331_1124 chr2A 191881485 A/G + G A AG + Excalibur_c18417_285 chr2A 194472892 T/C + C T CT + RAC875_c54971_197 chr2A 199032520 T/C - A G AG + RAC875_c5197_587 chr2A 199032969 T/C - A G AG + RFL_Contig3071_578 chr2A 199796308 T/C - A G AG + BS00091670_51 chr2A 200056856 T/C - A G AG + BS00068134_51 chr2A 200181854 A/G + G A AG + CAP7_rep_c12950_154 chr2A 200626585 T/C - A G AG + BS00048615_51 chr2A 200901088 T/G + G T AC - IACX6124 chr2A 200919450 A/G + G A CT - BS00076337_51 chr2A 202045939 A/G + A G CT - BS00086956_51 chr2A 202047333 T/C - G A CT - BS00039489_51 chr2A 203004127 A/G - C T AG - Tdurum_contig19560_273 chr2A 203459302 T/C - G A CT - RAC875_c11956_477 chr2A 205091611 T/C + C T CT + Kukri_c15325_1360 chr2A 205201694 T/C - A G CT - IAAV3570 chr2A 205217551 A/G + G A AG + IAAV1587 chr2A 206858198 T/C - G A CT - BobWhite_c37933_241 chr2A 207653960 A/G - C T CT + Jagger_c3061_53 chr2A 209386588 A/G - T C CT + BS00010932_51 chr2A 210470126 T/C - G A AG + BS00097263_51 chr2A 210470326 T/C - G A AG + Kukri_c20926_782 chr2A 211907695 T/G - A C AC + IAAV8481 chr2A 211911743 A/G - T C AG - Ku_c13673_1108 chr2A 211911743 T/C + T C AG - Kukri_c11455_628 chr2A 211917760 A/G + A G CT - Ra_c21065_625 chr2A 212901267 A/G - T C CT + RAC875_c15427_390 chr2A 214899983 A/G + A G AG + Kukri_rep_c70207_560 chr2A 216533379 A/G NA NA NA CT NA flanks do not match reference at this position Tdurum_contig100146_142 chr2A 218210926 T/C - A G AG + Excalibur_c7154_886 chr2A 222595233 A/G + A G AG + Tdurum_contig34143_327 chr2A 227626698 A/C + C A AC + RAC875_c29780_549 chr2A 227834030 T/C - A G CT - IAAV974 chr2A 233203752 A/G - T C AG - GENE-0875_887 chr2A 233460832 A/G + G A AG + IACX7433 chr2A 238002771 T/C + C T AG - IAAV3412 chr2A 239381463 A/G - T C AG - BS00031140_51 chr2A 241087111 T/C - G A AG + JD_c14920_380 chr2A 241973753 T/C - G A AG + Kukri_c53546_104 chr2A 250829281 A/G + A G CT - Ra_c4944_451 chr2A 252093351 T/C + T C CT + RAC875_c4944_914 chr2A 252094021 A/G + A G AG + IAAV1655 chr2A 257854792 T/C + T C AG - Excalibur_c24466_187 chr2A 261173057 A/G - T C AG - Excalibur_c11437_75 chr2A 275928717 T/C + T C CT + RAC875_c4346_111 chr2A 275929536 A/C - T G AC - Kukri_c5358_1252 chr2A 275932973 T/C + C T CT + CAP12_c1437_261 chr2A 276276570 A/G - T C AG - Excalibur_c4831_1182 chr2A 278920008 A/C - T G GT + BobWhite_c26666_152 chr2A 278992065 T/C + C T CT + BS00011045_51 chr2A 281756733 T/C + T C AG - Ku_c13599_707 chr2A 286598823 A/G - C T CT + Ku_c3575_879 chr2A 288288509 A/G - T C AG - BS00108004_51 chr2A 289759383 T/C - A G AG + BS00080997_51 chr2A 293892280 A/G + G A CT - RFL_Contig3805_680 chr2A 303730717 T/C + T C AG - Ra_c30247_628 chr2A 303743146 A/G - C T AG - BS00097694_51 chr2A 309691530 T/C - A G CT - IACX9256 chr2A 313297704 A/G - NA NA CT NA reference base G not among SNP alleles IAAV9197 chr2A 313770444 T/C - A G CT - Kukri_c38852_100 chr2A 313770444 A/G + A G CT - Ex_c101783_188 chr2A 313777608 T/C NA NA NA AG NA flanks do not match reference at this position BS00067792_51 chr2A 319045718 A/G + G A CT - RAC875_c13489_648 chr2A 323528637 A/G - T C CT + IAAV1691 chr2A 324292455 A/G - C T AG - BS00078923_51 chr2A 332044233 T/G - C A GT - BS00034382_51 chr2A 335393143 T/G + G T GT + IAAV6661 chr2A 335395798 A/G - C T CT + RAC875_c18698_550 chr2A 341627949 A/G + A G CT - Kukri_rep_c70265_167 chr2A 341921066 A/G + G A CT - BS00100472_51 chr2A 343886547 A/G + G A CT - IACX5145 chr2A 345162112 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00066310_51 chr2A 349721164 A/G - T C CT + Excalibur_rep_c107939_186 chr2A 353463033 T/C - A G CT - IAAV5457 chr2A 353470689 A/G + A G CT - RAC875_c38750_86 chr2A 353470953 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_rep_c107729_314 chr2A 355397967 A/G - T C AG - Kukri_c65433_431 chr2A 356723134 T/C + C T CT + IAAV8002 chr2A 360424958 T/C + T C AG - CAP11_c900_125 chr2A 360750986 T/C - A G CT - IAAV359 chr2A 361382615 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_rep_c67363_308 chr2A 362045790 T/C + T C AG - BS00042245_51 chr2A 367588277 T/C - A G CT - CAP11_s9154_121 chr2A 369832479 A/G - C T CT + RAC875_rep_c101788_71 chr2A 371045950 T/G + G T AC - Tdurum_contig13856_706 chr2A 371046969 T/C + C T AG - Tdurum_contig10818_618 chr2A 371341744 T/G - C A AC + Tdurum_contig10818_573 chr2A 371341789 A/C - T G AC - RAC875_c102123_187 chr2A 372229686 A/G - T C AG - RAC875_c102123_159 chr2A 372229714 A/G - T C AG - BS00052043_51 chr2A 376080025 A/C + C A AC + RAC875_c76620_361 chr2A 376752608 T/C - G A CT - GENE-0940_83 chr2A 379118345 T/C + T C CT + CAP7_rep_c6939_197 chr2A 379151189 T/C - G A CT - Ex_c5366_1904 chr2A 379945959 T/C - G A CT - Kukri_c41543_366 chr2A 379947688 A/G + A G CT - Excalibur_rep_c67624_422 chr2A 384332499 A/G + G A AG + Ex_c4639_2851 chr2A 384890683 A/G + A G AG + CAP12_rep_c8488_146 chr2A 387039611 A/G + A G AG + CAP11_c4420_138 chr2A 387086022 T/C + T C AG - Ra_c53882_371 chr2A 387642978 A/G - T C CT + IACX1022 chr2A 389222164 A/C - T G AC - RAC875_c30244_1396 chr2A 389222926 A/G + G A CT - Tdurum_contig15141_1198 chr2A 389438861 A/G + A G AG + BobWhite_c45978_111 chr2A 391111041 T/C - A G AG + CAP7_c239_267 chr2A 392729169 T/C + C T AG - Ra_c15346_447 chr2A 393515020 T/C - G A AG + IAAV6691 chr2A 394013586 T/C + C T CT + Ku_c19051_2450 chr2A 394013586 A/G - C T AG - Ku_c19051_834 chr2A 394015202 T/C - G A AG + Ra_c9532_3551 chr2A 406768927 A/C - T G AC - Kukri_rep_c72961_626 chr2A 406769596 T/C - A G CT - Ku_c40553_871 chr2A 408084283 T/C + C T CT + Ku_c13655_1180 chr2A 410878960 A/G + A G CT - Ex_c24398_831 chr2A 410879573 A/G + G A AG + BobWhite_rep_c53927_334 chr2A 412473206 A/G + A G AG + RAC875_c21173_213 chr2A 412510906 T/C + C T AG - GENE-0922_327 chr2A 412513820 A/G - T C AG - Excalibur_c18267_118 chr2A 413336341 T/C + T C CT + RAC875_c47395_652 chr2A 414985050 T/C - A G AG + IAAV2090 chr2A 414989797 T/C + T C AG - Tdurum_contig41914_544 chr2A 416008736 T/C - G A CT - Tdurum_contig41914_353 chr2A 416008927 T/C - A G CT - BobWhite_c8249_58 chr2A 420225818 T/G + T G GT + RAC875_c37015_73 chr2A 423190911 T/C + T C CT + Tdurum_contig11881_593 chr2A 423192027 A/G - T C CT + Excalibur_c9348_504 chr2A 423204812 A/C NA NA NA GT NA flanks do not match reference at this position Excalibur_c12620_225 chr2A 423778953 A/G - T C AG - BobWhite_c42875_115 chr2A 430708804 T/C + C T AG - BobWhite_c38716_323 chr2A 430951157 T/C - A G AG + BobWhite_c19806_217 chr2A 431653917 T/C - G A AG + JD_c4153_657 chr2A 431654671 T/C - G A AG + tplb0047f03_349 chr2A 432591993 T/G + G T AC - Excalibur_c42979_666 chr2A 433424558 A/G + A G AG + BobWhite_c23806_205 chr2A 433625081 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c29377_471 chr2A 437161097 A/G + A G CT - RAC875_c29377_521 chr2A 437161147 T/C + C T AG - BS00065921_51 chr2A 439398261 T/C + C T CT + RAC875_rep_c70769_95 chr2A 446526980 T/C + T C CT + Ra_c1257_2455 chr2A 447945825 A/G + A G CT - Kukri_rep_c71045_61 chr2A 449268936 A/G - T C CT + IAAV1361 chr2A 451026536 A/G - T C CT + RAC875_c9898_1212 chr2A 451026536 T/C + T C CT + RAC875_rep_c110421_111 chr2A 451567668 A/C - T G GT + RAC875_c61433_515 chr2A 454738295 A/G - T C CT + Ku_c69356_2165 chr2A 455353900 T/C + C T CT + Ra_c69516_1472 chr2A 455354133 A/G + G A AG + Ra_c37220_262 chr2A 459506343 A/G - C T AG - Kukri_c4810_211 chr2A 459516163 T/C + T C CT + Tdurum_contig10096_71 chr2A 460907487 T/G + T G GT + Tdurum_contig10096_142 chr2A 460907558 A/G + A G CT - RAC875_rep_c101689_504 chr2A 461389759 T/C - G A AG + RAC875_rep_c74447_79 chr2A 461390760 T/C + T C AG - Ra_c21219_503 chr2A 461417617 A/G + A G CT - BS00064090_51 chr2A 461727745 A/G + A G AG + Excalibur_rep_c66270_789 chr2A 461978957 T/C - G A AG + Tdurum_contig75565_1388 chr2A 461978957 A/G + G A AG + CAP7_c11156_108 chr2A 463251224 A/G + A G CT - Tdurum_contig52873_265 chr2A 463735973 A/G - C T AG - BobWhite_c36246_551 chr2A 468499572 A/G - T C AG - GENE-1057_41 chr2A 470237107 A/G - T C CT + RAC875_c41731_321 chr2A 470238277 A/G - C T AG - RAC875_rep_c71942_489 chr2A 475878029 A/G + A G AG + Kukri_rep_c76728_280 chr2A 478767070 T/C - G A AG + CAP8_c1480_140 chr2A 485047534 T/C + T C AG - BobWhite_c2099_337 chr2A 486204870 A/C + A C AC + Tdurum_contig42524_2432 chr2A 486209988 A/G + G A CT - Excalibur_c64727_82 chr2A 486898847 T/C - A G AG + RAC875_c30023_211 chr2A 486907595 T/C - A G CT - RAC875_c11682_1624 chr2A 494959633 A/G + A G AG + Kukri_c34327_343 chr2A 497449538 T/C + T C CT + Tdurum_contig76960_213 chr2A 497652462 T/C + T C AG - Ra_c1512_410 chr2A 498041002 A/G - T C CT + Ku_c59581_1412 chr2A 498043625 A/G + G A AG + Ra_c71628_188 chr2A 498044074 A/G - T C AG - RAC875_c41194_218 chr2A 498105407 A/G + G A AG + Ra_c22880_760 chr2A 498105776 A/G + A G AG + Ra_c26140_158 chr2A 501577056 A/G - C T AG - GENE-1350_36 chr2A 501850142 T/C - A G AG + Kukri_c57491_132 chr2A 502335108 A/G - T C AG - Kukri_c15489_626 chr2A 504076105 A/G - T C AG - Excalibur_c6290_1545 chr2A 504273396 A/G - T C AG - IAAV9024 chr2A 504273971 A/C - T G GT + Excalibur_c27023_134 chr2A 504275433 A/G + A G CT - RAC875_c21237_1064 chr2A 504276566 A/C - T G AC - Excalibur_c3869_427 chr2A 504277847 A/C - T G AC - CAP7_c3491_203 chr2A 504329412 T/C - A G CT - BobWhite_rep_c64242_111 chr2A 504344582 T/G - A C GT - Kukri_c15427_119 chr2A 504545547 T/C + T C AG - IAAV5270 chr2A 504545841 A/G - T C AG - CAP8_c607_659 chr2A 504711045 T/C + C T CT + IAAV444 chr2A 504711294 T/C + C T AG - BS00060653_51 chr2A 507159246 A/G + G A AG + Kukri_c11327_977 chr2A 507691422 T/G - A C GT - RAC875_c26283_54 chr2A 507692328 T/C + T C AG - BobWhite_rep_c50998_607 chr2A 508072248 T/C - G A CT - Ra_c29240_628 chr2A 508730959 A/G + G A CT - Tdurum_contig75336_402 chr2A 509356109 A/G - T C CT + CAP7_c4044_129 chr2A 510302424 T/C - A G AG + Kukri_c3740_94 chr2A 514746667 A/C + C A GT - BS00077693_51 chr2A 515945704 T/C - A G CT - TA002514-0825 chr2A 516432106 A/G NA NA NA CT NA flanks do not match reference at this position BS00061867_51 chr2A 517399093 A/C - T G AC - RAC875_c12686_683 chr2A 524330975 A/C + A C GT - RAC875_c69068_71 chr2A 526300474 T/C - G A CT - RAC875_c63386_948 chr2A 527108027 A/G + A G AG + BS00047176_51 chr2A 529635638 A/C - G T GT + RAC875_c5742_1357 chr2A 529954574 T/C - A G AG + BS00087428_51 chr2A 530745186 T/C - G A CT - BS00066607_51 chr2A 531602051 A/G + A G AG + GENE-1173_198 chr2A 532860097 T/C + C T AG - Kukri_rep_c72236_286 chr2A 533464545 T/C - G A CT - RFL_Contig5718_722 chr2A 533895316 A/G + A G CT - Kukri_c48516_73 chr2A 534622137 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c51281_802 chr2A 534631831 A/G - T C AG - Excalibur_c84687_162 chr2A 534934262 A/G + G A AG + BobWhite_c4505_531 chr2A 537250664 T/G - A C GT - IACX319 chr2A 539965347 A/G + A G CT - BobWhite_c31978_214 chr2A 542192468 A/G - T C CT + BS00040608_51 chr2A 542658559 T/C - G A AG + BS00056775_51 chr2A 542686937 T/C - G A AG + IACX85 chr2A 543122713 T/C + C T AG - Excalibur_c51073_82 chr2A 543124813 A/G + A G CT - Kukri_c77188_798 chr2A 543183218 A/G - C T CT + BS00045521_51 chr2A 543306885 A/G + G A CT - BS00055514_51 chr2A 543625494 T/C + T C CT + GENE-0672_87 chr2A 544307501 T/C + T C AG - Excalibur_rep_c103924_189 chr2A 546942319 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c20795_1027 chr2A 547134563 A/G + A G AG + IACX334 chr2A 549290522 T/G - A C GT - Kukri_c65721_427 chr2A 549679954 T/C + T C CT + Tdurum_contig50824_58 chr2A 550536139 A/G + A G CT - RAC875_c8721_212 chr2A 550540556 A/C + A C AC + CAP7_c2791_231 chr2A 551720316 T/C + C T AG - RFL_Contig852_4295 chr2A 553276200 T/C + C T CT + Tdurum_contig10579_790 chr2A 555333508 T/G - C A AC + RAC875_c31767_1093 chr2A 555341099 A/G + A G AG + BS00078116_51 chr2A 555342723 T/G + G T GT + Kukri_c61593_370 chr2A 555823957 T/C - A G CT - BobWhite_c28819_517 chr2A 556987610 T/C + C T CT + BobWhite_c28819_733 chr2A 556987826 T/C + T C AG - BobWhite_c28819_787 chr2A 556987880 A/G + G A CT - RAC875_c63975_307 chr2A 558527918 T/C - A G AG + RAC875_c53350_180 chr2A 558529026 T/C + T C CT + BS00085765_51 chr2A 558529565 T/C + C T AG - RAC875_rep_c71691_392 chr2A 558648943 A/G - T C AG - Excalibur_c1793_97 chr2A 558953050 A/C + C A AC + RAC875_c2154_1488 chr2A 558954505 T/G - C A GT - CAP12_c6044_69 chr2A 562509404 T/C + T C AG - BS00040336_51 chr2A 562509637 T/G + T G AC - BS00040337_51 chr2A 562509723 T/C + C T AG - Kukri_c9713_1999 chr2A 562527222 T/C + C T CT + RAC875_c992_718 chr2A 562604276 T/C - G A AG + Kukri_c12593_2960 chr2A 563772011 A/G + A G CT - BS00041707_51 chr2A 564265261 A/G + A G CT - BS00029224_51 chr2A 568411263 T/C - G A AG + BS00090129_51 chr2A 569584830 T/C - A G CT - BS00090128_51 chr2A 569585068 A/G - T C AG - Ex_c8505_307 chr2A 570013785 T/C + T C CT + Tdurum_contig28999_177 chr2A 572840899 T/C + C T AG - BobWhite_c1826_84 chr2A 573337693 A/G - C T CT + GENE-1264_25 chr2A 573378776 T/C - G A AG + BS00075635_51 chr2A 576067089 A/G - C T CT + BS00062628_51 chr2A 576359969 T/C + T C CT + Tdurum_contig25473_350 chr2A 578162677 A/G - T C AG - BS00068446_51 chr2A 579695692 A/G + A G CT - BS00049724_51 chr2A 579836715 A/G - C T CT + RAC875_c15367_553 chr2A 579890622 A/G + G A AG + Kukri_c23667_394 chr2A 580249278 A/G + G A CT - BS00027891_51 chr2A 580759038 T/C + T C CT + BS00027890_51 chr2A 580759259 T/G + G T AC - BS00036985_51 chr2A 580761150 T/C + T C AG - BobWhite_c2895_518 chr2A 582639677 T/C - A G AG + Tdurum_contig10906_867 chr2A 584510821 A/G - C T CT + Excalibur_c6894_792 chr2A 584512804 A/C + A C AC + IACX1369 chr2A 585139256 T/C - A G CT - Kukri_s112340_194 chr2A 585139256 A/G + A G AG + Ra_c16117_243 chr2A 585656613 A/G + A G AG + Excalibur_c2337_735 chr2A 585662263 A/G + A G AG + Tdurum_contig10019_1485 chr2A 586456780 T/C + T C CT + BobWhite_c9351_274 chr2A 587150381 A/G + A G AG + RFL_Contig89_774 chr2A 590974060 A/C - G T GT + RAC875_c54898_131 chr2A 593653474 T/C - G A CT - BS00022301_51 chr2A 597499367 A/C - G T GT + RAC875_c75351_370 chr2A 597850846 T/C + T C CT + BobWhite_c4743_63 chr2A 598617170 A/G - C T CT + Tdurum_contig27828_101 chr2A 602116290 A/C + C A AC + Kukri_c100543_472 chr2A 602117450 T/G + G T GT + RAC875_rep_c78728_248 chr2A 602128866 A/G - C T AG - RFL_Contig3658_193 chr2A 602450210 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c47535_389 chr2A 603548455 A/G - C T CT + Excalibur_c28017_641 chr2A 603560931 A/C + C A AC + IAAV80 chr2A 603686963 A/G - T C AG - Tdurum_contig30451_88 chr2A 603687297 T/C + C T CT + Kukri_c57078_153 chr2A 604750643 A/G + G A AG + Tdurum_contig11627_537 chr2A 604750873 T/C + T C CT + BS00049644_51 chr2A 605184956 A/G - C T CT + Tdurum_contig36267_169 chr2A 605635098 T/C - A G CT - Ku_c5710_312 chr2A 605800209 A/G - C T CT + Ku_c5710_310 chr2A 605800211 T/C - A G AG + Ra_c42714_1137 chr2A 605801495 A/G + A G AG + Kukri_c24064_2095 chr2A 606826148 T/G + G T GT + Tdurum_contig10586_545 chr2A 607485237 A/C + C A GT - BS00022903_51 chr2A 607827264 A/G + A G AG + Excalibur_c53423_245 chr2A 607830166 A/G + A G AG + BS00012126_51 chr2A 608608502 T/C + C T AG - JD_c10546_314 chr2A 608611087 A/C + A C AC + CAP8_rep_c3697_118 chr2A 610123524 T/C - A G AG + CAP11_rep_c6842_256 chr2A 612421764 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_c3509_1682 chr2A 614583402 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c23066_208 chr2A 617655359 A/G - T C CT + Tdurum_contig12980_500 chr2A 619240545 A/G - T C AG - Tdurum_contig12980_444 chr2A 619240601 T/C - A G AG + RFL_Contig2290_1009 chr2A 619857731 A/G NA NA NA CT NA flanks do not match reference at this position IACX794 chr2A 623546259 A/C + A C GT - GENE-4029_80 chr2A 623943330 A/G - C T AG - Excalibur_c34913_743 chr2A 624460552 T/C + C T CT + Tdurum_contig11421_212 chr2A 625028291 T/C - A G AG + BS00062658_51 chr2A 628095805 T/G + G T GT + Jagger_c3331_163 chr2A 628584758 T/G + T G GT + IAAV4464 chr2A 629108935 T/C - A G CT - JD_c3742_1130 chr2A 629108935 A/G + A G CT - Kukri_c25868_77 chr2A 630090041 A/G + A G AG + Excalibur_c995_949 chr2A 632952621 A/G - T C CT + Tdurum_contig19237_67 chr2A 635581184 T/C + T C AG - BS00063518_51 chr2A 636910094 A/G + A G AG + Kukri_c1905_232 chr2A 638306436 A/G + A G CT - RAC875_c38018_278 chr2A 639988472 T/C - G A AG + Kukri_rep_c108232_428 chr2A 640819599 T/C + C T AG - Kukri_c7622_912 chr2A 641600624 T/C - G A AG + Kukri_c7816_357 chr2A 641953150 A/G + A G CT - RAC875_c16339_265 chr2A 641957967 A/G - C T CT + BobWhite_c6356_87 chr2A 646627756 T/C - A G CT - Tdurum_contig27877_274 chr2A 647346269 T/G - A C GT - Kukri_c35671_162 chr2A 649694262 A/G - C T AG - BobWhite_c16053_183 chr2A 652291038 A/G + A G AG + IACX1471 chr2A 660513422 T/C + C T CT + Kukri_c5673_521 chr2A 662334444 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_rep_c104615_295 chr2A 662968916 T/C + T C CT + BS00022241_51 chr2A 663328967 A/C - T G GT + RAC875_c58127_53 chr2A 665843316 A/G - T C CT + Excalibur_c42050_861 chr2A 668220208 A/C + A C GT - Excalibur_c6807_825 chr2A 668450962 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_rep_c68360_1476 chr2A 668458705 T/C + T C AG - BobWhite_c10872_859 chr2A 671703415 T/C - A G CT - Excalibur_c41171_203 chr2A 671944289 A/G + G A CT - Excalibur_c74218_240 chr2A 674531815 A/G + A G AG + RAC875_c13247_1032 chr2A 675079416 A/G - T C AG - Ra_c13247_528 chr2A 675079920 A/G - C T CT + Excalibur_rep_c69799_1999 chr2A 675896548 T/C - G A CT - GENE-1792_560 chr2A 675938480 T/C + C T CT + GENE-1792_762 chr2A 675938678 T/C + T C CT + CAP7_c10780_405 chr2A 676160688 A/G + G A CT - BS00110586_51 chr2A 676232074 T/C + C T AG - BS00110587_51 chr2A 676232116 T/G + G T GT + BS00022377_51 chr2A 676238527 T/C - G A CT - BS00080654_51 chr2A 676238562 T/C - A G AG + BS00070005_51 chr2A 676244285 T/C - A G CT - RFL_Contig3780_644 chr2A 676246112 T/C - A G CT - BS00039406_51 chr2A 676383830 T/C - A G CT - RFL_Contig4528_217 chr2A 676392699 A/G - T C AG - Excalibur_rep_c69014_112 chr2A 676717419 T/C + T C CT + Tdurum_contig10794_2972 chr2A 676719076 T/G - C A GT - IACX6337 chr2A 676720118 A/G - C T AG - Tdurum_contig10794_1642 chr2A 676720406 A/C - T G GT + BS00027830_51 chr2A 676977112 T/C - A G CT - Kukri_rep_c69422_54 chr2A 676986657 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c34964_326 chr2A 677486325 A/G - T C CT + TA001859-0887 chr2A 677528969 A/C NA NA NA GT NA flanks do not match reference at this position GENE-0719_602 chr2A 678187794 T/C + T C CT + Excalibur_c2975_588 chr2A 679277041 T/C + T C AG - tplb0059b19_2378 chr2A 679505350 A/G - T C CT + GENE-0910_153 chr2A 679887395 T/C - A G CT - CAP12_c1276_171 chr2A 680278549 T/G - C A GT - IAAV2718 chr2A 681106757 T/C + T C CT + Kukri_c9785_384 chr2A 683012301 T/C + T C AG - IAAV5674 chr2A 683516603 A/C + NA NA GT NA reference base G not among SNP alleles BobWhite_c459_539 chr2A 684247861 A/G + A G CT - Excalibur_rep_c104910_124 chr2A 685222738 T/C + T C AG - BS00093447_51 chr2A 685223728 A/C + A C AC + Ra_c5443_527 chr2A 686862935 T/C + C T CT + Tdurum_contig41254_158 chr2A 688617876 A/G + A G AG + Tdurum_contig23247_547 chr2A 688619244 T/C + C T CT + Kukri_c32942_618 chr2A 688623591 T/G - C A GT - GENE-1381_132 chr2A 690932190 T/C - G A AG + GENE-1381_110 chr2A 690932208 T/G - A C GT - BobWhite_c3692_439 chr2A 691169437 T/C + C T CT + Ku_c8927_2075 chr2A 691217652 T/C - A G AG + Excalibur_c6660_746 chr2A 691218436 T/C - G A CT - Excalibur_c6660_716 chr2A 691218466 A/G - C T AG - IAAV2218 chr2A 691224022 T/C - A G CT - Kukri_c7193_3176 chr2A 691224866 A/G + G A AG + BobWhite_c15867_215 chr2A 691478585 A/G + A G CT - RAC875_c21906_247 chr2A 691478680 A/G - T C CT + BobWhite_c18506_419 chr2A 692530791 A/G + G A AG + Excalibur_c1604_2710 chr2A 692633239 A/G - T C CT + Kukri_c62142_683 chr2A 692636998 T/G + T G GT + RAC875_c52458_454 chr2A 692755051 T/C - A G CT - BobWhite_c23054_1464 chr2A 692841427 T/C - A G CT - Ra_c10607_524 chr2A 692934955 T/C - A G AG + BobWhite_c17403_635 chr2A 693241947 T/C - G A CT - BS00039422_51 chr2A 693292855 T/C - A G AG + BS00023214_51 chr2A 693294646 T/C + T C CT + RAC875_c8093_605 chr2A 694470714 T/C + C T AG - BobWhite_c12134_880 chr2A 694588952 A/G + A G AG + BS00035883_51 chr2A 694589208 T/G + T G GT + tplb0032k13_471 chr2A 694752979 A/G + A G CT - BS00089497_51 chr2A 694753643 A/G + G A AG + BS00022666_51 chr2A 694754648 A/G + G A CT - tplb0055a09_2355 chr2A 694906347 T/C - A G AG + Tdurum_contig25853_348 chr2A 695523746 A/G + A G AG + RAC875_rep_c73777_410 chr2A 696923033 T/C - G A AG + BS00011579_51 chr2A 696923072 A/G - C T CT + RAC875_c1781_1780 chr2A 696924419 A/G + A G CT - RAC875_c1781_1897 chr2A 696924536 T/C + T C CT + BobWhite_c3521_644 chr2A 697290647 A/C - G T AC - CAP12_rep_c6956_169 chr2A 697291164 T/C + T C AG - BS00077597_51 chr2A 699422777 A/G + G A CT - BS00000297_51 chr2A 699912092 T/C - G A AG + GENE-3975_194 chr2A 701485818 A/G - C T CT + GENE-3975_114 chr2A 701485886 T/G - C A GT - BS00083497_51 chr2A 701487889 A/G - T C AG - BobWhite_c41676_137 chr2A 703106230 T/C + C T CT + BobWhite_c20952_105 chr2A 703709493 A/G + G A CT - GENE-1182_349 chr2A 703880593 A/C + C A GT - Excalibur_c40617_983 chr2A 703976451 A/G - T C CT + Excalibur_c28325_140 chr2A 704710546 T/C + T C CT + Excalibur_c20933_416 chr2A 704771745 T/C + T C AG - GENE-1399_244 chr2A 704774996 A/G NA NA NA AG NA flanks do not match reference at this position GENE-1224_596 chr2A 705505042 A/G + G A AG + RAC875_c13861_1248 chr2A 705507123 T/C + C T CT + BS00029332_51 chr2A 705804860 T/C - A G CT - RFL_Contig4324_1348 chr2A 705826304 A/G - T C AG - BS00107804_51 chr2A 707040222 T/C + C T CT + IAAV56 chr2A 708185218 T/C + C T CT + BS00001059_51 chr2A 708185860 A/G + A G AG + Kukri_c21090_733 chr2A 709028553 A/C - T G AC - Ra_c70418_142 chr2A 709041048 A/C + A C AC + Ra_c70418_147 chr2A 709041053 A/C + A C AC + BobWhite_c31673_296 chr2A 709624934 T/C + T C CT + RAC875_rep_c108798_241 chr2A 709703439 T/C - A G CT - RAC875_c64377_350 chr2A 709711892 T/G - C A AC + Excalibur_c22687_1091 chr2A 709774673 A/G + A G AG + IAAV4899 chr2A 709836551 T/C - A G CT - RAC875_rep_c108548_253 chr2A 709836894 A/G - T C AG - Excalibur_c3171_416 chr2A 709850320 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c7282_285 chr2A 710099488 A/G + G A CT - BobWhite_rep_c64766_352 chr2A 711075336 T/G - C A GT - BS00022587_51 chr2A 711077223 A/G - C T AG - Excalibur_c5482_1264 chr2A 711637867 T/C - A G CT - Excalibur_c47219_820 chr2A 711640818 A/G - C T CT + Excalibur_c47219_186 chr2A 711641773 A/C - T G AC - IAAV6408 chr2A 711976227 A/G - T C CT + CAP12_c2521_103 chr2A 711980154 A/C - T G GT + BobWhite_c2512_1767 chr2A 712555325 T/C + T C AG - Kukri_rep_c69608_2762 chr2A 712573347 A/G - T C CT + Ku_c69608_894 chr2A 712577973 A/G - C T AG - Kukri_rep_c69608_375 chr2A 712578885 A/G - T C AG - RAC875_c13774_161 chr2A 712579995 T/C - G A AG + RAC875_rep_c102601_57 chr2A 712706817 A/G - C T CT + RAC875_c110838_165 chr2A 712721191 T/C + C T CT + Ku_c13700_1196 chr2A 712721629 A/G - C T CT + Ku_c13700_1189 chr2A 712721636 A/G - T C AG - Excalibur_c41125_360 chr2A 713444679 A/G - T C AG - RAC875_c81899_216 chr2A 714207640 T/C + T C CT + Ku_c9320_1234 chr2A 714210037 T/C + C T AG - TA005062-0529 chr2A 714625360 A/G - T C CT + RAC875_c58006_492 chr2A 715300463 A/G + A G AG + RAC875_c13390_1096 chr2A 715304163 A/G + G A CT - RAC875_c13390_1329 chr2A 715304396 A/G + G A CT - Kukri_c4027_151 chr2A 715333178 T/C + C T CT + Tdurum_contig40560_66 chr2A 715406447 T/C - A G CT - RAC875_c42648_115 chr2A 716169593 A/G + G A AG + RAC875_c42648_238 chr2A 716169716 A/G + A G CT - RAC875_c54927_800 chr2A 716178924 A/C + A C GT - Jagger_c9554_114 chr2A 716548942 T/C - G A AG + Kukri_c33828_801 chr2A 716918404 A/C - G T AC - Kukri_c47259_416 chr2A 717189499 A/G + A G CT - BS00110267_51 chr2A 717384851 T/C - A G CT - IACX1163 chr2A 717581668 T/G - C A GT - BS00065865_51 chr2A 717817040 A/C + A C AC + GENE-0703_5 chr2A 717824100 A/G - C T CT + Excalibur_c36481_519 chr2A 717941902 T/G - A C GT - BS00080752_51 chr2A 718355438 A/G + A G AG + BS00093201_51 chr2A 718571627 A/G - T C AG - BS00108775_51 chr2A 718722659 A/G + A G CT - BS00081506_51 chr2A 718730530 T/C + C T AG - RAC875_c16333_340 chr2A 721562498 A/G + G A CT - BS00064069_51 chr2A 721567998 T/C - A G CT - Excalibur_rep_c96883_147 chr2A 722138735 T/C - G A CT - Kukri_c3115_279 chr2A 722141663 T/C + T C AG - Excalibur_c57590_187 chr2A 722736066 T/C + T C AG - Kukri_c11022_549 chr2A 722736066 A/G NA NA NA CT NA flanks do not match reference at this position BS00079611_51 chr2A 723521375 T/G + G T AC - RAC875_c3378_1345 chr2A 723523936 T/C - A G AG + RFL_Contig3509_229 chr2A 723823710 T/G + T G AC - Kukri_c42324_656 chr2A 724528610 T/C - A G CT - BS00110450_51 chr2A 724620266 A/G - T C CT + RFL_Contig1691_2249 chr2A 724620773 A/C - T G AC - Kukri_c29592_559 chr2A 724622599 T/G - A C AC + BobWhite_c12090_117 chr2A 725346975 T/C + C T CT + GENE-1068_107 chr2A 725912844 T/G - C A AC + GENE-1068_60 chr2A 725912879 A/C - G T AC - GENE-2400_351 chr2A 726033446 T/C + T C AG - GENE-2400_109 chr2A 726033461 A/G + A G AG + Tdurum_contig12761_125 chr2A 727243399 A/C - T G GT + RAC875_rep_c107961_348 chr2A 727580363 T/C + C T CT + GENE-0638_1119 chr2A 728071406 A/C - T G AC - GENE-1908_331 chr2A 729169100 A/C + A C GT - TA013902-0228 chr2A 729287020 T/C NA NA NA CT NA flanks do not match reference at this position BS00057059_51 chr2A 729287911 A/G - C T AG - BS00057060_51 chr2A 729288308 T/C - G A AG + Kukri_c15340_1087 chr2A 732569649 T/C - G A AG + BS00082084_51 chr2A 732569776 T/C + C T CT + Tdurum_contig10574_864 chr2A 732585343 T/C - G A AG + BS00024921_51 chr2A 733091174 A/G - T C CT + Kukri_c25901_348 chr2A 733353526 T/G - A C AC + BobWhite_c8982_226 chr2A 733922154 A/G + G A CT - Kukri_c22047_313 chr2A 734148891 T/C + C T CT + BS00104083_51 chr2A 734256911 A/G + G A CT - BobWhite_c12767_148 chr2A 734346381 A/C + A C AC + RAC875_rep_c69619_260 chr2A 734349056 A/G - C T AG - RAC875_rep_c69619_78 chr2A 734352032 A/C NA NA NA AC NA flanks do not match reference at this position RAC875_rep_c111598_723 chr2A 734526222 T/C + T C AG - Kukri_c33884_632 chr2A 734526923 T/C - A G CT - BS00068413_51 chr2A 734596348 A/G + A G CT - RAC875_c46498_567 chr2A 734628858 A/C + C A AC + tplb0042l03_580 chr2A 734767492 A/G - C T AG - Excalibur_c42799_210 chr2A 734767753 A/G + G A AG + tplb0046b02_872 chr2A 734891198 A/G - C T CT + Excalibur_s116597_198 chr2A 734891399 A/G - T C AG - BS00009295_51 chr2A 734892014 A/G - T C CT + RFL_Contig1892_2214 chr2A 734892406 T/C + T C CT + RAC875_c19904_308 chr2A 734972837 A/G - T C CT + RAC875_c104160_61 chr2A 734973568 T/C - G A AG + BS00009817_51 chr2A 735007905 T/C + T C AG - BS00065808_51 chr2A 735565378 A/G - T C CT + BobWhite_c13525_262 chr2A 735787622 T/C - G A CT - Tdurum_contig4976_1138 chr2A 738989829 A/G + G A AG + BS00022265_51 chr2A 739254611 T/G + G T AC - Tdurum_contig60205_806 chr2A 739712583 T/C - A G CT - Tdurum_contig60205_509 chr2A 739712880 T/C - G A AG + BS00077768_51 chr2A 739923970 A/G + G A AG + BS00077769_51 chr2A 739924052 T/C + T C CT + BobWhite_c15766_562 chr2A 740012609 T/C - G A AG + Tdurum_contig10262_324 chr2A 740069090 A/G - T C CT + Excalibur_rep_c104620_183 chr2A 740360704 A/G + G A CT - Kukri_c25978_561 chr2A 740361107 T/C + C T CT + BobWhite_c25764_348 chr2A 740848583 T/C - A G CT - Ex_c5740_1133 chr2A 740848583 T/C - A G CT - Excalibur_c22696_316 chr2A 741371290 A/C + A C AC + BS00022813_51 chr2A 741371853 A/G + G A AG + Ku_c36209_204 chr2A 741827101 A/G - T C AG - Ku_c29409_324 chr2A 741984907 A/G - T C CT + BS00016238_51 chr2A 742134296 T/C NA NA NA AG NA flanks do not match reference at this position IAAV2861 chr2A 742134296 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c25848_122 chr2A 742720804 A/G - T C AG - IACX5800 chr2A 743096726 A/G + A G AG + BS00010098_51 chr2A 743096773 A/G - C T AG - RAC875_c8309_119 chr2A 743096893 T/C - A G AG + RAC875_c20564_881 chr2A 743097115 T/G + G T GT + GENE-4595_130 chr2A 743387531 T/G - C A GT - Ra_c3750_1082 chr2A 743574619 T/C - A G AG + Excalibur_c42110_210 chr2A 744283297 A/G - T C CT + IAAV3791 chr2A 744447878 A/G + G A AG + Tdurum_contig44139_1033 chr2A 744448070 A/G + G A CT - BS00030165_51 chr2A 744809705 A/G - C T AG - Tdurum_contig6086_269 chr2A 744809705 T/C + C T CT + Excalibur_c8009_325 chr2A 744811472 T/C - A G AG + BobWhite_c17783_174 chr2A 744820597 A/C - G T AC - GENE-0862_110 chr2A 745031425 A/G + A G AG + GENE-0862_322 chr2A 745031633 A/G + A G AG + Tdurum_contig12912_308 chr2A 745035377 T/G NA NA NA AC NA flanks do not match reference at this position Excalibur_rep_c67956_851 chr2A 746598709 T/C - A G AG + Tdurum_contig84245_154 chr2A 746761671 T/C - A G CT - BS00000209_51 chr2A 746763800 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c15615_254 chr2A 746764228 A/G + A G CT - BS00110516_51 chr2A 746975200 T/C - A G CT - IACX3245 chr2A 747089765 T/C + T C CT + BS00062732_51 chr2A 747090455 A/G + G A CT - BS00063236_51 chr2A 747144155 T/C - G A AG + RAC875_rep_c114621_122 chr2A 748964650 A/C - T G AC - BS00022446_51 chr2A 750066046 A/G + G A CT - BobWhite_c47555_106 chr2A 750550081 A/G + A G CT - CAP7_c1527_136 chr2A 750550192 T/C - A G AG + BS00053834_51 chr2A 750550273 A/G + A G AG + IACX987 chr2A 751006094 A/G - C T AG - BS00071660_51 chr2A 751008361 A/G + G A AG + Kukri_c30020_302 chr2A 751094065 T/C + T C CT + BobWhite_c5178_188 chr2A 751511217 T/C - A G CT - Kukri_c50391_219 chr2A 751511242 T/C + T C CT + BS00025880_51 chr2A 751609428 T/C + T C AG - BobWhite_c4517_120 chr2A 751663232 A/G - T C CT + BobWhite_c20335_236 chr2A 751892973 T/G + G T AC - RAC875_c35065_719 chr2A 752092718 A/G - T C AG - BobWhite_c15773_166 chr2A 752092859 T/C + C T AG - Excalibur_c9752_670 chr2A 752276901 T/C - A G AG + Excalibur_rep_c110586_1083 chr2A 752277464 T/C + C T CT + BS00064324_51 chr2A 752559649 T/C - A G CT - RFL_Contig2656_871 chr2A 753540797 A/G - T C CT + Excalibur_rep_c66606_2065 chr2A 753980276 T/C - A G CT - Excalibur_c20439_825 chr2A 753987428 T/C + T C AG - BS00023075_51 chr2A 754339185 A/G + A G CT - Tdurum_contig47508_250 chr2A 754339185 T/C - A G CT - Kukri_c27894_369 chr2A 754354408 T/G + T G GT + BS00063368_51 chr2A 754356931 T/C + T C AG - Excalibur_c35919_107 chr2A 754461555 A/G + G A AG + BS00074648_51 chr2A 755248799 A/G + G A CT - BS00067663_51 chr2A 755434392 T/G - C A AC + RAC875_c1706_1888 chr2A 755776336 A/G + A G CT - IAAV880 chr2A 755788434 T/C + C T CT + Tdurum_contig61938_424 chr2A 755788761 T/C - A G CT - BS00096927_51 chr2A 755789414 T/C + C T CT + CAP12_c575_105 chr2A 755794967 A/G - T C CT + BobWhite_c5191_362 chr2A 755974850 T/C NA NA NA AG NA flanks do not match reference at this position BobWhite_c5191_563 chr2A 755975155 T/C + T C CT + Excalibur_c10018_356 chr2A 757635777 A/G - C T CT + BobWhite_c42181_327 chr2A 757942874 A/G + A G AG + Excalibur_c39151_104 chr2A 757946889 A/G + G A CT - RAC875_c21013_1187 chr2A 757947956 T/C - G A CT - Excalibur_c52319_257 chr2A 757948238 T/C - G A CT - RAC875_c21013_841 chr2A 757948302 A/G - C T AG - Tdurum_contig25539_248 chr2A 758287054 A/G + G A AG + RAC875_c96399_610 chr2A 758388461 A/C + A C GT - IAAV3800 chr2A 758396116 A/G + A G CT - Excalibur_c923_837 chr2A 758396241 T/C + T C AG - Ku_c72620_132 chr2A 758396715 A/C + A C AC + Excalibur_c4372_363 chr2A 758396922 A/G + G A AG + RAC875_rep_c102485_468 chr2A 758397306 A/G NA NA NA AG NA flanks do not match reference at this position IAAV6070 chr2A 758399278 T/C + T C CT + Tdurum_contig53038_714 chr2A 758420888 T/C - G A AG + Tdurum_contig53038_684 chr2A 758420918 A/G - C T AG - BS00011539_51 chr2A 758421352 T/C + C T CT + Excalibur_c31864_179 chr2A 758532616 T/C - G A AG + RAC875_c22328_490 chr2A 759813947 T/C + T C CT + RAC875_c16727_1826 chr2A 759828703 T/C - A G AG + Tdurum_contig52350_902 chr2A 759829874 T/C - G A CT - Tdurum_contig52350_170 chr2A 759830792 T/G - A C AC + RAC875_c259_1339 chr2A 759830917 T/C + T C CT + BobWhite_c17943_633 chr2A 759869637 A/G NA NA NA CT NA flanks do not match reference at this position Tdurum_contig16904_167 chr2A 760564780 A/G + A G AG + BS00097473_51 chr2A 760564862 T/G - C A AC + IAAV6102 chr2A 760565582 T/C - A G CT - Excalibur_c71561_356 chr2A 760574464 T/C - A G AG + JD_c246_260 chr2A 761859799 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c15518_236 chr2A 762286198 A/C + A C GT - Kukri_c498_2381 chr2A 762289860 A/G + A G AG + RAC875_c5082_1098 chr2A 762623613 A/G + G A CT - BobWhite_c5756_516 chr2A 763047572 T/C + T C AG - CAP12_c449_277 chr2A 763368990 A/G + A G AG + GENE-0686_804 chr2A 763693598 T/C + T C AG - BS00012014_51 chr2A 764089681 A/C - T G AC - BS00072462_51 chr2A 765055795 T/C - A G CT - RAC875_c3259_276 chr2A 765705705 A/G + G A CT - Excalibur_c2311_1116 chr2A 765708562 T/G + T G GT + RAC875_c42539_151 chr2A 766400360 A/G + A G CT - BobWhite_c1523_269 chr2A 766982014 A/G - T C AG - tplb0060e06_1793 chr2A 767781808 A/G - C T AG - Excalibur_c21501_219 chr2A 769004638 T/G - A C AC + RAC875_c51691_82 chr2A 769221796 T/C + T C CT + RFL_Contig5495_563 chr2A 770013124 A/G - T C CT + BobWhite_rep_c63940_205 chr2A 770358453 T/C + C T AG - GENE-0762_185 chr2A 770412672 A/G - T C CT + RAC875_rep_c101664_297 chr2A 771238395 A/G + A G CT - RFL_Contig5277_1283 chr2A 771512413 T/C - A G CT - RFL_Contig5277_888 chr2A 771513348 T/C - G A AG + BS00091763_51 chr2A 773186043 A/G - T C AG - RAC875_c5998_1056 chr2A 774568995 T/C + T C AG - Excalibur_rep_c67599_272 chr2A 774569325 T/C + T C CT + IAAV1322 chr2A 774573507 T/C - G A CT - Kukri_c17_967 chr2A 774853537 T/C - A G AG + Tdurum_contig10295_374 chr2A 775018588 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c50116_107 chr2A 776214859 A/G - C T CT + Kukri_rep_c104982_217 chr2A 776219534 A/G - T C CT + tplb0043n06_2291 chr2A 776290836 T/G + T G AC - BS00022965_51 chr2A 776394975 A/G NA NA NA CT NA flanks do not match reference at this position BS00099801_51 chr2A 776394994 T/C + T C AG - Kukri_c53501_305 chr2A 776552712 A/G - T C CT + Excalibur_c38714_170 chr2A 777497208 A/G - T C AG - Tdurum_contig52627_726 chr2A 777515561 A/G - T C AG - BS00068691_51 chr2A 777518471 A/G - T C AG - BobWhite_c24069_257 chr2A 778425899 T/C - G A CT - BS00027799_51 chr2A 778442536 A/G - C T CT + BS00011392_51 chr2A 778919253 A/C - T G GT + Kukri_c706_702 chr2A 779205237 A/G - C T AG - BS00024643_51 chr2A 779207379 T/C - G A CT - CAP8_c3129_381 chr2A 779269585 A/G NA NA NA CT NA flanks do not match reference at this position BS00064813_51 chr2A 779295432 A/G + A G CT - tplb0025l18_1788 chr2A 779646054 T/C + C T CT + RAC875_c51459_311 chr2A 779670974 A/G - T C AG - Tdurum_contig50720_482 chr2A 779818505 A/C - T G GT + RAC875_c35688_382 chr2A 779882017 T/C + C T CT + Tdurum_contig92425_3144 chr2A 779991253 A/G + A G CT - Tdurum_contig8350_350 chr2A 780714622 A/G - T C AG - IAAV4880 chr2A 780714729 A/C + A C AC + RAC875_c27611_467 chr2B 1251436 T/C + T C AG - BS00084668_51 chr2B 1832807 A/G + A G CT - BS00044332_51 chr2B 2109722 T/C - A G CT - BS00023068_51 chr2B 3300107 T/C - A G CT - BS00046538_51 chr2B 3312649 T/C - A G CT - Ra_c2544_1566 chr2B 4185728 A/C - G T GT + Kukri_c30847_344 chr2B 4664247 A/G + A G CT - BS00061187_51 chr2B 4790129 T/C + T C CT + RAC875_rep_c71112_400 chr2B 4990423 A/G - T C CT + IAAV1970 chr2B 5609620 T/C + T C AG - Excalibur_rep_c107769_116 chr2B 5666766 A/G + A G CT - Tdurum_contig12189_1334 chr2B 5670462 A/G + A G CT - Kukri_rep_c97239_133 chr2B 6210157 A/G - T C AG - Excalibur_c39493_251 chr2B 6210321 A/G - T C AG - BS00028028_51 chr2B 6253562 T/C + C T AG - Excalibur_c17250_104 chr2B 6263196 T/C + T C CT + RAC875_c35090_398 chr2B 6263619 A/G - T C CT + Excalibur_c17250_646 chr2B 6263737 A/G + G A AG + Excalibur_c17250_751 chr2B 6263842 A/G NA NA NA AG NA flanks do not match reference at this position tplb0034e07_1869 chr2B 6311327 T/C - G A CT - tplb0034e07_718 chr2B 6313903 A/G - C T CT + GENE-1442_78 chr2B 6337735 A/C + A C GT - Excalibur_c29417_499 chr2B 7429446 T/C - G A CT - RAC875_c45166_1174 chr2B 7429616 A/C - T G GT + BS00101972_51 chr2B 7430458 A/G + A G CT - BS00031118_51 chr2B 7435627 A/G + G A AG + Kukri_c6306_1151 chr2B 7436667 T/C - A G CT - BS00058815_51 chr2B 7436731 T/C + T C AG - BS00083763_51 chr2B 7443043 T/C + C T AG - BS00083768_51 chr2B 7443154 T/C + T C CT + BS00101456_51 chr2B 7645606 A/G + A G CT - BS00074254_51 chr2B 8567346 A/G - C T AG - BobWhite_c2963_1880 chr2B 8593100 A/G - C T CT + Kukri_c3701_330 chr2B 9730916 A/G + A G AG + Kukri_c3701_392 chr2B 9730978 T/C + T C CT + Kukri_c6626_57 chr2B 9871591 T/C + T C CT + BS00099465_51 chr2B 10781806 T/C + T C AG - BS00099469_51 chr2B 10784146 A/G + A G AG + BobWhite_c11397_231 chr2B 10784233 T/G - A C GT - Excalibur_c1747_429 chr2B 11462831 A/C NA NA NA AC NA flanks do not match reference at this position BS00081871_51 chr2B 12076610 A/C + C A GT - BS00022126_51 chr2B 12076713 T/G + T G GT + BobWhite_c19945_341 chr2B 12881061 T/G - A C GT - RAC875_c6538_123 chr2B 13166108 A/G - C T AG - BS00077463_51 chr2B 13757971 A/G - C T CT + BS00077462_51 chr2B 13758119 T/C - G A AG + BS00076139_51 chr2B 13767909 A/G + G A CT - BobWhite_c26803_89 chr2B 14047064 T/C + C T CT + Kukri_c22513_1780 chr2B 14047161 A/G - C T AG - Excalibur_c25445_1061 chr2B 14048067 T/C + T C CT + Excalibur_c476_266 chr2B 16815952 T/C - G A CT - Excalibur_c1787_1199 chr2B 16827992 T/C + T C AG - Excalibur_c3524_318 chr2B 16898003 A/G - C T CT + Kukri_c16758_443 chr2B 17389176 T/G - C A GT - Excalibur_c841_609 chr2B 17390904 T/C + C T AG - BS00065556_51 chr2B 17456915 T/C - A G AG + Excalibur_c42928_135 chr2B 17564545 T/C - A G CT - Kukri_c56081_307 chr2B 17570892 A/G + A G CT - BS00110996_51 chr2B 17572453 A/G - T C CT + GENE-1018_99 chr2B 17783428 A/G - C T CT + Kukri_c27673_289 chr2B 17787291 A/G + A G AG + RAC875_c87052_193 chr2B 18176463 T/C - A G CT - tplb0058m16_1152 chr2B 18177366 T/C - G A CT - Excalibur_c14396_1629 chr2B 18939220 A/G - T C CT + TA003865-0902 chr2B 20076011 A/G + A G AG + BS00061979_51 chr2B 20077015 T/C - G A CT - BS00077642_51 chr2B 20373384 T/C - G A CT - RAC875_c21646_496 chr2B 21911562 A/G + A G CT - Excalibur_c60081_474 chr2B 21912494 T/C - G A AG + RAC875_c30161_82 chr2B 21952499 A/G + G A CT - RFL_Contig5625_912 chr2B 22320051 A/C - G T AC - Excalibur_c94336_68 chr2B 22788919 A/C + A C GT - Excalibur_c94336_103 chr2B 22788954 T/C + C T CT + BS00063251_51 chr2B 22789330 A/C + C A GT - GENE-1711_304 chr2B 23543308 A/G NA NA NA AG NA flanks do not match reference at this position GENE-1422_774 chr2B 24239830 T/G + G T AC - BS00109330_51 chr2B 24264502 T/C - G A AG + Excalibur_rep_c108189_683 chr2B 25019247 A/G - T C AG - IAAV5802 chr2B 25021122 A/C + A C GT - Kukri_c63748_1453 chr2B 25021434 A/G - C T CT + Ku_c63748_1264 chr2B 25021826 T/C - G A CT - tplb0058j01_762 chr2B 25072004 A/G - T C AG - BS00038498_51 chr2B 25236588 A/G + A G CT - RAC875_c15909_659 chr2B 26100866 A/G + A G AG + RAC875_c47161_100 chr2B 26337247 A/C - T G AC - BS00009263_51 chr2B 26564155 T/C + T C CT + CAP8_c5108_139 chr2B 26567971 A/G - C T AG - BS00065036_51 chr2B 26581602 T/G - C A GT - Excalibur_c2454_333 chr2B 26581945 T/C - A G AG + RAC875_c52926_871 chr2B 27728467 T/C + T C AG - GENE-1676_57 chr2B 28293627 A/G + A G CT - Excalibur_c40567_1857 chr2B 28368534 A/G + G A AG + CAP11_c585_134 chr2B 28416207 A/C - T G GT + Kukri_c48_1257 chr2B 29039311 T/C NA NA NA AG NA flanks do not match reference at this position RFL_Contig5031_526 chr2B 30496930 A/C + A C GT - BS00067046_51 chr2B 31422132 A/G + G A CT - Kukri_c53810_137 chr2B 31622741 T/C + T C CT + BS00076982_51 chr2B 32871698 T/C + C T CT + BobWhite_c2988_421 chr2B 33839721 T/C + T C CT + Kukri_rep_c106786_230 chr2B 33839886 T/C - G A AG + BobWhite_c2988_2161 chr2B 33841462 T/C + C T CT + IAAV3478 chr2B 34063517 T/C - A G CT - GENE-1123_531 chr2B 35390985 T/C - G A CT - BS00064704_51 chr2B 39368562 A/G + G A AG + Excalibur_c50192_149 chr2B 39736466 T/C + C T AG - BS00012081_51 chr2B 41144291 A/G - T C CT + RAC875_c15844_348 chr2B 41145515 T/C + T C AG - RAC875_c31358_214 chr2B 41145744 A/G + G A CT - BS00055665_51 chr2B 41153199 T/C + T C AG - Tdurum_contig42153_5854 chr2B 41155090 T/G - A C AC + Tdurum_contig42153_4175 chr2B 41157022 A/G NA NA NA AG NA flanks do not match reference at this position BS00109853_51 chr2B 42277344 T/G - A C AC + BS00077914_51 chr2B 42281570 T/C - A G AG + RAC875_c2014_153 chr2B 42943582 A/G + G A CT - BS00071995_51 chr2B 42944370 T/C + T C AG - RAC875_rep_c105164_545 chr2B 42945359 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c29807_713 chr2B 42947270 T/C - A G AG + Kukri_c29807_476 chr2B 42948061 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_rep_c103893_875 chr2B 42953625 T/C + T C AG - BobWhite_rep_c63363_160 chr2B 43615989 T/C - A G AG + BobWhite_c5072_107 chr2B 44191094 T/C + T C CT + BobWhite_rep_c65082_84 chr2B 44352849 A/G - T C AG - JD_c49544_37 chr2B 44360570 T/C NA NA NA AG NA flanks do not match reference at this position BS00022950_51 chr2B 44404953 A/G - C T CT + BS00093755_51 chr2B 44424336 T/C - G A CT - RAC875_rep_c79427_59 chr2B 44426840 A/G - C T CT + Excalibur_c21220_88 chr2B 44922004 T/C + T C AG - Ku_c41677_924 chr2B 45537579 T/C + T C AG - TA002079-5951 chr2B 45788713 T/G - A C AC + BS00036721_51 chr2B 46088370 T/C - G A AG + Kukri_c28478_750 chr2B 46090280 A/C + A C AC + Excalibur_c26099_106 chr2B 46115201 T/C - G A CT - GENE-1421_802 chr2B 46880030 A/G NA NA NA AG NA flanks do not match reference at this position GENE-1421_706 chr2B 46880122 A/G - C T CT + BS00022382_51 chr2B 46894037 T/C - A G CT - Kukri_c29640_92 chr2B 47168996 A/G + A G AG + BS00022487_51 chr2B 47169671 A/G + G A CT - RAC875_c17720_436 chr2B 47181365 T/C + T C CT + RAC875_c17720_501 chr2B 47181430 A/G + G A CT - RAC875_c17720_570 chr2B 47181499 A/G + G A CT - IAAV2277 chr2B 47427272 T/C + C T CT + Ex_c12051_875 chr2B 47427954 T/C + T C CT + IAAV4206 chr2B 47430632 T/C + T C CT + RAC875_c12766_461 chr2B 47430632 A/G - T C CT + Ku_c34562_480 chr2B 47454569 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c23425_208 chr2B 47839525 T/C + T C CT + BS00064155_51 chr2B 50290471 T/C - A G AG + BS00009807_51 chr2B 52669991 T/C - G A CT - IAAV3165 chr2B 52670346 A/G - T C AG - Kukri_c37311_136 chr2B 52700856 T/C + C T CT + Kukri_c37311_790 chr2B 52701512 A/G + A G AG + BS00095573_51 chr2B 52701779 T/C - A G CT - IACX445 chr2B 52872936 T/C - G A CT - BobWhite_c8734_91 chr2B 52911796 A/G + G A AG + Tdurum_contig11803_850 chr2B 54531395 T/C - A G CT - Tdurum_contig51706_895 chr2B 54532358 T/C - G A CT - Tdurum_contig51706_157 chr2B 54533105 A/G - T C AG - Kukri_c16479_765 chr2B 54778663 A/G - T C CT + BobWhite_c3448_80 chr2B 57651517 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c4349_1050 chr2B 57654517 T/C + T C AG - IACX1098 chr2B 58324675 A/G + G A AG + Tdurum_contig54704_176 chr2B 58325008 A/G - C T AG - BobWhite_c41535_52 chr2B 58979444 T/C + T C AG - Excalibur_c23201_970 chr2B 64205007 T/C - A G CT - BS00038820_51 chr2B 64988290 T/C - G A CT - BS00067962_51 chr2B 65100056 A/G - C T CT + RAC875_c26469_480 chr2B 65100754 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c26469_363 chr2B 65100871 A/G - C T CT + RAC875_c61801_299 chr2B 65106996 T/G - A C AC + RAC875_c15229_108 chr2B 65114029 T/C + T C AG - BobWhite_c47608_273 chr2B 65317192 A/G + G A CT - BS00096182_51 chr2B 65370483 A/G + G A CT - Excalibur_c25234_143 chr2B 66214720 A/G - T C AG - BobWhite_c11739_325 chr2B 66544151 A/G - C T CT + BobWhite_c31129_60 chr2B 68201601 T/C + C T CT + Tdurum_contig9716_2337 chr2B 68219192 T/C - A G CT - Tdurum_contig9716_1460 chr2B 68220785 T/C - G A CT - Excalibur_c1233_669 chr2B 68223331 A/G - T C CT + Tdurum_contig9716_553 chr2B 68223859 A/G - C T CT + Ku_c5725_892 chr2B 68363434 A/G - T C AG - Ku_c5725_615 chr2B 68363711 T/C - G A CT - Kukri_rep_c107572_121 chr2B 68365355 A/G - C T CT + Tdurum_contig42636_1245 chr2B 68599654 T/C - G A AG + RAC875_c95948_614 chr2B 69370567 T/C - A G AG + Tdurum_contig45255_3473 chr2B 69410759 T/C - A G CT - RAC875_c22429_249 chr2B 69414814 A/G - T C CT + BS00065105_51 chr2B 69648893 T/C - A G CT - RAC875_c22619_364 chr2B 72577254 A/G + A G AG + BS00010055_51 chr2B 72610551 A/G - C T AG - IACX8565 chr2B 72610551 T/C + C T AG - Tdurum_contig61293_131 chr2B 73989699 T/C - A G CT - Kukri_c29272_363 chr2B 75693581 T/C + T C CT + CAP12_rep_c5926_51 chr2B 75694948 T/C + C T AG - CAP12_rep_c5926_115 chr2B 75695012 T/C + C T CT + Kukri_c43403_594 chr2B 76817000 T/C - G A CT - Excalibur_c20058_339 chr2B 76817110 T/G - A C GT - Kukri_c43403_346 chr2B 76817378 T/C - A G AG + IAAV7837 chr2B 76916492 T/C - G A CT - Jagger_c8098_88 chr2B 76916706 A/G - T C AG - RAC875_c8780_441 chr2B 76929459 A/G - T C AG - Tdurum_contig7526_301 chr2B 77170014 T/G - C A AC + BS00110490_51 chr2B 77170646 T/C + C T AG - Excalibur_rep_c101660_546 chr2B 77172619 A/G + A G AG + Tdurum_contig29620_285 chr2B 77172888 T/C - G A CT - Tdurum_contig29620_207 chr2B 77172966 A/G - C T CT + Excalibur_rep_c101660_869 chr2B 77173029 A/G + G A AG + Tdurum_contig29620_125 chr2B 77173048 A/G - T C AG - IAAV8040 chr2B 77174828 A/C + A C AC + Tdurum_contig74936_264 chr2B 77290852 T/G + G T AC - Tdurum_contig74936_387 chr2B 77290975 A/G + A G CT - Tdurum_contig11350_827 chr2B 77902878 T/G - A C AC + Tdurum_contig11350_629 chr2B 77905076 A/G - T C CT + Kukri_rep_c69288_529 chr2B 87350805 T/C - A G CT - RAC875_rep_c119905_116 chr2B 87351774 A/G + A G CT - Excalibur_c6097_2208 chr2B 87355011 A/G + A G CT - Kukri_c44_1704 chr2B 89312335 A/G NA NA NA AG NA flanks do not match reference at this position BS00022422_51 chr2B 89491655 T/C + T C AG - BS00081428_51 chr2B 89491845 T/C + T C AG - CAP8_c1227_166 chr2B 89709330 T/C + C T AG - RAC875_c54625_78 chr2B 90011806 T/C + T C CT + RAC875_c54625_250 chr2B 90011978 A/G + A G AG + RAC875_c86069_65 chr2B 91547558 A/G + A G CT - Excalibur_rep_c68899_1400 chr2B 91836588 A/G - T C CT + IAAV1101 chr2B 91837050 A/G - C T CT + Ku_c68678_924 chr2B 91837050 T/C + C T CT + Excalibur_rep_c68899_218 chr2B 91837770 A/C - T G GT + Ra_c37244_428 chr2B 92797308 A/C NA NA NA GT NA flanks do not match reference at this position BS00022966_51 chr2B 92996902 A/G - C T AG - RAC875_rep_c118993_717 chr2B 93111974 A/C - G T AC - IACX6223 chr2B 93409767 T/C + C T CT + Tdurum_contig62458_179 chr2B 94033158 T/C + C T CT + Tdurum_contig60978_352 chr2B 94192783 A/G - T C CT + BS00023221_51 chr2B 94199666 A/G + A G AG + Excalibur_rep_c104347_86 chr2B 94223687 A/C + A C AC + RAC875_c37837_197 chr2B 94224869 T/C - A G CT - Jagger_c36_213 chr2B 94927862 A/C - T G AC - Kukri_c36879_83 chr2B 95761959 A/G + G A AG + IACX2309 chr2B 95797357 A/T - A T AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00067337_51 chr2B 97188902 T/C + T C CT + BobWhite_c30112_275 chr2B 97441940 T/G + T G AC - CAP7_c1018_75 chr2B 97442031 T/C - A G CT - Excalibur_c17039_436 chr2B 97953825 T/G + T G GT + RAC875_c76533_442 chr2B 98360670 T/G + G T GT + BobWhite_c12687_131 chr2B 99759474 T/C + C T AG - RAC875_c6370_1433 chr2B 99759654 T/C - G A CT - tplb0045o20_1440 chr2B 99760417 T/C - A G CT - tplb0045o20_699 chr2B 99765448 A/G NA NA NA AG NA flanks do not match reference at this position BS00029713_51 chr2B 99773056 T/G + T G GT + BS00038217_51 chr2B 99961084 T/C + T C AG - Excalibur_c43482_141 chr2B 100088851 A/G + A G CT - Excalibur_c15953_544 chr2B 100089293 A/G - T C CT + Tdurum_contig1653_190 chr2B 100095144 T/C + C T CT + BobWhite_rep_c66302_289 chr2B 100342141 A/G + A G CT - RAC875_c52061_153 chr2B 101234910 A/G - T C CT + Excalibur_c4303_184 chr2B 101236651 T/C - A G CT - Tdurum_contig36804_220 chr2B 101524919 A/G + A G CT - Excalibur_rep_c69459_270 chr2B 102421642 T/G - A C GT - RAC875_c52481_852 chr2B 102423479 A/G + A G CT - RAC875_c3302_1411 chr2B 102977102 T/C + T C AG - Tdurum_contig62852_538 chr2B 104063791 T/C + T C AG - Excalibur_c25430_183 chr2B 104063845 T/C - A G AG + Tdurum_contig62852_592 chr2B 104063845 A/G + A G AG + Kukri_c49298_598 chr2B 104234303 A/C + C A AC + Excalibur_rep_c67391_476 chr2B 104236762 T/C + C T CT + BS00079213_51 chr2B 104237413 T/C + T C AG - Tdurum_contig81323_291 chr2B 104237413 A/G - T C AG - GENE-0787_549 chr2B 104239416 A/G - T C AG - Kukri_c66123_88 chr2B 104242981 T/C + T C AG - Excalibur_c17633_111 chr2B 104243134 A/G - T C CT + Kukri_c49522_313 chr2B 104245494 T/C + T C AG - RFL_Contig2231_346 chr2B 104574455 A/G + G A AG + Tdurum_contig68806_537 chr2B 104578573 A/G - T C CT + BS00021923_51 chr2B 104578598 A/G + A G AG + BS00010514_51 chr2B 104579560 T/C + T C CT + BS00103461_51 chr2B 104580548 A/G - C T CT + BS00021675_51 chr2B 104792516 T/C + C T AG - Excalibur_c27716_544 chr2B 104817889 T/C - G A AG + Tdurum_contig14542_858 chr2B 105694450 T/C - A G AG + Kukri_c13747_464 chr2B 105908974 T/C - A G AG + Tdurum_contig82821_324 chr2B 105909244 T/C - G A CT - Kukri_c67276_103 chr2B 105909328 T/C - A G AG + Kukri_c67276_76 chr2B 105909355 T/C - A G CT - Kukri_c4790_154 chr2B 105913020 T/C - G A AG + Kukri_rep_c85389_715 chr2B 105991618 T/C - G A CT - BobWhite_s65298_124 chr2B 105991909 T/C - G A CT - BS00067975_51 chr2B 107081066 T/C + T C CT + Kukri_c40637_223 chr2B 108238043 T/C - G A AG + Ku_c57425_413 chr2B 108905234 A/G - C T AG - Ku_c7195_2622 chr2B 109140343 A/G + A G AG + Excalibur_rep_c98947_669 chr2B 110465853 T/C + T C CT + Excalibur_c41536_808 chr2B 110479892 T/C - G A CT - RAC875_c22552_380 chr2B 110480414 A/G - T C AG - RAC875_c10009_615 chr2B 111662167 A/G + A G AG + BS00063710_51 chr2B 111663938 T/C + C T AG - RAC875_c102761_297 chr2B 113605770 T/C - A G CT - CAP7_c9792_139 chr2B 114045238 T/C - A G CT - CAP7_c9792_109 chr2B 114045268 T/C - A G CT - Excalibur_c37649_125 chr2B 114045525 T/C - G A CT - RAC875_rep_c109864_61 chr2B 114060955 T/C - G A CT - BobWhite_c7723_354 chr2B 114376341 T/G + G T AC - Jagger_c6529_119 chr2B 114647529 T/C + C T AG - RAC875_c63111_151 chr2B 114763388 A/G + G A AG + RAC875_rep_c107451_541 chr2B 115210838 A/G + A G CT - RAC875_c61111_489 chr2B 115211536 A/G + A G AG + RAC875_rep_c80477_180 chr2B 115380863 T/C - A G CT - RAC875_c32133_452 chr2B 115836599 T/C - A G CT - RAC875_c21378_474 chr2B 116323220 T/C + T C CT + RAC875_c58652_80 chr2B 116323292 A/C - T G AC - Kukri_c24586_923 chr2B 116324280 T/G + G T AC - Excalibur_c74162_625 chr2B 116469302 A/G + G A AG + RAC875_rep_c105961_329 chr2B 117117724 T/C + T C AG - RAC875_c7699_325 chr2B 117606474 T/C + T C CT + GENE-0767_62 chr2B 117620063 T/G + T G AC - Ra_c31463_148 chr2B 117876153 T/C - A G CT - Excalibur_c7324_542 chr2B 118061318 A/G - C T CT + Ku_c4042_576 chr2B 118287554 T/C - G A CT - Kukri_s106211_65 chr2B 118693210 A/G - C T AG - RAC875_c5753_1087 chr2B 118693944 A/G + A G AG + Tdurum_contig77602_931 chr2B 120589912 A/G - T C AG - Excalibur_c2430_844 chr2B 120589976 A/G - C T AG - Kukri_c11935_65 chr2B 121355777 T/C + T C AG - Kukri_rep_c104810_341 chr2B 121357812 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_rep_c104810_301 chr2B 121357970 A/G - T C AG - BobWhite_c12088_261 chr2B 121361298 A/G - T C AG - RAC875_c14076_105 chr2B 121368798 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c7818_970 chr2B 121369573 A/G - T C CT + BS00003404_51 chr2B 121370808 T/C - A G CT - BS00022486_51 chr2B 121371060 T/G - A C GT - Kukri_c46621_143 chr2B 121677036 T/C + C T CT + RAC875_rep_c112117_67 chr2B 121679928 A/G - T C CT + BS00070001_51 chr2B 122010450 A/G + G A CT - JD_c14855_506 chr2B 122265753 A/G - T C AG - TA014111-0612 chr2B 122266002 T/C + T C CT + Kukri_c20247_53 chr2B 122696519 A/G + A G CT - IAAV980 chr2B 122697195 A/G - C T AG - Tdurum_contig42112_2432 chr2B 122699994 T/C - A G CT - Kukri_c48909_163 chr2B 122713307 T/C NA NA NA CT NA flanks do not match reference at this position BobWhite_c10238_127 chr2B 122756813 T/C - A G CT - BS00022969_51 chr2B 123062357 T/C - G A CT - BS00014923_51 chr2B 126731281 T/G - C A AC + RAC875_c52566_551 chr2B 126949323 A/G + A G CT - RAC875_rep_c69211_652 chr2B 129661621 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_c4632_115 chr2B 129662554 A/G - T C AG - BS00065030_51 chr2B 130137733 A/G + A G AG + BS00083078_51 chr2B 131130470 A/G + G A AG + GENE-1364_133 chr2B 131570189 T/C - G A CT - Excalibur_c6537_849 chr2B 131571821 T/C + T C CT + Kukri_rep_c70983_803 chr2B 131572883 A/G - T C CT + Kukri_rep_c103845_165 chr2B 131575347 A/C - T G GT + RFL_Contig747_1012 chr2B 131575999 T/C - G A CT - RFL_Contig747_899 chr2B 131576112 A/C - G T GT + Kukri_c13884_74 chr2B 131583607 A/G + A G AG + BS00022657_51 chr2B 132340633 A/G - T C AG - BS00063577_51 chr2B 132518531 T/C + T C CT + Ku_c23446_2209 chr2B 133009104 A/G - T C CT + Kukri_c106282_114 chr2B 133015691 T/C + C T AG - RAC875_c9091_360 chr2B 133023491 T/C - A G CT - JD_c39990_130 chr2B 133169443 A/G - C T CT + Kukri_rep_c104148_764 chr2B 133169534 T/C - G A CT - Kukri_rep_c104676_292 chr2B 133169570 T/C - A G CT - Kukri_rep_c104676_265 chr2B 133169597 T/C - A G CT - Tdurum_contig83066_276 chr2B 133689893 T/G - C A AC + BS00065994_51 chr2B 133704710 T/C + C T CT + BobWhite_c22503_605 chr2B 134090339 T/C - G A CT - Ra_c6728_590 chr2B 134090349 T/C - A G AG + Tdurum_contig94806_361 chr2B 134090349 A/G + A G CT - BS00088575_51 chr2B 135003886 T/C + C T CT + RAC875_c79857_301 chr2B 135007973 T/C - G A AG + Excalibur_c35414_986 chr2B 135093797 T/G - C A AC + RAC875_rep_c74419_1298 chr2B 135094332 A/G - T C AG - Ra_c106376_879 chr2B 135100851 A/G + A G AG + Excalibur_c13339_561 chr2B 136150897 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_rep_c102657_575 chr2B 136154805 T/C + T C CT + RAC875_c14362_529 chr2B 136175493 A/G - T C AG - Tdurum_contig98206_211 chr2B 136430768 A/G + G A AG + Excalibur_c26042_260 chr2B 138117669 T/C - G A CT - BS00059315_51 chr2B 138536901 T/G - C A GT - Excalibur_c15031_73 chr2B 139068437 T/C - A G AG + IAAV2381 chr2B 139068437 A/G + A G AG + Kukri_c11665_1877 chr2B 139069067 T/C - A G AG + BobWhite_c48532_625 chr2B 139070719 T/C + T C CT + Kukri_c15574_204 chr2B 139074209 A/C - T G AC - Kukri_c11156_366 chr2B 139341892 T/C + C T AG - Tdurum_contig15512_407 chr2B 139351601 T/C + C T CT + Tdurum_contig15512_429 chr2B 139351623 T/C + C T AG - RAC875_c27716_720 chr2B 139802261 A/G + A G AG + RAC875_rep_c112008_519 chr2B 139812784 A/G + A G AG + Kukri_c28266_705 chr2B 139814207 A/G - T C CT + Excalibur_c65206_621 chr2B 139816005 T/C + T C CT + Excalibur_c23185_155 chr2B 140750254 A/G + A G CT - RAC875_c12191_77 chr2B 140772477 T/C + C T AG - BS00022944_51 chr2B 140775148 T/C - G A AG + BS00099097_51 chr2B 140775160 T/C - A G AG + Kukri_c36026_68 chr2B 140776052 T/C + T C CT + RAC875_rep_c106400_276 chr2B 140776870 A/G NA NA NA AG NA flanks do not match reference at this position BS00022949_51 chr2B 140850052 T/C + C T AG - BS00099361_51 chr2B 140850078 A/G + G A AG + RFL_Contig1385_326 chr2B 141559396 A/G + A G AG + RFL_Contig1385_1575 chr2B 141564719 T/G + T G GT + BS00069627_51 chr2B 141641187 A/C + C A GT - RFL_Contig3604_398 chr2B 141987452 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_rep_c118376_304 chr2B 143773951 A/C - T G AC - Jagger_c3660_88 chr2B 143774036 A/C - T G AC - TA004478-0271 chr2B 143774181 T/C NA NA NA AG NA flanks do not match reference at this position IAAV6994 chr2B 144431599 T/C + C T AG - GENE-4359_102 chr2B 144432957 A/G - C T CT + BobWhite_c2280_95 chr2B 144603038 A/G + A G AG + RAC875_rep_c117760_181 chr2B 144653359 T/C - A G CT - BobWhite_c45174_86 chr2B 144654869 T/C + C T AG - Kukri_c9387_372 chr2B 146717673 A/G - T C AG - Kukri_c9387_112 chr2B 146717932 T/G - C A GT - Ra_c2110_1660 chr2B 146732976 A/G - T C AG - Ra_c2110_494 chr2B 146735843 T/C - A G AG + RAC875_c89991_411 chr2B 146954989 A/G - T C CT + RAC875_c23721_165 chr2B 146956128 T/C + T C CT + CAP8_c708_406 chr2B 146956140 T/C + C T CT + RAC875_c50279_1180 chr2B 148239141 A/G - T C AG - RAC875_c22567_273 chr2B 148242398 T/C + C T AG - Kukri_rep_c110613_729 chr2B 148404382 A/G + G A AG + BS00030130_51 chr2B 148590036 A/G - C T CT + Kukri_c9490_1024 chr2B 149024915 A/G - T C AG - Ku_c103035_323 chr2B 149842992 T/C + T C CT + RAC875_rep_c105424_254 chr2B 149842996 A/G - T C AG - Excalibur_c107556_105 chr2B 149843020 A/G - T C CT + Tdurum_contig27024_67 chr2B 150599208 T/C - A G CT - Tdurum_contig10994_617 chr2B 150607850 A/G - C T CT + GENE-1031_48 chr2B 150714236 A/G - T C CT + Tdurum_contig99313_288 chr2B 150882517 A/G + G A CT - RFL_Contig1483_1765 chr2B 151644876 T/C - A G AG + RFL_Contig2931_1687 chr2B 151907594 T/C - G A AG + Tdurum_contig71387_65 chr2B 152175265 A/C + C A GT - BobWhite_c662_148 chr2B 152569080 A/G + A G CT - BobWhite_c662_648 chr2B 152569580 T/C + T C CT + BS00073447_51 chr2B 152709138 T/C + C T AG - BS00087793_51 chr2B 153223664 T/G - A C AC + Tdurum_contig92963_204 chr2B 153223758 T/C + C T AG - tplb0031k24_1315 chr2B 153223867 A/G - T C CT + tplb0031k24_648 chr2B 153225405 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c98208_135 chr2B 153226003 A/G + A G AG + BS00031143_51 chr2B 153610498 A/C + A C GT - BobWhite_c18690_420 chr2B 153610573 A/G - C T AG - RFL_Contig189_894 chr2B 153612682 A/G + A G AG + RAC875_c16822_186 chr2B 153761461 T/C + T C CT + RAC875_c16822_362 chr2B 153761637 T/C + T C AG - Kukri_c42263_278 chr2B 153858749 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c47353_350 chr2B 153859877 T/C + T C AG - Kukri_c10858_206 chr2B 154245252 T/C + T C CT + GENE-2904_757 chr2B 154250491 T/C - A G CT - GENE-2904_476 chr2B 154250768 T/C - A G AG + Kukri_c6973_344 chr2B 154251253 A/G + G A AG + Tdurum_contig94521_738 chr2B 154270600 A/G + A G AG + Excalibur_c15412_647 chr2B 154270900 T/C + C T CT + Excalibur_c15412_900 chr2B 154271152 T/C + C T AG - Excalibur_c15412_1135 chr2B 154271387 T/C + T C CT + Ku_c34010_1016 chr2B 154719959 A/G - C T AG - Excalibur_c26167_174 chr2B 154722000 A/G - C T CT + CAP7_c937_55 chr2B 154934169 A/G - T C CT + Excalibur_c30636_487 chr2B 155044303 T/C - G A AG + Tdurum_contig76426_861 chr2B 156593851 T/G - C A AC + BobWhite_c32236_139 chr2B 157041002 A/G - T C AG - RAC875_rep_c74590_606 chr2B 157693838 T/C - G A CT - JD_c767_567 chr2B 157695245 A/C + C A GT - RAC875_c30227_210 chr2B 158618593 T/G + G T AC - Excalibur_c9248_771 chr2B 158618852 T/G + T G GT + RAC875_c13835_173 chr2B 158624409 T/G + T G AC - Jagger_c7840_145 chr2B 158624569 A/G + G A CT - Jagger_c7840_166 chr2B 158624590 T/C + C T CT + Excalibur_c45094_602 chr2B 158643756 T/C - G A AG + Kukri_rep_c115151_99 chr2B 158643992 A/G - T C CT + IACX1412 chr2B 159205817 A/G NA NA NA CT NA flanks do not match reference at this position GENE-1389_59 chr2B 159207015 T/C + T C CT + Excalibur_rep_c106124_239 chr2B 159207418 A/G + A G AG + Kukri_c3100_236 chr2B 159367818 T/C - A G CT - RAC875_c25760_147 chr2B 159891625 T/C - A G CT - BS00073426_51 chr2B 160201102 A/G - T C AG - RAC875_c36366_181 chr2B 160407109 T/C + T C CT + GENE-0724_612 chr2B 160904114 A/G + A G CT - TA005635-0459 chr2B 161406179 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c23723_141 chr2B 161409259 T/C + T C CT + BS00070091_51 chr2B 163714341 T/C + T C CT + Kukri_c34029_920 chr2B 164088218 A/G - T C AG - RAC875_c14645_162 chr2B 164422886 A/G + A G CT - RAC875_rep_c70857_1559 chr2B 164426742 A/G + A G CT - IACX2953 chr2B 165115668 T/C - G A AG + Tdurum_contig28126_609 chr2B 165116040 T/C - G A AG + BS00064626_51 chr2B 165117895 A/G - T C CT + Kukri_c108216_193 chr2B 165505350 T/C - A G CT - Kukri_c34353_821 chr2B 165506841 T/C - A G CT - Excalibur_c4440_923 chr2B 167085979 T/C + T C AG - RAC875_c32503_134 chr2B 167469340 A/G + A G CT - RAC875_c32503_241 chr2B 167469447 T/C + T C AG - BS00031814_51 chr2B 167798344 T/C + C T AG - IAAV4497 chr2B 167798344 A/G - C T AG - Kukri_c53629_239 chr2B 168610742 T/G - C A AC + IAAV2018 chr2B 168622535 A/G + A G AG + Kukri_rep_c102367_278 chr2B 171024930 T/C - A G CT - RAC875_c16899_219 chr2B 173204216 T/C + C T AG - Kukri_rep_c113077_284 chr2B 174343718 A/G - C T CT + BobWhite_rep_c50371_343 chr2B 174344372 T/C + C T CT + RAC875_c16697_1686 chr2B 174393990 A/G - C T CT + Excalibur_c20885_365 chr2B 174923613 T/G - C A GT - Kukri_c42244_809 chr2B 174930204 T/C - G A CT - Kukri_c42244_605 chr2B 174930601 T/C - A G AG + BobWhite_c42064_338 chr2B 175060472 A/G + A G AG + tplb0058k14_1155 chr2B 175628775 A/C - T G AC - RAC875_c14514_209 chr2B 176406760 A/C + A C GT - BobWhite_rep_c66732_270 chr2B 176410004 T/C + T C AG - RAC875_c1786_2335 chr2B 177649774 A/G - T C AG - RAC875_c1786_2227 chr2B 177649882 A/G - T C CT + Excalibur_c43358_463 chr2B 177650159 T/C - A G AG + Tdurum_contig42091_1912 chr2B 177652439 A/G + A G AG + Tdurum_contig42091_2860 chr2B 177657361 A/G + A G CT - Excalibur_c47286_281 chr2B 179398264 A/G + G A AG + RAC875_c19210_348 chr2B 179399007 A/C + A C AC + BS00011164_51 chr2B 180568905 T/C - A G CT - BobWhite_c948_52 chr2B 180616436 T/C + T C AG - Excalibur_c12626_588 chr2B 180822548 A/G - T C AG - RAC875_c11149_422 chr2B 181355683 T/C - G A CT - RAC875_c11149_381 chr2B 181355724 T/C - G A AG + RAC875_c11149_351 chr2B 181355754 T/C - G A AG + Kukri_rep_c94009_116 chr2B 182361037 A/G - T C CT + Ex_c101393_1898 chr2B 182708311 T/G - C A AC + BS00043103_51 chr2B 183200569 T/C + C T CT + BS00091007_51 chr2B 183262736 T/G + T G GT + RAC875_c28583_451 chr2B 183317338 T/C - G A AG + Excalibur_c44495_105 chr2B 184118517 T/G + G T AC - BobWhite_c647_668 chr2B 184331540 T/C + C T CT + RAC875_c7933_570 chr2B 184492858 A/G + A G AG + BS00037278_51 chr2B 184661676 A/G - T C CT + Ku_c4777_2494 chr2B 185760745 T/C - G A CT - Kukri_c9281_71 chr2B 185761574 A/G + G A AG + Kukri_c4777_685 chr2B 185762852 T/C - G A CT - RAC875_rep_c110508_698 chr2B 185806440 T/C - A G AG + RAC875_rep_c116562_245 chr2B 185806940 A/G - T C AG - Excalibur_c2301_401 chr2B 185815344 T/C - A G AG + Kukri_rep_c102276_688 chr2B 186286661 A/G + A G AG + Kukri_rep_c102276_751 chr2B 186286724 T/C + T C AG - Excalibur_c338_651 chr2B 188022454 T/G + T G AC - Ra_c24071_210 chr2B 188149238 A/C + A C AC + Kukri_c21300_323 chr2B 188720791 T/C NA NA NA AG NA flanks do not match reference at this position BS00034315_51 chr2B 189603683 T/C + C T CT + Excalibur_c2557_103 chr2B 189603711 T/G + G T AC - Ex_c3769_791 chr2B 189612751 A/G - T C CT + IACX6743 chr2B 189617131 T/C + C T AG - Kukri_rep_c107921_128 chr2B 189619456 A/C + A C AC + Excalibur_c41397_485 chr2B 189745218 T/C - A G CT - Excalibur_c41397_439 chr2B 189745264 T/C - A G CT - RAC875_c33839_393 chr2B 189745524 T/C - A G CT - Ex_c8832_2521 chr2B 190015995 T/C - G A AG + RFL_Contig5138_2366 chr2B 190018608 T/C + T C CT + Kukri_c49479_771 chr2B 190019134 T/C + T C AG - Kukri_c49479_1173 chr2B 190019627 T/C + T C CT + IAAV1296 chr2B 190658482 A/G - C T CT + Excalibur_c16646_1056 chr2B 190971636 A/C + A C GT - RAC875_c9894_1320 chr2B 191542234 A/C + A C GT - Kukri_c12900_270 chr2B 191752685 A/G - T C CT + RAC875_c34679_177 chr2B 191752753 T/C - A G AG + RAC875_c57195_129 chr2B 192360332 A/G - T C AG - RAC875_c62674_357 chr2B 192364775 T/C - G A AG + Jagger_c9472_305 chr2B 195664018 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c35762_123 chr2B 197724380 A/G - T C CT + RAC875_c35762_86 chr2B 197724417 A/G - T C CT + RAC875_c92198_360 chr2B 198756065 A/G - C T CT + RAC875_c12968_1526 chr2B 199021553 A/G - T C CT + RAC875_c12968_1429 chr2B 199021650 A/G - T C CT + BobWhite_c12129_801 chr2B 199021890 A/G - T C AG - RAC875_c8045_231 chr2B 199763074 T/C - G A CT - RFL_Contig5290_1493 chr2B 200385482 A/C + C A AC + RAC875_rep_c71760_550 chr2B 200902043 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_rep_c71760_57 chr2B 200905079 T/G - A C AC + CAP11_c1363_55 chr2B 202484257 A/C + A C GT - Excalibur_rep_c70384_663 chr2B 202484888 A/G + G A CT - RAC875_c5080_915 chr2B 206113216 A/G - C T AG - RAC875_c57901_354 chr2B 206373684 A/G - C T AG - Kukri_rep_c73015_130 chr2B 206376049 A/G + A G AG + Ra_c23048_474 chr2B 206681480 T/C + T C CT + Ku_c6546_718 chr2B 206752112 T/C - G A CT - BobWhite_c33574_552 chr2B 207598761 T/G + T G AC - Excalibur_c90811_88 chr2B 208625051 A/G + G A AG + RAC875_c5077_437 chr2B 209085432 T/C + T C CT + RFL_Contig2370_1129 chr2B 209252917 T/C + T C AG - RAC875_c46661_184 chr2B 209253010 T/G - C A AC + RAC875_c3752_890 chr2B 210262587 A/G - T C AG - BS00065558_51 chr2B 210455799 A/G - C T AG - CAP8_c5800_150 chr2B 210652242 A/G + G A AG + tplb0035h18_465 chr2B 210665652 T/C - A G CT - BS00078506_51 chr2B 210842786 T/C - A G CT - BobWhite_c14115_378 chr2B 211153750 T/G - C A AC + RAC875_c19235_631 chr2B 211528770 A/G - T C AG - BobWhite_c892_73 chr2B 211535314 T/C - A G AG + Excalibur_c47589_448 chr2B 212772677 A/G + G A AG + Kukri_c12290_360 chr2B 212780166 T/G - A C GT - RFL_Contig356_812 chr2B 212943614 A/G - C T AG - BobWhite_c18911_103 chr2B 213253762 A/C - T G AC - GENE-1243_338 chr2B 213254490 A/G + A G CT - Kukri_c18462_601 chr2B 213803894 T/C - G A AG + Tdurum_contig29618_321 chr2B 213804336 A/G + A G AG + RFL_Contig1523_470 chr2B 214288757 A/G + A G AG + Excalibur_c41356_1047 chr2B 214314587 A/G + A G AG + Kukri_c87767_121 chr2B 214375944 A/G - T C AG - RAC875_c20628_111 chr2B 214587400 T/C - A G AG + Kukri_c24793_454 chr2B 214588711 A/G NA NA NA CT NA flanks do not match reference at this position IAAV6765 chr2B 214590843 A/C + C A GT - Ex_c4328_1408 chr2B 214593242 A/G + A G CT - Kukri_c8900_251 chr2B 214596657 T/C + T C AG - Kukri_c19524_87 chr2B 215202085 T/C + T C AG - RFL_Contig1418_3465 chr2B 215203280 A/G + G A CT - Excalibur_c15089_881 chr2B 215204939 T/G - A C GT - Excalibur_c15089_758 chr2B 215205062 T/C - A G AG + Tdurum_contig8048_84 chr2B 215593652 T/G + G T AC - BobWhite_c2235_121 chr2B 216449458 T/C + T C CT + Kukri_rep_c68124_672 chr2B 216463274 A/G + A G CT - Tdurum_contig50509_805 chr2B 216467652 T/C + T C AG - BS00034245_51 chr2B 216467919 T/G + G T AC - RAC875_c13106_271 chr2B 216853977 A/G - T C CT + RAC875_c2944_486 chr2B 217405059 T/G + T G AC - Kukri_c66550_167 chr2B 217405584 A/C - T G GT + RAC875_c2944_1383 chr2B 217405956 A/G + A G AG + Kukri_c11636_1023 chr2B 217407356 T/C + T C CT + Tdurum_contig28831_292 chr2B 217793084 A/C - T G GT + Kukri_c40290_73 chr2B 221089015 A/G + A G AG + Kukri_c27713_131 chr2B 221921302 A/G + A G AG + Kukri_rep_c115206_141 chr2B 221925343 A/C + A C AC + BobWhite_c21338_749 chr2B 222591713 A/G + G A AG + RFL_Contig5279_1859 chr2B 225260646 T/C + T C CT + Excalibur_rep_c67816_2354 chr2B 225587963 T/C + C T AG - Kukri_c5121_1826 chr2B 227083021 A/G - C T AG - Excalibur_c5691_2947 chr2B 228980201 T/C - G A CT - Excalibur_c5691_2277 chr2B 228980871 T/C - A G AG + Excalibur_c5691_2088 chr2B 228981060 T/C - A G AG + RFL_Contig522_678 chr2B 230218463 T/C + T C AG - RAC875_c56101_368 chr2B 231971783 T/C + T C CT + BobWhite_rep_c54808_282 chr2B 231971900 A/G + G A AG + RAC875_rep_c105780_64 chr2B 232793101 T/C - A G CT - Tdurum_contig36029_347 chr2B 233267058 A/G - T C AG - CAP7_c3814_330 chr2B 233268166 T/C NA NA NA AG NA flanks do not match reference at this position CAP7_c3814_216 chr2B 233268394 A/C - T G AC - Tdurum_contig52063_1077 chr2B 233269103 A/C + C A GT - Excalibur_c58566_284 chr2B 233554407 T/C NA NA NA AG NA flanks do not match reference at this position RFL_Contig4230_544 chr2B 234368927 T/C - G A AG + Kukri_rep_c70153_1757 chr2B 234633243 A/G - T C CT + RAC875_c30936_318 chr2B 234634296 T/G + T G AC - RAC875_c30936_411 chr2B 234634389 A/C + A C AC + Kukri_c5711_112 chr2B 234636098 A/G + G A AG + BobWhite_c5852_685 chr2B 234636215 A/G - C T AG - BobWhite_c5852_103 chr2B 234636794 T/G - A C AC + Excalibur_c30286_835 chr2B 236048486 T/G + T G GT + Excalibur_c8013_432 chr2B 236166575 A/G - C T AG - RAC875_rep_c109975_192 chr2B 236805761 T/C - G A AG + BS00111324_51 chr2B 237177078 T/C - G A CT - BobWhite_rep_c61602_139 chr2B 237967261 A/G + A G AG + Tdurum_contig20589_247 chr2B 238961035 T/C - A G CT - RAC875_c63112_460 chr2B 239646059 T/C + T C AG - BS00061269_51 chr2B 239846796 A/C + C A AC + BS00061268_51 chr2B 239847284 T/G + T G GT + TA004199-0831 chr2B 239854053 A/G - T C CT + Kukri_c22419_541 chr2B 239854131 A/C + A C AC + Ku_c32730_715 chr2B 240309433 A/C + A C AC + tplb0040e02_1293 chr2B 240318304 A/G + A G CT - Excalibur_c20647_643 chr2B 242825134 A/G - T C AG - CAP8_rep_c3775_324 chr2B 243080886 T/C - A G CT - BS00091671_51 chr2B 243363192 A/G - T C CT + RAC875_c44395_481 chr2B 243363320 T/C - G A CT - Kukri_c58974_141 chr2B 243364846 A/G - T C AG - RAC875_rep_c72449_111 chr2B 243570189 T/C - A G AG + CAP12_c2565_239 chr2B 243790172 A/G - T C AG - RAC875_c96504_413 chr2B 243830209 A/G + A G CT - RAC875_c63545_85 chr2B 244572477 T/C - A G CT - RAC875_c41899_238 chr2B 245008463 A/G - C T CT + BS00075410_51 chr2B 245129264 A/C + C A GT - Kukri_c26474_540 chr2B 245790742 T/G - C A AC + Excalibur_c584_726 chr2B 245888169 T/C - G A AG + Tdurum_contig19560_212 chr2B 246002628 T/G - A C AC + RAC875_c18786_858 chr2B 246067490 T/C - G A CT - Excalibur_c3851_1815 chr2B 247920861 T/G + G T GT + Kukri_c3907_96 chr2B 247924666 A/G - T C AG - TA001505-1171 chr2B 247934117 T/C - A G AG + Excalibur_c4709_576 chr2B 247934995 A/G - C T AG - RAC875_s109189_188 chr2B 248149824 T/C + T C AG - Kukri_c47336_687 chr2B 248157093 A/G + A G AG + BS00071346_51 chr2B 249198170 T/C + C T CT + Excalibur_s114390_149 chr2B 249207826 A/G - C T AG - TA002306-1975 chr2B 249264147 T/G + T G GT + RAC875_rep_c108711_131 chr2B 249264573 A/C - G T GT + RAC875_c102981_396 chr2B 249369169 T/C - A G CT - Excalibur_c65830_82 chr2B 249370504 A/G + G A CT - BS00072689_51 chr2B 249371836 T/C - G A CT - RAC875_c57938_94 chr2B 249374614 A/G + G A AG + GENE-0753_696 chr2B 249524526 T/G - C A AC + RAC875_c55227_129 chr2B 249669173 A/G - C T CT + Jagger_c699_176 chr2B 250070288 A/G - T C AG - Kukri_c17916_107 chr2B 250255235 A/G + A G AG + Kukri_c52154_193 chr2B 250256038 T/C + C T AG - Kukri_c17916_1370 chr2B 250257076 T/C + T C CT + Kukri_rep_c114375_259 chr2B 250742706 A/C + A C AC + Excalibur_c56259_212 chr2B 251371270 A/G - T C AG - BobWhite_c44175_495 chr2B 251373054 A/G + G A AG + Excalibur_c60255_473 chr2B 251373087 A/G - T C AG - BobWhite_c23362_393 chr2B 251770339 T/C + C T CT + RAC875_c67415_289 chr2B 253267402 A/G - T C CT + Excalibur_c36632_142 chr2B 253269409 T/G + T G AC - RAC875_c9786_438 chr2B 254133492 A/G - C T AG - RAC875_c9786_202 chr2B 254133728 T/C - A G CT - RAC875_c9786_162 chr2B 254133768 T/G - A C GT - RAC875_c101453_216 chr2B 254137377 A/G + A G CT - RAC875_rep_c108394_471 chr2B 254875306 T/G - A C AC + RAC875_c11881_301 chr2B 256963627 T/C + C T CT + Kukri_c3934_1569 chr2B 257904102 T/C - A G CT - GENE-0875_506 chr2B 258030716 A/G + A G AG + GENE-0875_620 chr2B 258030822 T/C + T C CT + RAC875_c50475_252 chr2B 258155963 T/C - A G CT - Excalibur_rep_c101083_218 chr2B 258775842 A/G + A G AG + Excalibur_c27620_327 chr2B 260606627 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c9079_296 chr2B 262899780 T/C + T C AG - Excalibur_c7539_195 chr2B 262900711 A/G - T C AG - GENE-0976_223 chr2B 265222749 T/C - A G CT - Excalibur_c44703_69 chr2B 265435226 T/C + C T CT + Kukri_rep_c69087_1014 chr2B 269374597 T/C + T C AG - Kukri_c34763_58 chr2B 272485655 T/G + T G AC - BS00063599_51 chr2B 272673046 T/C - G A CT - RAC875_rep_c105450_779 chr2B 272770119 T/C + T C CT + Kukri_c23475_1485 chr2B 273052248 A/G - T C AG - Kukri_c61350_341 chr2B 274299200 A/G - T C CT + Excalibur_c16957_104 chr2B 277308740 A/C + A C AC + RAC875_c172_1121 chr2B 277318634 T/C + T C CT + Excalibur_c3546_624 chr2B 280474875 A/G - T C AG - RAC875_c22378_496 chr2B 280475444 T/C - A G AG + Excalibur_c47422_106 chr2B 280484216 A/G - T C CT + Kukri_c6836_1462 chr2B 283018432 A/G + G A CT - Excalibur_c39881_355 chr2B 285054304 T/C + T C CT + Tdurum_contig23591_137 chr2B 286976402 A/C - T G AC - Kukri_c8562_1650 chr2B 288936596 A/G - T C AG - Ex_c27097_826 chr2B 291601056 T/C - A G AG + Ex_c27097_736 chr2B 291601242 T/G NA NA NA GT NA flanks do not match reference at this position RFL_Contig4194_1665 chr2B 296013085 A/G - T C CT + RAC875_c17375_910 chr2B 296013131 A/G - T C CT + BobWhite_c2842_95 chr2B 302039752 A/G + A G CT - RAC875_c11878_100 chr2B 302084680 A/G - T C CT + Kukri_c61568_73 chr2B 303094389 T/C + T C CT + Excalibur_c28380_608 chr2B 303098610 T/G + T G GT + Excalibur_c28380_1177 chr2B 303100672 A/C + A C AC + Excalibur_rep_c66565_108 chr2B 305328099 T/C + C T CT + Excalibur_rep_c66565_387 chr2B 305328378 A/G + A G CT - Kukri_c12626_240 chr2B 306175661 A/G - C T AG - BobWhite_c7823_914 chr2B 306885150 A/G - C T AG - RAC875_c29686_113 chr2B 308725799 T/G + T G AC - RAC875_rep_c105294_121 chr2B 309485736 T/C - G A CT - Kukri_c3096_1411 chr2B 313481278 T/G - A C AC + CAP8_c1655_298 chr2B 314151715 A/C - G T AC - BS00066873_51 chr2B 315664154 T/C + C T AG - RAC875_c673_1812 chr2B 315665767 A/C + C A GT - Kukri_c16415_747 chr2B 316049128 T/C + C T AG - Kukri_c11515_175 chr2B 317237904 A/C + A C GT - Kukri_c683_1401 chr2B 318176485 A/C - T G GT + Kukri_c43458_209 chr2B 319360751 A/G - T C AG - Kukri_rep_c103379_99 chr2B 320745182 T/C - A G CT - Excalibur_c44851_267 chr2B 320745997 T/C + C T AG - RAC875_c14841_1079 chr2B 323085774 T/C + T C AG - RAC875_c32593_174 chr2B 323099884 A/G - T C CT + Excalibur_c6746_61 chr2B 323101644 A/G - T C AG - RFL_Contig5615_1867 chr2B 325844664 T/C - A G AG + CAP12_c4999_56 chr2B 326286764 T/G - A C AC + Kukri_c22175_123 chr2B 329472716 T/C + C T CT + RAC875_c52617_595 chr2B 329474728 T/C + C T CT + RAC875_c17634_1185 chr2B 330443228 A/G - T C AG - Kukri_rep_c69553_1891 chr2B 330445132 T/C + T C CT + Kukri_c34305_308 chr2B 330487175 T/G + T G GT + RAC875_c9009_1205 chr2B 331229679 A/G - T C AG - RAC875_c29073_149 chr2B 335377216 A/G + A G CT - Kukri_c36275_88 chr2B 335526455 A/G - T C CT + Excalibur_c13293_1074 chr2B 337072521 A/G + A G CT - Tdurum_contig33403_231 chr2B 339166919 A/G - C T CT + Excalibur_c29827_491 chr2B 339911842 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c12408_134 chr2B 347078744 T/C - G A AG + RAC875_rep_c72963_109 chr2B 354073272 A/G - T C AG - Kukri_rep_c72730_483 chr2B 354078147 A/G - T C CT + BobWhite_c14209_871 chr2B 356594887 A/C - G T AC - BobWhite_c14209_478 chr2B 356595730 A/G - T C CT + BobWhite_rep_c52619_1091 chr2B 356600432 A/G + A G AG + Tdurum_contig33943_52 chr2B 357884746 T/C - G A AG + Excalibur_c3364_1075 chr2B 357916049 T/C + T C CT + RAC875_c50571_108 chr2B 358672636 A/G + A G CT - BobWhite_rep_c50481_121 chr2B 358673071 T/C + T C AG - RAC875_c78196_64 chr2B 358760853 T/C - A G CT - Excalibur_c58010_77 chr2B 359311605 A/G - T C AG - Kukri_c39899_318 chr2B 359609035 T/C - G A CT - Excalibur_c22164_248 chr2B 359611853 A/G + G A AG + Kukri_c6309_58 chr2B 359859283 T/C + T C CT + Kukri_c6284_1623 chr2B 359870931 T/C + C T AG - Excalibur_c854_1459 chr2B 359871047 A/C - G T GT + Kukri_c101770_328 chr2B 359872356 T/C + C T AG - CAP7_c1394_430 chr2B 360481637 A/C - T G AC - Kukri_c12511_57 chr2B 360981479 A/G + A G CT - tplb0060o20_752 chr2B 361128363 T/C + T C CT + RAC875_c12399_148 chr2B 361578034 A/G - T C AG - CAP11_c3038_102 chr2B 361638297 T/C - A G AG + RAC875_rep_c101788_88 chr2B 364135586 T/C - A G AG + RAC875_c56586_221 chr2B 364327553 A/G - T C AG - Tdurum_contig28617_220 chr2B 364677456 A/G + G A CT - Tdurum_contig28617_277 chr2B 364677513 A/G + A G AG + Kukri_c9600_882 chr2B 364682847 T/C - A G AG + Excalibur_c16019_419 chr2B 366021399 T/C + T C CT + Kukri_c21460_315 chr2B 367790835 A/G + A G AG + RAC875_c10117_1497 chr2B 368954061 T/C - G A AG + Ku_c70277_1276 chr2B 368960757 A/G + A G AG + Kukri_c9197_1171 chr2B 369477282 A/G - C T AG - Kukri_rep_c101425_563 chr2B 369496620 A/G + A G CT - Jagger_c2095_150 chr2B 371166445 A/G - T C CT + tplb0059n08_808 chr2B 371166496 A/G - C T CT + Kukri_c10235_411 chr2B 371556988 T/C - A G CT - BobWhite_c1557_734 chr2B 371561412 T/C - A G AG + Excalibur_c44649_181 chr2B 371930887 A/G - T C CT + Kukri_c14213_320 chr2B 371935293 A/G + A G AG + RFL_Contig4941_214 chr2B 373301795 A/G + A G CT - RAC875_c23413_172 chr2B 373303126 A/G NA NA NA CT NA flanks do not match reference at this position Ra_c52002_77 chr2B 373303817 T/C + T C CT + RFL_Contig3765_322 chr2B 373309844 A/G + A G AG + Excalibur_c6958_138 chr2B 373314417 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c54440_401 chr2B 373480870 A/C + A C AC + RAC875_c26467_115 chr2B 373490275 A/G + G A CT - Kukri_c10862_792 chr2B 373494779 T/C - A G CT - CAP7_c8488_312 chr2B 373747252 A/C + A C AC + BobWhite_c16508_212 chr2B 373754131 A/G - T C AG - RAC875_c9008_1730 chr2B 373754161 T/C - A G CT - Excalibur_c15998_208 chr2B 373983528 A/G - T C AG - RAC875_c13343_130 chr2B 373991600 T/C + T C CT + Kukri_c6931_1209 chr2B 374682230 T/C + T C AG - BobWhite_c13719_365 chr2B 374799648 T/C + C T CT + Kukri_c23571_681 chr2B 375134268 A/G + A G AG + Tdurum_contig31113_328 chr2B 375171993 A/G + A G CT - Excalibur_c4159_1134 chr2B 375544909 A/G - T C AG - CAP11_rep_c8683_78 chr2B 375545926 T/C - A G CT - Kukri_rep_c73960_55 chr2B 377526791 T/C + T C AG - Kukri_c4360_1755 chr2B 377528009 T/C - A G CT - Kukri_c22318_315 chr2B 379095209 A/C + A C GT - CAP12_c3437_227 chr2B 379788364 A/G - T C AG - CAP11_c6321_202 chr2B 379833325 A/G - T C AG - Excalibur_c85610_72 chr2B 381914197 T/G - C A AC + tplb0046p14_350 chr2B 381914617 T/C - A G CT - tplb0046p14_329 chr2B 381914638 A/G - T C AG - BS00062485_51 chr2B 382083910 T/G - C A AC + RAC875_s119681_325 chr2B 382597847 A/G + A G AG + BobWhite_c9772_361 chr2B 383056657 T/C - G A CT - BobWhite_c9772_251 chr2B 383056767 T/C - G A AG + RAC875_c11809_1784 chr2B 383279969 A/G + A G AG + RAC875_c11809_1851 chr2B 383280036 A/C + A C AC + Kukri_rep_c109422_74 chr2B 383566623 A/G - T C AG - Excalibur_c59178_338 chr2B 383928584 T/C - A G AG + RAC875_c19043_841 chr2B 384318586 T/C - G A CT - BobWhite_c10453_396 chr2B 384319875 A/G NA NA NA AG NA flanks do not match reference at this position CAP8_rep_c9587_147 chr2B 384341874 T/C - G A AG + BobWhite_c45456_70 chr2B 384397805 A/C - T G GT + Kukri_c42510_147 chr2B 384677389 T/C + T C AG - Excalibur_c13028_683 chr2B 384749502 A/C - T G GT + RAC875_c65712_353 chr2B 385192418 T/C - G A CT - Excalibur_rep_c69554_168 chr2B 385201431 A/G + A G CT - Excalibur_c4984_162 chr2B 385201729 A/G - T C AG - Ku_c14843_504 chr2B 385202015 T/C NA NA NA AG NA flanks do not match reference at this position IACX1028 chr2B 385564299 A/G - C T CT + Kukri_c23221_1071 chr2B 385573142 T/C + T C CT + Excalibur_c5171_88 chr2B 385771955 A/C + A C AC + Excalibur_c42447_852 chr2B 386313122 A/G - T C AG - Excalibur_c42447_638 chr2B 386313336 A/C - G T AC - BobWhite_c13455_112 chr2B 387103786 A/G - T C AG - BobWhite_c13455_93 chr2B 387103805 A/G - T C CT + BobWhite_c35005_81 chr2B 387104802 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_c28000_321 chr2B 387104823 A/C - G T GT + BobWhite_rep_c53927_391 chr2B 387105553 T/C NA NA NA AG NA flanks do not match reference at this position Tdurum_contig3868_343 chr2B 387106089 T/C + C T CT + Excalibur_c7347_87 chr2B 388104523 T/C + C T CT + Excalibur_c42562_172 chr2B 388116741 T/C + T C AG - CAP7_c12133_170 chr2B 388503942 T/C + C T AG - RAC875_rep_c117320_114 chr2B 388945969 T/C - A G CT - RAC875_c18011_1286 chr2B 388946172 A/G - T C CT + Tdurum_contig15345_1044 chr2B 389409017 A/C - G T AC - Tdurum_contig42041_2081 chr2B 389465023 T/C + T C CT + Excalibur_rep_c69187_151 chr2B 389471745 A/G + A G AG + Kukri_rep_c71938_573 chr2B 389472421 A/G - T C AG - RFL_Contig4748_1076 chr2B 390116879 A/C - T G GT + Tdurum_contig28787_125 chr2B 390117495 T/G - A C AC + IAAV3148 chr2B 390362984 T/C - A G CT - Excalibur_c20367_505 chr2B 390807157 A/G - T C AG - Excalibur_c10703_89 chr2B 390812103 T/G - A C AC + RAC875_c67707_84 chr2B 390923589 T/C + T C CT + RAC875_c67707_113 chr2B 390923618 A/G + G A AG + RAC875_rep_c92405_249 chr2B 390941782 A/C - T G AC - RAC875_rep_c83983_171 chr2B 390941950 A/G - T C CT + Kukri_rep_c69962_1081 chr2B 390942868 T/C - A G AG + Kukri_rep_c84168_305 chr2B 390971519 A/G - T C AG - RAC875_c51853_241 chr2B 390975771 T/C - A G AG + RFL_Contig1329_1065 chr2B 392895907 A/C + A C GT - Kukri_rep_c71838_1273 chr2B 393464392 A/C + A C GT - Excalibur_c14735_146 chr2B 393469036 T/C + C T CT + Kukri_c11686_224 chr2B 393473317 A/G - T C CT + Excalibur_c8480_1301 chr2B 394246272 T/G - A C GT - RAC875_c16159_1090 chr2B 395537901 T/C + T C CT + Kukri_c11850_1711 chr2B 395542859 A/G - T C AG - Kukri_c11850_361 chr2B 395545033 A/C - T G AC - Excalibur_rep_c69016_57 chr2B 396338353 T/C + T C AG - Kukri_rep_c72413_423 chr2B 396338513 A/G - C T AG - RAC875_c13105_125 chr2B 396568493 T/C - G A AG + CAP8_c7066_68 chr2B 397606912 T/G - A C AC + Kukri_c5609_565 chr2B 397920069 A/G - T C AG - BobWhite_c3757_55 chr2B 398707071 A/C - T G AC - Kukri_c59854_248 chr2B 399353283 T/C NA NA NA AG NA flanks do not match reference at this position BobWhite_c25856_223 chr2B 399708366 A/G + A G CT - BobWhite_c25856_263 chr2B 399708406 A/G + G A AG + Kukri_c46628_699 chr2B 399938819 A/G - T C AG - Kukri_c46628_243 chr2B 399941328 T/C - A G CT - Excalibur_c71681_53 chr2B 402369358 T/G + T G AC - Tdurum_contig29316_210 chr2B 402679585 T/G + T G GT + Kukri_c47231_219 chr2B 402679690 A/G - T C AG - CAP7_c2854_46 chr2B 403084894 T/C + T C AG - CAP7_c1066_165 chr2B 403557859 A/C + A C AC + CAP7_rep_c5496_70 chr2B 403561987 T/G + T G AC - Kukri_rep_c100990_597 chr2B 403698956 A/C - G T AC - Excalibur_c52458_796 chr2B 403698989 T/G + G T GT + CAP12_rep_c6582_70 chr2B 404113616 T/C + T C AG - Excalibur_c36002_143 chr2B 404427757 T/C + T C CT + RAC875_rep_c85921_842 chr2B 404746340 A/G + A G AG + RAC875_c23621_413 chr2B 406081524 A/G - T C CT + RAC875_c9898_576 chr2B 406083651 T/C - A G CT - Jagger_c8683_58 chr2B 406091172 T/G + T G GT + RAC875_c6806_532 chr2B 406891763 A/G - C T CT + RAC875_c6806_361 chr2B 406891934 A/G - T C AG - Excalibur_c3839_2483 chr2B 407237657 T/G - A C AC + BobWhite_c11800_96 chr2B 407909983 T/C + T C CT + BobWhite_c11800_119 chr2B 407910006 A/G + A G AG + Ku_c46339_317 chr2B 408194806 T/G + G T GT + Kukri_c46339_441 chr2B 408194930 A/G + A G AG + IAAV3295 chr2B 409338453 T/C + T C AG - RAC875_c67138_696 chr2B 409339426 A/G NA NA NA CT NA flanks do not match reference at this position Jagger_c3269_107 chr2B 409342240 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_rep_c54390_73 chr2B 409344507 A/G - T C CT + BobWhite_rep_c48743_691 chr2B 410062345 A/G - C T CT + BobWhite_rep_c48743_625 chr2B 410062411 A/C - T G AC - Tdurum_contig15870_823 chr2B 410264923 T/G - C A GT - Kukri_c673_677 chr2B 411141599 T/C - G A AG + Kukri_c673_510 chr2B 411141766 T/C - A G AG + Kukri_c673_452 chr2B 411141922 A/G - T C AG - RFL_Contig3353_125 chr2B 411143395 A/G - T C AG - Kukri_c61942_61 chr2B 411493110 A/G + A G AG + Kukri_c11488_874 chr2B 411517128 A/C + C A GT - BobWhite_c18672_757 chr2B 412659516 T/C + T C CT + RAC875_c26460_807 chr2B 412665217 T/C + T C CT + RAC875_c26460_1040 chr2B 412665450 T/C + T C CT + Ex_c7628_2392 chr2B 412665511 A/G + G A CT - RAC875_c400_3016 chr2B 412719173 A/G + A G AG + Excalibur_rep_c102353_307 chr2B 412990277 A/G + A G CT - Kukri_rep_c101330_1009 chr2B 412992442 A/G + G A AG + tplb0050c06_1036 chr2B 413063735 A/G + G A CT - RAC875_c35084_141 chr2B 413449524 T/C - G A CT - Kukri_c2507_1183 chr2B 413865666 T/G - A C AC + Ex_c66545_551 chr2B 413865723 A/G + G A CT - Ex_c66545_567 chr2B 413865739 A/C + C A AC + Kukri_c2507_962 chr2B 413865887 A/C - G T AC - Ex_c66545_1078 chr2B 413866250 A/C + C A AC + Kukri_c2507_382 chr2B 413866467 T/G - C A GT - RFL_Contig3301_510 chr2B 415055295 A/G - T C AG - Excalibur_c60716_53 chr2B 416056315 T/C - G A AG + Kukri_c7670_220 chr2B 416831939 A/C - T G GT + Ra_c8602_465 chr2B 416832085 T/C + T C CT + Excalibur_c26375_144 chr2B 417079971 T/C + T C CT + RAC875_c4850_1427 chr2B 417080160 T/C - A G AG + tplb0038f13_1219 chr2B 417080273 T/C - G A CT - RAC875_c87421_408 chr2B 417645491 A/G - C T AG - Excalibur_c5137_430 chr2B 418777023 T/G + T G AC - Excalibur_c21991_725 chr2B 418956665 A/C - T G GT + RFL_Contig351_632 chr2B 419322061 A/C - T G GT + Kukri_rep_c103414_607 chr2B 421084441 T/C - A G AG + BobWhite_c5589_132 chr2B 421711637 T/G NA NA NA AC NA flanks do not match reference at this position RAC875_c47701_768 chr2B 422508963 T/C + C T AG - Kukri_c57399_314 chr2B 422732037 T/C + C T CT + Kukri_c42289_502 chr2B 422732104 A/G + A G AG + Kukri_c42289_582 chr2B 422732184 T/G + G T GT + Kukri_c42289_667 chr2B 422732269 A/C + A C AC + Excalibur_rep_c111672_114 chr2B 423661778 A/G - T C CT + RAC875_c25425_262 chr2B 423665746 A/C + A C GT - Kukri_c9665_185 chr2B 423666215 T/C + T C CT + Kukri_c9665_318 chr2B 423666348 T/C + C T CT + Excalibur_rep_c106537_63 chr2B 424331287 T/C - A G AG + BobWhite_c21530_1111 chr2B 424332519 T/G + T G GT + tplb0023l22_1420 chr2B 425796688 A/G + A G CT - BobWhite_c3166_310 chr2B 426478544 A/G + G A AG + BobWhite_c3166_675 chr2B 426481767 A/G + A G CT - Kukri_c55095_118 chr2B 427952638 T/C + T C AG - Excalibur_c8457_130 chr2B 427952764 A/G - C T CT + Excalibur_c4323_2123 chr2B 429147526 A/G + A G CT - BobWhite_c3693_85 chr2B 429261148 A/C - G T AC - Excalibur_rep_c104001_94 chr2B 429486217 A/G - T C CT + Kukri_rep_c107732_99 chr2B 429487828 T/C + T C AG - RAC875_c59828_163 chr2B 429488602 T/C - A G CT - Tdurum_contig42524_4725 chr2B 429491270 A/G + A G AG + RFL_Contig1263_696 chr2B 429650626 A/G - T C AG - RAC875_c13717_192 chr2B 430234251 T/C - A G AG + CAP12_c2890_214 chr2B 432135118 A/G + G A AG + BobWhite_rep_c49813_867 chr2B 432140081 T/G + G T GT + Tdurum_contig11871_88 chr2B 432558051 A/G + G A AG + Kukri_c6866_440 chr2B 434229412 T/C - A G CT - BobWhite_c1654_440 chr2B 434691710 T/C + C T AG - BobWhite_c4640_420 chr2B 434695366 T/C - A G CT - Ku_c3858_1078 chr2B 435341227 T/C - A G AG + IAAV8980 chr2B 435341981 A/G + G A CT - BobWhite_c27675_201 chr2B 436944988 T/C + T C CT + Kukri_rep_c70962_1545 chr2B 436961186 T/G + G T GT + Excalibur_rep_c107546_206 chr2B 437008599 T/G NA NA NA AC NA flanks do not match reference at this position Ku_c14053_772 chr2B 437009757 A/G + A G CT - Ra_c6266_136 chr2B 440214913 A/G - T C CT + Kukri_c57491_156 chr2B 440825074 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c60230_122 chr2B 440825282 T/C NA NA NA CT NA flanks do not match reference at this position tplb0034a02_1566 chr2B 441078843 A/G + G A AG + BobWhite_c10215_242 chr2B 441079831 A/G - C T AG - GENE-0951_398 chr2B 441860881 A/G NA NA NA AG NA flanks do not match reference at this position tplb0061i01_209 chr2B 442308099 A/G - T C AG - Kukri_c17888_243 chr2B 442338782 A/G - T C AG - Kukri_c47082_109 chr2B 442514862 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_rep_c66700_743 chr2B 442519267 T/C - A G CT - IAAV3255 chr2B 442522681 T/G + T G GT + BobWhite_c16735_131 chr2B 442569592 A/G + A G CT - BobWhite_c16735_176 chr2B 442569637 A/C + C A AC + tplb0038i24_1548 chr2B 442792380 A/G - T C AG - RAC875_c21237_166 chr2B 442792856 T/C + T C AG - RAC875_c11355_1215 chr2B 442794561 T/C + C T CT + CAP12_c6259_207 chr2B 442794798 A/G + G A AG + CAP12_c6259_236 chr2B 442794827 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_rep_c91092_553 chr2B 442795565 T/C - A G AG + Kukri_rep_c91092_72 chr2B 442796046 A/G - C T CT + Kukri_c31049_127 chr2B 442797166 T/G + T G AC - Excalibur_c25322_2231 chr2B 442797420 A/G + A G CT - Excalibur_c44190_297 chr2B 447745464 T/C - G A AG + CAP8_rep_c9095_407 chr2B 448080910 T/G + G T GT + Excalibur_s115514_168 chr2B 449167818 T/C + T C AG - Kukri_rep_c108265_141 chr2B 449167818 A/G - T C CT + Excalibur_c89062_180 chr2B 449170335 T/C - A G AG + RFL_Contig4562_142 chr2B 449516010 T/G - A C GT - RAC875_c3039_101 chr2B 450181335 A/G + G A AG + Kukri_c20819_497 chr2B 450184271 T/C + C T CT + RAC875_c5438_403 chr2B 450758924 A/G + A G CT - Excalibur_c19567_88 chr2B 450759997 A/G - C T AG - Kukri_c2541_976 chr2B 452772932 A/G - T C CT + Kukri_c2541_385 chr2B 452773523 A/G - T C CT + BS00066545_51 chr2B 452811220 A/G - C T AG - RAC875_c6201_933 chr2B 453019422 T/C + C T AG - Tdurum_contig27794_582 chr2B 453078759 T/C - A G AG + BobWhite_c34233_205 chr2B 453272780 T/C - G A AG + Kukri_c8595_953 chr2B 453752054 T/C + T C AG - Kukri_c9932_568 chr2B 453809862 T/C + T C CT + CAP7_rep_c6934_84 chr2B 453815171 A/G - T C CT + BobWhite_c9557_347 chr2B 453815599 T/C - G A AG + Kukri_c40347_584 chr2B 454018958 T/C + T C AG - Excalibur_c18275_211 chr2B 454326756 A/G NA NA NA CT NA flanks do not match reference at this position Ra_c21042_617 chr2B 456025530 T/C - A G AG + IAAV1993 chr2B 456025682 T/C - G A AG + BobWhite_c7326_70 chr2B 456172695 A/G + A G CT - RAC875_rep_c70107_184 chr2B 456174110 T/C + T C AG - Ku_c33341_260 chr2B 456341610 A/C - G T AC - BobWhite_c31523_130 chr2B 457343204 T/C + C T CT + BobWhite_c31986_324 chr2B 457684372 T/C - G A AG + RAC875_c41250_256 chr2B 457684399 T/C - A G CT - RAC875_c31376_399 chr2B 458081880 A/G + A G AG + Excalibur_c6911_126 chr2B 458246871 A/G - T C AG - TA002013-0438 chr2B 458622067 T/G NA NA NA GT NA flanks do not match reference at this position Excalibur_c4273_1921 chr2B 458622277 T/C - G A AG + Excalibur_c17576_2239 chr2B 458849772 A/G - C T CT + Kukri_rep_c110858_173 chr2B 458849895 T/C + C T CT + Kukri_rep_c110858_213 chr2B 458849935 A/G + A G CT - Kukri_c2746_3488 chr2B 459251122 A/G - T C CT + Kukri_c2746_1520 chr2B 459259314 A/G - T C AG - Excalibur_c45331_251 chr2B 459575759 T/C + C T CT + BobWhite_c27816_523 chr2B 459575972 T/C + C T AG - Excalibur_rep_c66988_471 chr2B 461736025 A/G - C T CT + Excalibur_rep_c66988_312 chr2B 461736184 A/G - T C CT + Excalibur_c6471_598 chr2B 461738256 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c6471_877 chr2B 461739351 A/G + G A CT - Tdurum_contig14531_347 chr2B 461741333 T/G + G T GT + Kukri_c57811_86 chr2B 462947184 A/G - T C CT + Excalibur_c6651_111 chr2B 462949436 A/C - T G GT + Kukri_c17062_426 chr2B 463283813 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c17991_1295 chr2B 463769617 A/G + A G AG + BobWhite_c14686_86 chr2B 463771117 T/G - A C AC + Kukri_c35305_684 chr2B 464289062 T/C + T C AG - Kukri_c35305_736 chr2B 464289114 A/G + G A AG + RFL_Contig4849_702 chr2B 464290358 T/C - A G CT - RAC875_c26168_84 chr2B 464681669 T/C - A G AG + Kukri_rep_c69034_146 chr2B 466190056 A/G - C T CT + Kukri_rep_c69034_100 chr2B 466190102 T/C - A G AG + Excalibur_rep_c67308_109 chr2B 466190188 A/C - T G GT + BobWhite_c12365_719 chr2B 466190452 A/G + G A CT - RAC875_rep_c105654_818 chr2B 466191425 A/G - T C CT + Kukri_rep_c106481_51 chr2B 467792398 T/C + C T AG - RAC875_c18298_171 chr2B 467863495 T/G + T G AC - RAC875_c18298_1105 chr2B 467870236 A/C + A C AC + Kukri_c23938_347 chr2B 470058742 T/C + C T CT + Tdurum_contig19642_362 chr2B 470913459 T/C + T C CT + BobWhite_c1617_799 chr2B 471442156 T/C + T C AG - RAC875_c29452_487 chr2B 471442933 A/G + G A AG + Excalibur_rep_c66758_1193 chr2B 472899477 T/G + T G AC - Kukri_c1913_107 chr2B 475604965 T/C + C T CT + CAP11_c6226_278 chr2B 475607690 A/G NA NA NA AG NA flanks do not match reference at this position CAP8_c6219_239 chr2B 476406298 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c26144_490 chr2B 476406307 T/C - A G CT - Tdurum_contig61682_187 chr2B 476407626 A/G - T C AG - RAC875_c26144_340 chr2B 476407666 T/C - A G CT - Jagger_c8101_134 chr2B 476408343 T/C - A G CT - Kukri_c13225_806 chr2B 476559723 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c5711_1043 chr2B 476560823 T/G + G T GT + Tdurum_contig11172_443 chr2B 476563278 A/G - C T AG - Tdurum_contig31448_78 chr2B 477332356 T/C - G A CT - Excalibur_c1655_1711 chr2B 478108296 A/G + A G AG + Excalibur_c18658_281 chr2B 478115952 T/G + G T GT + Excalibur_c18658_1053 chr2B 478117848 T/C + T C CT + Kukri_c1300_840 chr2B 478896398 T/C + C T CT + RAC875_c13882_454 chr2B 478909676 T/C - G A AG + Kukri_c28941_439 chr2B 480410625 T/C + T C CT + Excalibur_c36122_250 chr2B 481164569 T/C + C T AG - CAP11_rep_c6932_58 chr2B 481629418 A/G + G A CT - Kukri_c66566_59 chr2B 481880211 T/C - G A CT - Kukri_rep_c112089_211 chr2B 482721599 T/C - A G AG + RAC875_c22084_325 chr2B 482721635 T/C NA NA NA CT NA flanks do not match reference at this position BobWhite_rep_c64927_86 chr2B 482722645 A/G - T C AG - Excalibur_c59970_127 chr2B 482732878 T/C + C T CT + CAP7_c3162_138 chr2B 482734172 T/G + T G AC - Excalibur_c26599_213 chr2B 483458419 A/G + G A AG + tplb0046i10_1224 chr2B 483548149 T/C + T C AG - BS00063995_51 chr2B 483664860 T/C + T C CT + RFL_Contig1953_421 chr2B 484934130 T/C - A G CT - tplb0028k07_1268 chr2B 485040252 T/C - A G CT - tplb0062c03_292 chr2B 485871353 T/C NA NA NA CT NA flanks do not match reference at this position RFL_Contig4366_1075 chr2B 485925097 A/G - C T AG - CAP12_c1165_112 chr2B 486191885 T/C - A G CT - Excalibur_c12998_855 chr2B 486841262 A/G - T C AG - RAC875_c18953_153 chr2B 488011763 T/C - A G CT - BobWhite_c7977_412 chr2B 488192497 T/C + T C CT + BobWhite_rep_c50597_63 chr2B 488193032 A/C + C A GT - BobWhite_rep_c50597_84 chr2B 488193053 T/C + T C AG - Kukri_c11006_797 chr2B 488198818 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c27301_185 chr2B 488863798 T/C + T C CT + tplb0043g07_1291 chr2B 489851031 T/C + T C CT + BobWhite_rep_c63058_327 chr2B 491181550 A/G + A G AG + BobWhite_rep_c65893_87 chr2B 491181709 A/G - T C CT + Tdurum_contig27567_78 chr2B 491183101 T/C - A G CT - Jagger_c950_438 chr2B 491183345 A/G - T C AG - CAP12_c3182_123 chr2B 492289271 A/G - T C AG - RAC875_c25810_791 chr2B 493563022 T/C + C T CT + Excalibur_c42789_1093 chr2B 493564774 T/C + T C AG - Excalibur_c22285_501 chr2B 493986719 A/G - T C AG - Excalibur_c80177_123 chr2B 494284234 A/G - T C AG - Tdurum_contig64751_231 chr2B 494375313 T/C - A G CT - BobWhite_c21705_722 chr2B 494375520 T/C + C T CT + Excalibur_c19093_530 chr2B 494878823 A/C + C A AC + Kukri_c48530_131 chr2B 495167170 A/G - T C AG - Tdurum_contig12562_690 chr2B 495168309 A/C - T G AC - BobWhite_c1044_413 chr2B 495905990 T/G + T G AC - RAC875_c40420_134 chr2B 497798099 A/G - T C AG - Excalibur_c37712_728 chr2B 497799411 A/G + A G AG + Excalibur_rep_c68622_59 chr2B 497853808 T/C + T C CT + Excalibur_c92631_491 chr2B 498417143 T/C - A G CT - Kukri_c323_285 chr2B 499551529 T/C - A G CT - Kukri_c5749_2872 chr2B 500189704 T/C - A G CT - Kukri_c5749_371 chr2B 500192619 A/G - T C AG - RAC875_c22926_1596 chr2B 501010010 A/G + A G AG + RAC875_c10004_1708 chr2B 503447435 T/C + C T CT + RAC875_c17926_176 chr2B 503452284 A/G + A G CT - RFL_Contig1369_596 chr2B 503453394 T/C - A G AG + Excalibur_c13004_537 chr2B 505498202 A/G + G A AG + RAC875_c17266_60 chr2B 505933127 A/G + A G AG + Kukri_c15571_1564 chr2B 505934324 T/C + T C AG - RAC875_rep_c70556_1472 chr2B 506212266 A/G - T C CT + Excalibur_c18880_90 chr2B 506214027 A/G - T C CT + BobWhite_c31583_303 chr2B 507828147 T/C + C T CT + Kukri_c23852_72 chr2B 508648057 T/C + T C AG - Kukri_c23852_585 chr2B 508649716 T/C NA NA NA CT NA flanks do not match reference at this position RFL_Contig2023_575 chr2B 510399515 A/G - T C AG - RFL_Contig2023_547 chr2B 510399543 A/G - T C AG - Excalibur_c64378_109 chr2B 511278178 A/C + A C GT - Kukri_rep_c69580_249 chr2B 513496971 T/C - G A CT - Kukri_rep_c69580_162 chr2B 513497058 T/C - A G CT - Kukri_rep_c104061_598 chr2B 513498027 A/G - T C CT + CAP11_c7178_371 chr2B 513589658 A/C + C A GT - Excalibur_c56092_976 chr2B 514031620 A/G + A G CT - Excalibur_c46393_2446 chr2B 514035619 T/C - A G CT - BobWhite_c3208_97 chr2B 514038804 T/C - A G AG + Tdurum_contig54074_979 chr2B 514324641 A/G + G A AG + Excalibur_c4388_96 chr2B 514353222 A/G - T C AG - Excalibur_c27916_623 chr2B 514863196 T/C - A G CT - RAC875_c8721_80 chr2B 514864374 A/G - T C CT + Kukri_c11019_956 chr2B 514868354 T/C + T C AG - RAC875_c61100_694 chr2B 514882215 T/G - C A AC + Tdurum_contig12589_325 chr2B 516531695 A/G - T C AG - Kukri_c65721_158 chr2B 517382644 T/C - A G CT - Kukri_c39313_434 chr2B 518049637 T/C - G A CT - Kukri_c24374_397 chr2B 518517291 T/C - A G CT - RAC875_c730_234 chr2B 518741046 T/C + T C AG - Excalibur_c12721_319 chr2B 518741626 T/G + G T GT + Excalibur_c12721_376 chr2B 518741683 T/C + C T AG - RFL_Contig3840_969 chr2B 519015424 A/G + A G CT - IACX597 chr2B 519017350 A/C - G T GT + BobWhite_c7749_396 chr2B 521332912 A/C - G T AC - Kukri_c10642_271 chr2B 523265783 A/G + A G CT - Ra_c15365_530 chr2B 523266368 A/C + A C GT - Tdurum_contig42017_2877 chr2B 523774410 A/G - T C AG - Excalibur_rep_c103458_980 chr2B 524008385 T/C - G A CT - Excalibur_c11617_75 chr2B 524026630 T/C + C T CT + Excalibur_c11617_122 chr2B 524026677 T/C + C T CT + Excalibur_c11617_409 chr2B 524027082 A/G + A G AG + Kukri_c3163_328 chr2B 524176244 A/G + A G AG + RAC875_c17292_483 chr2B 525074945 T/C - G A CT - BobWhite_c34115_137 chr2B 525250429 T/C - G A AG + Kukri_c2664_180 chr2B 525827185 A/C + A C AC + BS00034167_51 chr2B 526733398 A/G - T C AG - Kukri_c15082_2790 chr2B 528202556 T/C - A G AG + Ex_c7958_1923 chr2B 529102584 T/C - A G CT - Ku_c6050_678 chr2B 529102910 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c57842_264 chr2B 529262820 A/G - C T CT + RAC875_c30053_167 chr2B 529537361 T/G - A C GT - Kukri_c9455_942 chr2B 529537627 A/G + A G CT - Tdurum_contig19607_147 chr2B 529698110 A/G - C T CT + Tdurum_contig64416_441 chr2B 530046503 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig27880_199 chr2B 530098933 T/G + G T GT + BobWhite_c7386_184 chr2B 530307613 T/C + T C AG - Jagger_c1810_163 chr2B 530730830 A/G - T C AG - BobWhite_rep_c59776_439 chr2B 531135703 T/C + T C CT + BobWhite_c54696_56 chr2B 531467034 T/C + C T CT + BobWhite_c54119_160 chr2B 531467366 T/C + T C CT + BobWhite_c54909_261 chr2B 531467393 A/G - C T CT + Excalibur_c40199_132 chr2B 531467807 A/C - G T AC - BobWhite_c39987_95 chr2B 532082360 T/G + T G AC - Excalibur_rep_c114468_327 chr2B 532091120 T/C + T C AG - Kukri_c16024_1368 chr2B 532092788 A/G + A G AG + RAC875_c18993_893 chr2B 532094721 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_rep_c69189_183 chr2B 534844953 T/G - A C GT - IAAV9070 chr2B 536639227 T/C + T C CT + RAC875_rep_c114453_166 chr2B 536639625 A/G + G A AG + Kukri_c39999_55 chr2B 536818870 T/C + T C CT + Excalibur_c79940_363 chr2B 538954426 T/G + T G AC - Excalibur_c79940_386 chr2B 538954449 T/C + C T AG - Excalibur_c79940_527 chr2B 538954590 T/C + T C CT + RAC875_c16393_576 chr2B 539476833 A/C + A C AC + RAC875_c16393_780 chr2B 539477037 T/C + T C AG - Excalibur_c4363_357 chr2B 539648834 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c1042_954 chr2B 539650985 A/G + A G AG + Excalibur_rep_c68587_90 chr2B 539804957 T/C + C T CT + RAC875_rep_c70357_296 chr2B 539805204 T/C + T C CT + RAC875_c14727_730 chr2B 539811444 T/C + T C CT + Excalibur_c29734_1152 chr2B 539961920 A/C NA NA NA AC NA flanks do not match reference at this position Kukri_c35153_956 chr2B 539965351 A/G + A G AG + Excalibur_c8894_836 chr2B 540425040 A/C - G T GT + BobWhite_c13063_381 chr2B 540428733 T/C + T C AG - Excalibur_c2005_359 chr2B 540438282 T/C + C T CT + tplb0036a07_596 chr2B 541105356 A/G + A G AG + RFL_Contig3104_1300 chr2B 541201003 A/G - T C CT + Excalibur_c77235_87 chr2B 541203004 T/C + T C AG - RFL_Contig890_1341 chr2B 542355316 T/C - G A AG + RFL_Contig890_1146 chr2B 542355511 A/G - T C AG - RAC875_c8722_2032 chr2B 543190205 A/G - T C CT + Kukri_rep_c93426_93 chr2B 544763488 T/G - A C AC + BS00009962_51 chr2B 545267408 T/C + C T CT + tplb0052b22_504 chr2B 545365603 A/G + A G CT - BS00010745_51 chr2B 546201924 T/C - A G AG + BS00010829_51 chr2B 546201931 T/C - A G AG + Ra_c111671_555 chr2B 546201966 A/G - C T CT + RFL_Contig5677_2285 chr2B 546202023 T/G - A C GT - IACX7505 chr2B 546202095 T/C + T C AG - RAC875_c29716_322 chr2B 546202737 A/G + A G CT - RAC875_c29716_871 chr2B 546203286 A/G + A G AG + GENE-1667_528 chr2B 546424815 A/G + G A CT - Excalibur_c84741_99 chr2B 547095911 T/C - A G AG + Tdurum_contig92604_368 chr2B 547096011 T/G + G T GT + BobWhite_c13285_245 chr2B 547837140 A/G + G A CT - RAC875_c25051_396 chr2B 547837386 T/C + T C AG - RAC875_c24668_362 chr2B 549191577 A/G + G A CT - CAP8_c711_201 chr2B 550045003 T/C + T C AG - Kukri_rep_c102199_232 chr2B 553166524 A/G + A G AG + Kukri_rep_c102199_1228 chr2B 553168105 T/C + T C AG - IAAV211 chr2B 553613770 A/G - C T CT + RAC875_c49672_304 chr2B 553614971 A/G - T C CT + GENE-1252_145 chr2B 553617541 A/C + A C GT - RFL_Contig4718_1269 chr2B 553623420 A/G + G A AG + RFL_Contig4718_1323 chr2B 553623474 A/C + A C GT - Excalibur_c36069_286 chr2B 553650432 A/G - T C CT + Tdurum_contig26542_457 chr2B 554292531 A/G - C T AG - Tdurum_contig26542_281 chr2B 554292707 T/C - G A CT - RFL_Contig1987_3440 chr2B 555840834 A/G - C T AG - Kukri_c23066_287 chr2B 556202548 T/C - A G AG + Excalibur_c9580_1142 chr2B 556685795 T/C NA NA NA CT NA flanks do not match reference at this position BobWhite_c24013_285 chr2B 556981060 A/G + A G AG + RAC875_s118762_119 chr2B 557229811 A/G - C T CT + RFL_Contig2290_463 chr2B 559430032 A/G NA NA NA CT NA flanks do not match reference at this position RFL_Contig2290_184 chr2B 559430384 T/C - A G CT - TA006140-0798 chr2B 560894898 T/C - A G AG + Kukri_c4097_898 chr2B 561226903 A/G + A G CT - BobWhite_c16130_362 chr2B 561283604 T/C - A G AG + BobWhite_rep_c53204_309 chr2B 563043721 T/G - C A GT - BobWhite_rep_c53204_212 chr2B 563043818 A/G - T C CT + BobWhite_c26981_66 chr2B 563045881 T/C - A G CT - CAP8_c3408_117 chr2B 563182680 T/C - A G CT - BobWhite_c25778_421 chr2B 563182781 A/G - C T CT + BobWhite_c45218_687 chr2B 563184889 A/C + C A AC + BobWhite_c39858_132 chr2B 563310772 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c41584_1172 chr2B 563860532 A/G + G A CT - RAC875_c15396_90 chr2B 564234162 A/G - T C CT + IACX11084 chr2B 564874571 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00100563_51 chr2B 564877374 A/G + A G AG + Excalibur_c114791_328 chr2B 564921622 T/C + T C AG - RAC875_c29297_122 chr2B 565211837 A/G + A G AG + Excalibur_c45120_560 chr2B 568658784 A/C + A C AC + CAP8_c1858_350 chr2B 569528707 T/C + T C AG - RAC875_c13876_313 chr2B 569980265 T/C + C T CT + BobWhite_c7477_707 chr2B 571144245 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_s118338_239 chr2B 572588931 T/C - G A AG + Excalibur_c6922_373 chr2B 573199214 T/C + C T AG - Excalibur_c6922_1393 chr2B 573200420 A/G + A G AG + RAC875_c20358_353 chr2B 575871817 A/G - T C CT + Tdurum_contig19264_355 chr2B 576091391 A/C + A C GT - Excalibur_rep_c82971_206 chr2B 576695760 A/G + A G AG + tplb0055d13_2123 chr2B 578136502 A/G - T C CT + tplb0055d13_2014 chr2B 578136611 T/C - A G AG + Kukri_c43745_1935 chr2B 578601210 T/C + T C AG - BobWhite_c744_614 chr2B 580020374 T/G - A C AC + CAP12_c733_120 chr2B 581468073 A/G + A G AG + Kukri_c28974_177 chr2B 581593908 T/G + T G GT + RAC875_c12920_274 chr2B 581594692 T/C - G A CT - RAC875_c12920_245 chr2B 581594721 A/G - T C AG - Ku_c71357_859 chr2B 581704094 T/C + T C CT + RAC875_rep_c106201_305 chr2B 581704779 T/C + C T CT + RFL_Contig2377_413 chr2B 582805780 T/C NA NA NA AG NA flanks do not match reference at this position RFL_Contig4181_1239 chr2B 583067672 A/G - T C AG - Excalibur_c14105_1257 chr2B 583415974 T/C + T C AG - Excalibur_c24738_965 chr2B 583531571 A/G - C T AG - RAC875_c22892_918 chr2B 583674692 T/G - A C GT - RAC875_rep_c69581_662 chr2B 583679225 T/C - A G CT - Kukri_c18494_341 chr2B 584117560 A/G + A G AG + RFL_Contig1361_542 chr2B 584823093 A/G - T C CT + RAC875_c56111_61 chr2B 585892127 A/G + A G CT - RFL_Contig4856_1483 chr2B 586119124 A/G - T C CT + RFL_Contig4856_71 chr2B 586120536 T/C - A G CT - BS00012320_51 chr2B 589879471 A/C + A C AC + Kukri_c79815_483 chr2B 589879943 T/C - G A AG + BS00035335_51 chr2B 591915666 A/G - C T CT + Kukri_c16453_913 chr2B 591916390 A/G - C T AG - BS00064448_51 chr2B 592039400 A/G + A G AG + IAAV5350 chr2B 592584190 A/C + A C AC + BS00019285_51 chr2B 592585152 A/C - T G AC - IAAV717 chr2B 592585152 T/G + T G GT + BobWhite_c22601_282 chr2B 593648614 T/C + T C CT + BS00091068_51 chr2B 593658786 A/C + C A AC + Kukri_c18949_113 chr2B 593659533 T/C - A G CT - Kukri_c12700_740 chr2B 593674566 A/G - C T CT + BobWhite_rep_c48906_1137 chr2B 593674602 A/G - T C CT + Kukri_c12700_122 chr2B 593676306 A/G - T C AG - BobWhite_rep_c48906_121 chr2B 593678289 T/G - C A GT - Kukri_c19751_873 chr2B 594172437 A/G - T C AG - Tdurum_contig30930_184 chr2B 594201501 T/C - G A AG + BobWhite_c38456_119 chr2B 594683384 A/G - C T CT + Kukri_c25815_263 chr2B 594849586 A/G - T C AG - BS00093992_51 chr2B 595126929 A/G + A G AG + CAP7_c2175_306 chr2B 596897930 A/G - C T CT + RAC875_c90702_249 chr2B 598958905 A/G + A G AG + BobWhite_c18969_556 chr2B 599597293 A/G - T C AG - IACX5850 chr2B 599813155 A/G + G A AG + Excalibur_c17833_222 chr2B 600704941 T/C + T C AG - Kukri_c32700_104 chr2B 601334100 T/C + C T CT + RAC875_c12016_880 chr2B 601334340 T/C + C T AG - BS00055427_51 chr2B 601892005 A/G - T C AG - BobWhite_c7354_462 chr2B 602993937 A/G - T C CT + Ex_c55735_1012 chr2B 605000674 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_rep_c112675_676 chr2B 605001459 A/C + A C GT - BobWhite_c26698_121 chr2B 607049209 A/G - C T CT + Ku_c11652_1720 chr2B 607244065 T/C + C T AG - CAP8_c407_255 chr2B 607246589 T/G + T G GT + Excalibur_rep_c74217_186 chr2B 607339931 A/G - T C AG - Kukri_c18031_2282 chr2B 608219573 T/C - A G CT - Ra_c72477_2165 chr2B 608223413 A/C - T G GT + Ra_c6367_387 chr2B 608231168 T/C + C T CT + Kukri_c31165_835 chr2B 608942339 A/G - T C CT + Kukri_c31165_812 chr2B 608942362 T/G - C A GT - Kukri_rep_c78141_398 chr2B 610419984 T/G + T G AC - BobWhite_c23462_53 chr2B 610421802 T/C - A G CT - BobWhite_c7143_223 chr2B 610595514 A/C - T G GT + BobWhite_c37602_265 chr2B 610595615 A/G + G A AG + RAC875_c100017_620 chr2B 611057951 T/C - A G CT - Ku_c12037_482 chr2B 611065411 T/C + T C CT + CAP12_c2472_60 chr2B 611282888 A/G + G A CT - Ex_c30517_1207 chr2B 612682941 A/G - C T CT + RAC875_c25035_958 chr2B 612684669 T/C + T C AG - RAC875_c14316_584 chr2B 612686386 A/G + G A AG + Ra_c14316_850 chr2B 612686734 A/G + A G CT - GENE-1352_214 chr2B 614908009 A/G NA NA NA CT NA flanks do not match reference at this position BobWhite_c7585_65 chr2B 614908503 T/G - A C GT - BobWhite_c2510_320 chr2B 615365163 A/G - C T AG - BobWhite_c2510_130 chr2B 615365353 T/C - A G AG + BobWhite_c12853_660 chr2B 616474263 T/G - A C GT - RAC875_c7540_366 chr2B 616928762 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c7540_118 chr2B 616929010 T/C - G A CT - Tdurum_contig13295_374 chr2B 616932826 T/C - A G AG + RAC875_c26278_459 chr2B 616935050 A/G - C T CT + Excalibur_c19649_1500 chr2B 616955965 T/C + C T AG - RAC875_c66657_91 chr2B 616956508 T/C + T C CT + Excalibur_c31737_169 chr2B 616963410 T/C + T C CT + RAC875_c12803_916 chr2B 616964984 A/G - T C AG - Kukri_rep_c69169_334 chr2B 616969769 A/G + A G AG + Kukri_rep_c69169_1153 chr2B 616970835 T/G + G T GT + Excalibur_rep_c67411_210 chr2B 616971046 T/C - G A CT - Kukri_c920_1379 chr2B 617141016 A/G - C T CT + Excalibur_c5064_765 chr2B 617141464 A/G + G A AG + Ex_c69493_1208 chr2B 617142915 T/C + T C AG - Kukri_c56872_402 chr2B 617528123 A/G + A G AG + Tdurum_contig25958_148 chr2B 617932761 T/C + T C CT + Tdurum_contig25958_262 chr2B 617932875 T/C + T C CT + Tdurum_contig25958_271 chr2B 617932884 T/C + T C AG - RAC875_c54947_108 chr2B 619044538 A/G - C T AG - Excalibur_c6302_1036 chr2B 619753475 T/C + T C CT + Excalibur_c6302_1072 chr2B 619753511 A/G + A G CT - Ra_c108387_863 chr2B 619753710 A/G + A G AG + JG_c2092_196 chr2B 620594828 T/C + C T CT + Tdurum_contig66317_77 chr2B 621185388 T/C - A G CT - Kukri_c17992_1382 chr2B 622476949 T/C + T C CT + Kukri_c31988_367 chr2B 622907123 T/C - A G AG + BobWhite_c10016_431 chr2B 622918512 T/C - A G CT - Tdurum_contig65349_140 chr2B 622918545 T/C + T C AG - BobWhite_c10016_302 chr2B 622918641 A/G - T C CT + Kukri_c64145_373 chr2B 622918758 A/G - T C AG - CAP8_rep_c8335_68 chr2B 624535157 A/G - T C CT + GENE-1174_236 chr2B 624538489 A/G - T C CT + Tdurum_contig34640_411 chr2B 624538605 T/G + T G GT + RAC875_c32066_684 chr2B 624539187 T/C + C T AG - Excalibur_c18989_1026 chr2B 629022609 A/G - T C AG - Kukri_c90752_89 chr2B 631330846 T/G + T G AC - Kukri_c19664_973 chr2B 631441478 T/C - A G CT - BobWhite_c2356_154 chr2B 631441918 A/G - T C CT + BobWhite_c19838_290 chr2B 631723028 A/G - C T AG - RAC875_c75222_346 chr2B 631802906 A/G - T C AG - RAC875_rep_c81149_203 chr2B 632168825 A/G + A G AG + Kukri_rep_c108258_397 chr2B 632170773 T/C + T C CT + Kukri_rep_c68955_239 chr2B 632171578 A/G - C T CT + Ra_c18654_370 chr2B 632381287 A/C + A C GT - Excalibur_c6111_411 chr2B 632386764 T/C - A G AG + BobWhite_c47936_113 chr2B 632387003 A/C + C A AC + Ex_c960_746 chr2B 634203265 A/G - T C AG - Ku_c10415_662 chr2B 635073893 A/G NA NA NA CT NA flanks do not match reference at this position BS00070861_51 chr2B 635075945 A/G - C T CT + RAC875_c3780_1317 chr2B 635078031 A/G + A G CT - Ku_c6970_2174 chr2B 635199128 T/G - C A GT - Tdurum_contig7144_248 chr2B 635206667 A/G + G A CT - Tdurum_contig7144_602 chr2B 635207021 T/C + T C CT + Excalibur_rep_c66864_74 chr2B 636112529 A/C + A C AC + Excalibur_c4252_75 chr2B 636112889 T/C + T C AG - Excalibur_c8499_723 chr2B 636200744 T/C - A G AG + Excalibur_c8499_282 chr2B 636201396 A/G - C T AG - Excalibur_c8499_165 chr2B 636201513 A/G - T C AG - Excalibur_c30728_218 chr2B 636549612 A/G + G A AG + RFL_Contig4034_1700 chr2B 636778978 A/C + A C AC + BS00088489_51 chr2B 637573913 A/G - C T CT + BobWhite_c19554_544 chr2B 637574105 A/G - T C AG - RFL_Contig337_1432 chr2B 637574237 A/G + A G CT - Tdurum_contig54925_415 chr2B 637574237 T/C - A G CT - Tdurum_contig54925_358 chr2B 637574294 T/C - G A CT - Tdurum_contig54925_291 chr2B 637574361 T/C - G A CT - Tdurum_contig54925_225 chr2B 637574427 T/C - A G AG + RFL_Contig337_1645 chr2B 637574450 T/G + T G GT + Tdurum_contig54925_202 chr2B 637574450 A/C - T G AC - Ra_c4051_1010 chr2B 638261899 T/C - G A CT - TA002671-0128-w chr2B 638630217 T/G - A C GT - BS00064528_51 chr2B 638955436 T/C - A G CT - Kukri_c20930_159 chr2B 640103289 T/G - C A GT - Excalibur_c16425_2096 chr2B 640340661 T/G + G T GT + CAP11_rep_c8975_202 chr2B 640377501 A/G - T C CT + BS00041922_51 chr2B 640489948 T/C - G A AG + RAC875_c12817_450 chr2B 640691751 A/C + C A GT - Ku_c66734_472 chr2B 640691822 T/G + G T GT + BS00069685_51 chr2B 640794808 T/C - A G AG + Excalibur_c30477_352 chr2B 640985969 A/G - T C CT + Kukri_c53850_730 chr2B 640987297 A/C NA NA NA AC NA flanks do not match reference at this position Excalibur_c4997_1208 chr2B 641101151 T/C - G A CT - Kukri_c35838_296 chr2B 641174138 T/C NA NA NA CT NA flanks do not match reference at this position BS00105315_51 chr2B 641877282 A/G + A G AG + BobWhite_rep_c50458_213 chr2B 641943063 A/G + G A CT - Excalibur_c11392_1193 chr2B 641943184 A/G + G A AG + Kukri_c9785_62 chr2B 643682925 A/G + G A CT - RAC875_rep_c80745_106 chr2B 643684175 T/C - A G CT - Kukri_c9785_1557 chr2B 643684667 A/G + G A AG + Ex_c9729_126 chr2B 643685066 T/G - C A GT - Kukri_c1460_1032 chr2B 644151555 A/G - T C CT + Kukri_c11600_1038 chr2B 645308160 T/C + T C AG - IAAV5675 chr2B 645309795 A/G + G A CT - BS00012036_51 chr2B 646215599 T/C + T C AG - BS00023154_51 chr2B 646215657 T/C + T C AG - Kukri_c38601_375 chr2B 646416757 T/C + C T CT + RAC875_c12037_1913 chr2B 646417069 T/G + T G AC - Tdurum_contig31911_195 chr2B 646417340 T/G - C A GT - Kukri_c32234_274 chr2B 646957818 T/C - A G CT - RAC875_rep_c114597_51 chr2B 646959207 A/C - T G AC - Tdurum_contig12831_69 chr2B 647104611 A/C NA NA NA AC NA flanks do not match reference at this position GENE-0675_104 chr2B 647105402 T/C + C T CT + GENE-0675_161 chr2B 647105455 T/C + T C AG - Ra_c68109_376 chr2B 647108830 A/G - T C AG - Tdurum_contig35492_150 chr2B 647109508 A/G + G A AG + RAC875_rep_c72879_435 chr2B 647114207 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c20187_1081 chr2B 647316638 A/G + A G AG + RAC875_c29892_138 chr2B 648083086 A/C - T G AC - TA001720-0874 chr2B 648481689 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_c71500_231 chr2B 648482734 A/C + A C GT - Kukri_c97631_275 chr2B 648912714 T/C - G A AG + Kukri_c4294_371 chr2B 648920752 A/G - C T AG - BobWhite_c4555_1950 chr2B 650284076 A/G + A G AG + Excalibur_c27279_699 chr2B 650402368 A/G NA NA NA CT NA flanks do not match reference at this position BobWhite_c12775_188 chr2B 650790339 T/C + T C CT + BobWhite_c12775_299 chr2B 650790549 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_c89760_431 chr2B 651352187 A/G - C T AG - Tdurum_contig10380_87 chr2B 651358139 A/G - T C CT + Kukri_c44276_88 chr2B 651734870 T/C - A G CT - Tdurum_contig12459_664 chr2B 651932274 A/G - T C AG - Excalibur_c45355_418 chr2B 651932348 A/G - C T CT + Tdurum_contig12459_491 chr2B 651932447 T/C - A G AG + Kukri_c65315_82 chr2B 651932533 T/C + T C AG - Tdurum_contig12459_405 chr2B 651932533 A/G - T C AG - CAP11_c6003_257 chr2B 652407574 A/G + A G AG + BobWhite_rep_c49922_132 chr2B 652414345 A/C + A C GT - Tdurum_contig74826_330 chr2B 652613163 T/C + T C AG - BS00057475_51 chr2B 652615059 A/G + A G CT - Kukri_c3965_374 chr2B 653259872 A/G + G A CT - Tdurum_contig84620_175 chr2B 653620438 A/G - T C AG - Tdurum_contig22828_244 chr2B 653914439 A/C + C A GT - Tdurum_contig25423_72 chr2B 653914722 T/C + C T CT + BS00047891_51 chr2B 654374967 T/C + C T CT + RAC875_c20016_298 chr2B 655004949 A/G - C T CT + RAC875_c20016_202 chr2B 655005045 T/C - G A AG + RAC875_rep_c73704_83 chr2B 655005229 T/C - A G CT - RAC875_rep_c72476_295 chr2B 655007158 T/G NA NA NA GT NA flanks do not match reference at this position BS00105409_51 chr2B 655014328 A/G - T C AG - BobWhite_c59027_169 chr2B 655304910 A/G - T C CT + Kukri_c10749_489 chr2B 655602096 A/G - T C AG - Excalibur_c3762_715 chr2B 655602876 T/C - A G AG + Excalibur_c7755_1321 chr2B 655605853 A/G - T C AG - Excalibur_c25414_806 chr2B 656228477 T/C - A G CT - BS00010567_51 chr2B 657195995 T/C + C T CT + IAAV7130 chr2B 657792718 T/C - A G AG + GENE-1444_162 chr2B 657844054 A/G + G A CT - IAAV677 chr2B 657844969 A/G - T C CT + TA005500-0404 chr2B 657845485 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_c23046_293 chr2B 658606153 A/G + G A AG + Kukri_c216_842 chr2B 658613006 T/C - A G AG + Kukri_c49007_501 chr2B 658615065 T/C - G A CT - Kukri_c4060_2424 chr2B 658616248 T/C + T C CT + BS00079013_51 chr2B 660114463 T/C - G A AG + RAC875_c3947_441 chr2B 660461061 T/C + T C CT + BobWhite_c4500_882 chr2B 660465483 T/C - G A CT - BobWhite_c12134_1140 chr2B 660465997 T/C + C T CT + Kukri_c75902_395 chr2B 662685326 A/G + A G CT - Kukri_c857_1332 chr2B 663127461 A/C - T G GT + RAC875_rep_c106437_83 chr2B 663128008 T/C - A G CT - RAC875_s118711_279 chr2B 664128690 T/C - A G CT - RAC875_c66557_403 chr2B 664213442 A/G + A G AG + Kukri_rep_c112754_101 chr2B 664213676 T/C + T C CT + BS00098739_51 chr2B 664214070 T/C - G A AG + Tdurum_contig68666_570 chr2B 664214138 A/G + A G CT - BS00011545_51 chr2B 664219708 A/G - T C AG - BS00009247_51 chr2B 664219711 T/C - G A CT - RAC875_rep_c73777_74 chr2B 664220215 T/G - A C GT - Kukri_rep_c101529_553 chr2B 664220483 A/C - G T GT + BobWhite_c5543_492 chr2B 664934844 A/G + G A CT - BobWhite_c22106_204 chr2B 665189392 A/C + C A AC + Tdurum_contig59522_420 chr2B 665189392 T/G - C A GT - Tdurum_contig59522_262 chr2B 665189653 T/C - G A AG + RAC875_c14039_299 chr2B 665668954 A/G + A G AG + Tdurum_contig76090_916 chr2B 666482800 T/C - A G AG + BobWhite_rep_c64679_73 chr2B 666650024 A/C + A C GT - Tdurum_contig13837_573 chr2B 667416863 A/G - T C AG - RFL_Contig5721_851 chr2B 668171070 T/C - A G AG + BobWhite_c44310_299 chr2B 668171122 T/C + C T CT + tplb0021c16_1440 chr2B 668383314 A/G + A G AG + Tdurum_contig5691_526 chr2B 668570132 A/G - C T AG - Ra_c31353_172 chr2B 669436096 A/G + G A CT - BS00080967_51 chr2B 669436308 A/G - C T AG - BobWhite_c3056_2737 chr2B 669436685 T/C - G A AG + Kukri_rep_c108192_147 chr2B 670166269 A/G - T C CT + Excalibur_c6769_1371 chr2B 670750811 A/G - T C AG - Excalibur_c6769_758 chr2B 670752004 A/G - T C CT + BS00094373_51 chr2B 670752276 T/C - A G CT - BS00022518_51 chr2B 670837337 T/C - G A CT - BS00067992_51 chr2B 670842171 A/G - T C CT + tplb0049b10_696 chr2B 671742659 T/C - G A AG + Kukri_c20973_606 chr2B 672021092 T/C + T C CT + BS00049974_51 chr2B 672023695 T/G + G T AC - BobWhite_c47573_560 chr2B 673961576 T/C + C T AG - Excalibur_c16983_1471 chr2B 674039597 A/G + A G CT - Excalibur_c16983_1626 chr2B 674039752 T/C + T C CT + Excalibur_c1685_1270 chr2B 674305492 A/G + A G AG + Tdurum_contig18858_324 chr2B 675340491 A/C - G T AC - Excalibur_c76236_105 chr2B 675344396 T/C - G A CT - Excalibur_c64983_65 chr2B 675345867 T/C + T C CT + Tdurum_contig30325_334 chr2B 675347647 A/G - C T AG - BS00033942_51 chr2B 675352302 T/C - A G CT - GENE-1224_119 chr2B 676127011 T/C - A G AG + Excalibur_c1353_1364 chr2B 676128399 T/C - G A AG + Excalibur_c1353_1100 chr2B 676128663 A/G - C T CT + BobWhite_c1072_100 chr2B 677218397 A/G + G A CT - BS00027945_51 chr2B 677356607 T/C + C T AG - GENE-1283_1105 chr2B 677805459 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c59539_158 chr2B 679627519 T/C - A G CT - RAC875_c817_2282 chr2B 679743097 T/C + T C CT + Excalibur_c22637_235 chr2B 679898851 T/C + T C AG - Excalibur_c362_330 chr2B 680042264 T/C + C T AG - IACX6497 chr2B 680044413 T/C + T C AG - BS00022790_51 chr2B 680044771 A/G + A G AG + Excalibur_c19407_326 chr2B 680044895 A/G - T C CT + BS00093777_51 chr2B 680045001 A/G + G A AG + BS00080797_51 chr2B 680237625 T/G - A C GT - BS00022383_51 chr2B 680237719 A/C - T G AC - BS00022717_51 chr2B 680573506 A/G - C T AG - BobWhite_c3146_128 chr2B 680574689 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c76598_570 chr2B 681539627 A/G - C T AG - RAC875_c28108_400 chr2B 681540452 T/C + C T AG - RAC875_c28108_523 chr2B 681540575 T/C + T C CT + IACX8470 chr2B 681542496 T/C + C T AG - Excalibur_rep_c114675_101 chr2B 682016810 T/C - A G AG + Kukri_c31131_223 chr2B 682039542 T/C + T C CT + Kukri_c31131_369 chr2B 682039688 T/C + T C AG - Kukri_c26622_867 chr2B 682041159 T/C NA NA NA CT NA flanks do not match reference at this position CAP11_c2194_115 chr2B 682217702 T/C - A G CT - BobWhite_c18540_97 chr2B 682848350 A/G + A G CT - BobWhite_c18540_351 chr2B 682848604 A/G + A G CT - BobWhite_rep_c60776_638 chr2B 682849392 A/G + A G CT - BobWhite_rep_c60776_1019 chr2B 682850494 A/G + A G AG + Kukri_rep_c68130_626 chr2B 682851216 A/G - T C CT + GENE-1000_141 chr2B 683003193 T/C + C T CT + GENE-1000_186 chr2B 683003222 T/C + T C AG - Kukri_rep_c108243_143 chr2B 683028761 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_rep_c108243_88 chr2B 683028816 A/C - T G GT + BS00016650_51 chr2B 683029170 A/G + G A CT - BS00023124_51 chr2B 683046930 T/C + C T AG - BS00081231_51 chr2B 683758793 T/C - A G CT - BS00086322_51 chr2B 686834821 A/G - C T CT + GENE-0966_173 chr2B 686836489 T/C - A G CT - Ra_c13679_2284 chr2B 687205342 A/G - C T AG - Excalibur_c76665_98 chr2B 687206986 T/C + T C AG - BS00088621_51 chr2B 687248334 T/C + T C CT + CAP11_c1993_434 chr2B 687469102 T/C - G A CT - BS00013013_51 chr2B 687473521 A/G - T C CT + Excalibur_c65759_335 chr2B 687473563 T/C - A G CT - BS00011630_51 chr2B 688459169 T/C - G A CT - CAP12_c2521_413 chr2B 688462604 A/G - C T CT + CAP8_rep_c8162_101 chr2B 689106051 T/G + G T AC - Excalibur_c5619_1110 chr2B 689871010 T/C - A G AG + Excalibur_c5619_990 chr2B 689871130 T/C - A G CT - Excalibur_c5619_136 chr2B 689871984 A/C - T G GT + GENE-0808_1110 chr2B 690028365 T/C - A G CT - GENE-0808_745 chr2B 690028435 A/C - G T GT + Kukri_c66502_108 chr2B 690033210 T/G + G T GT + BS00104667_51 chr2B 690218325 A/G + A G CT - Kukri_c26311_891 chr2B 690588623 A/G + A G AG + tplb0048g05_866 chr2B 690777813 A/G + A G CT - BS00067572_51 chr2B 691055963 A/C + A C GT - IAAV6424 chr2B 691780716 T/C - G A CT - IACX8096 chr2B 691780864 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RFL_Contig2612_826 chr2B 692461536 T/C + C T CT + Kukri_c31059_130 chr2B 692468899 A/G - T C CT + RAC875_c3397_274 chr2B 694050185 A/C + A C GT - RFL_Contig3172_2652 chr2B 694055160 A/G - T C CT + RFL_Contig3172_2394 chr2B 694055505 A/G NA NA NA AG NA flanks do not match reference at this position BS00072324_51 chr2B 695374463 T/C - A G CT - Ku_c9369_1726 chr2B 695374677 T/G + T G GT + Ku_c9369_1965 chr2B 695374916 T/C + T C AG - Excalibur_c65341_303 chr2B 695581355 A/G + A G AG + RAC875_c54927_1000 chr2B 695582709 A/C + C A AC + IAAV2633 chr2B 695689202 A/G - T C AG - IAAV3474 chr2B 695693402 A/G + A G CT - RAC875_c41026_274 chr2B 695840386 A/G - C T AG - IACX2158 chr2B 695992436 A/G - T C CT + IACX2142 chr2B 696080499 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c3257_729 chr2B 696356897 A/C NA NA NA AC NA flanks do not match reference at this position RAC875_c14885_1184 chr2B 696371900 T/C - A G AG + RAC875_c14885_1027 chr2B 696372160 A/C NA NA NA GT NA flanks do not match reference at this position GENE-3588_374 chr2B 696373359 T/C - A G CT - GENE-0746_101 chr2B 696373405 A/G - C T CT + RAC875_c14885_243 chr2B 696373840 T/C - A G CT - Kukri_c21044_1231 chr2B 696375250 A/G + A G CT - RAC875_c17455_653 chr2B 696678113 T/G - A C AC + CAP11_c1716_97 chr2B 697435688 T/C + T C AG - BobWhite_c17220_314 chr2B 697435752 T/C - G A AG + BS00046164_51 chr2B 697510373 A/C + A C AC + IAAV2917 chr2B 697511636 A/G - T C AG - Excalibur_c36280_764 chr2B 697512104 A/C + A C GT - Excalibur_rep_c110697_196 chr2B 697978823 A/G + A G CT - BS00021713_51 chr2B 698208610 T/C - A G CT - BS00021682_51 chr2B 698212114 A/C - G T AC - RAC875_c12313_898 chr2B 698214233 A/G - T C AG - RAC875_c103094_120 chr2B 698303834 A/C + A C AC + RAC875_c103094_572 chr2B 698304284 A/G + A G AG + Excalibur_c2819_2310 chr2B 698963683 A/G - T C CT + BobWhite_c47357_535 chr2B 698968757 A/G + A G CT - BobWhite_c2521_117 chr2B 699106309 T/C + T C AG - Kukri_c2343_108 chr2B 699108379 A/G - T C AG - RAC875_c4465_549 chr2B 699108736 A/G - C T AG - RAC875_c4465_81 chr2B 699109204 A/G - T C AG - IAAV3067 chr2B 699173434 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RFL_Contig2519_341 chr2B 699178314 T/C NA NA NA AG NA flanks do not match reference at this position Ex_c16948_754 chr2B 699827018 A/G - T C AG - BobWhite_c2244_259 chr2B 700456923 A/G + A G AG + BS00095643_51 chr2B 702714575 T/G + G T GT + Kukri_c8502_120 chr2B 702726892 A/G - T C CT + Ku_c12447_2002 chr2B 703976259 T/G + G T GT + GENE-3548_191 chr2B 705205423 A/G + A G CT - BobWhite_c16923_64 chr2B 706269885 T/C + T C AG - Tdurum_contig27907_359 chr2B 708197437 T/G - C A GT - Tdurum_contig27907_216 chr2B 708197580 A/G - C T AG - Excalibur_c60964_203 chr2B 708436756 A/G + G A CT - BS00046744_51 chr2B 708437945 T/C - G A AG + Tdurum_contig21896_174 chr2B 709423590 T/C NA NA NA CT NA flanks do not match reference at this position Ku_c53298_1284 chr2B 709821485 A/G + G A CT - BobWhite_c64697_215 chr2B 710897340 A/C - G T GT + CAP8_c2432_370 chr2B 711534453 T/C - A G CT - Excalibur_rep_c78626_295 chr2B 711718118 T/C - A G CT - RFL_Contig3016_1771 chr2B 711727805 T/C + C T CT + IACX10927 chr2B 712601684 A/C - T G GT + GENE-0713_444 chr2B 712601823 T/C + C T AG - BS00083821_51 chr2B 712603382 T/C - A G CT - tplb0024l03_910 chr2B 713675758 T/C + T C CT + Excalibur_c80601_83 chr2B 713675815 T/C + C T AG - Excalibur_c80601_278 chr2B 713676010 A/G + G A AG + Excalibur_c80601_308 chr2B 713676040 A/G + A G CT - Excalibur_c27629_473 chr2B 714132936 A/G + A G CT - BS00047073_51 chr2B 714779769 T/C - A G CT - BS00047070_51 chr2B 714779851 A/G - C T CT + Ku_c51309_212 chr2B 714791625 A/G + A G CT - IAAV3100 chr2B 715028611 A/G - T C CT + BS00022618_51 chr2B 715030126 A/G - T C CT + BS00073735_51 chr2B 715310673 A/G + A G AG + BobWhite_c32938_264 chr2B 715599509 T/C - G A CT - BobWhite_c29596_649 chr2B 715601569 A/C + A C AC + TA004922-0553 chr2B 715926681 T/C NA NA NA AG NA flanks do not match reference at this position BS00093566_51 chr2B 715927063 A/G + A G CT - BobWhite_c1472_528 chr2B 715927162 T/C - A G AG + BS00093546_51 chr2B 715927329 T/C + T C CT + IACX6492 chr2B 716594566 T/C - G A CT - BS00025650_51 chr2B 716780342 T/C + T C CT + JD_c9115_954 chr2B 716782453 A/C + C A GT - BS00022547_51 chr2B 716815921 A/G + G A AG + Kukri_c60849_248 chr2B 716816050 T/C + C T AG - Excalibur_c2484_2113 chr2B 717474744 T/C - A G CT - IAAV307 chr2B 717475063 A/T + NA NA AT NA reference base C not among SNP alleles Excalibur_c2484_1659 chr2B 717475198 T/C - G A AG + BobWhite_c10837_533 chr2B 718603595 T/C + C T AG - Tdurum_contig54784_485 chr2B 718967996 A/G - C T AG - Excalibur_c13180_336 chr2B 719522056 T/C + C T AG - Ku_c674_915 chr2B 719522108 A/G - T C AG - RAC875_c81984_707 chr2B 719800816 T/C - G A CT - Tdurum_contig42046_1390 chr2B 719800816 T/C - G A CT - Tdurum_contig32221_462 chr2B 719964987 T/G NA NA NA AC NA flanks do not match reference at this position BS00110588_51 chr2B 719965157 T/C - A G CT - TA001163-0861 chr2B 719980045 T/G - C A GT - Kukri_c16601_822 chr2B 720479473 T/C + C T AG - Tdurum_contig10246_1749 chr2B 720576358 A/G - T C AG - BS00090406_51 chr2B 720582136 T/C + C T CT + Tdurum_contig78534_314 chr2B 720807493 T/C - A G CT - Excalibur_rep_c71150_423 chr2B 721112319 A/G - T C AG - BS00003939_51 chr2B 721112655 A/G - T C AG - Kukri_c101063_1234 chr2B 721113525 A/G + A G CT - Kukri_c20719_949 chr2B 721700935 T/C - A G AG + BS00063365_51 chr2B 721922228 T/C - G A AG + Excalibur_c5801_177 chr2B 722085721 A/C - T G AC - BobWhite_c1841_868 chr2B 722620262 A/G NA NA NA AG NA flanks do not match reference at this position BS00101105_51 chr2B 722628686 A/C + C A GT - BS00101113_51 chr2B 722628916 A/C + A C AC + TA001249-1083 chr2B 722633335 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c10218_944 chr2B 722633928 A/G + A G CT - CAP11_c2607_294 chr2B 722633988 T/C - A G CT - Kukri_c35798_308 chr2B 723331919 T/C - A G AG + Ex_c13213_2594 chr2B 723333707 A/G + G A AG + Ex_c13213_2992 chr2B 723334105 T/C + C T CT + Kukri_c7953_513 chr2B 723442967 A/G + A G CT - RAC875_c5689_1052 chr2B 723443351 T/G + T G AC - Tdurum_contig48260_249 chr2B 723443416 A/G - C T AG - BS00081095_51 chr2B 724741267 A/C - T G GT + BS00022399_51 chr2B 724741283 T/C - A G AG + CAP8_c5161_541 chr2B 725960659 A/G + A G AG + Jagger_c6543_220 chr2B 725961161 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_c411_1775 chr2B 726547514 A/G - C T CT + Kukri_c411_1530 chr2B 726547759 A/C - T G GT + BS00022674_51 chr2B 726547785 T/C - A G CT - Tdurum_contig56876_1078 chr2B 726550408 A/G NA NA NA CT NA flanks do not match reference at this position GENE-1176_361 chr2B 726551293 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c24410_754 chr2B 729767125 A/G - C T CT + Kukri_rep_c68903_301 chr2B 730188559 T/C + T C CT + GENE-0342_117 chr2B 730188720 T/C + T C CT + Kukri_rep_c68903_708 chr2B 730189372 T/C + T C AG - Kukri_rep_c68903_1100 chr2B 730190673 T/G + G T GT + Kukri_rep_c68903_1118 chr2B 730190691 T/G + G T GT + Tdurum_contig82393_484 chr2B 730562664 A/C + C A AC + Tdurum_contig82393_581 chr2B 730562761 T/G + T G AC - BS00004224_51 chr2B 730563020 T/C - A G CT - Excalibur_c14201_111 chr2B 730563981 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c2259_1052 chr2B 730565527 T/C + T C AG - GENE-3157_174 chr2B 730613799 T/G - C A GT - Kukri_c2363_702 chr2B 730851132 T/C - A G CT - BobWhite_c17614_194 chr2B 730998248 A/G NA NA NA CT NA flanks do not match reference at this position BobWhite_c17614_323 chr2B 730998377 T/C + T C AG - BS00086676_51 chr2B 730998473 A/G + A G CT - RAC875_c97355_297 chr2B 730998473 A/G + A G AG + BS00015253_51 chr2B 730998548 T/G + T G GT + IAAV2337 chr2B 730998548 A/C - T G AC - Excalibur_c52268_92 chr2B 731001044 A/G + A G AG + tplb0048j22_125 chr2B 731001729 A/G - T C CT + RAC875_c53285_834 chr2B 731305719 T/G - A C AC + Excalibur_s109809_129 chr2B 731305746 T/C - A G AG + RAC875_rep_c106542_272 chr2B 731311073 A/G NA NA NA CT NA flanks do not match reference at this position BS00082137_51 chr2B 731481384 A/C - G T GT + RAC875_c91522_523 chr2B 731562376 A/G + G A CT - GENE-1236_418 chr2B 731605360 A/G + A G CT - CAP12_rep_c7164_108 chr2B 731609334 T/C + C T CT + BobWhite_c35150_107 chr2B 731609586 A/G - C T AG - BobWhite_c6365_540 chr2B 731894809 T/C NA NA NA AG NA flanks do not match reference at this position BobWhite_c6365_385 chr2B 731895391 T/C - G A AG + Excalibur_c60164_137 chr2B 732607386 T/C - A G CT - Excalibur_c95944_72 chr2B 732607743 A/G + G A AG + Kukri_c529_1414 chr2B 733714407 T/C - A G CT - BS00110721_51 chr2B 734050220 A/G - T C AG - BS00022295_51 chr2B 734050376 T/C - A G CT - Kukri_c57014_168 chr2B 734127065 A/C + A C GT - BS00081109_51 chr2B 734453472 T/C - G A AG + Excalibur_c35074_257 chr2B 734495342 T/C - A G CT - Excalibur_c35074_106 chr2B 734495493 T/C - G A CT - Kukri_c64884_106 chr2B 735520958 T/C + T C AG - IAAV4101 chr2B 735521084 A/G + A G CT - BobWhite_rep_c52106_349 chr2B 736245457 A/C + A C AC + BobWhite_c55700_273 chr2B 736247209 T/C - G A CT - Excalibur_c33221_681 chr2B 736408809 A/G - T C CT + Kukri_c38497_174 chr2B 736790823 T/C + T C CT + Tdurum_contig71365_233 chr2B 738410414 A/G + G A AG + RFL_Contig4096_605 chr2B 738411171 T/C + C T AG - RFL_Contig4499_204 chr2B 738681209 A/G + A G CT - RFL_Contig4499_785 chr2B 738681790 T/C + C T AG - RFL_Contig4499_1145 chr2B 738682150 T/C + T C CT + RFL_Contig4499_1817 chr2B 738682913 A/G + A G AG + RAC875_c54085_51 chr2B 738684687 A/G + A G CT - BS00111236_51 chr2B 738686705 A/G + A G CT - Tdurum_contig77036_338 chr2B 740218272 T/C - G A CT - BS00035380_51 chr2B 740313563 A/G + A G AG + Excalibur_rep_c111396_152 chr2B 740314226 A/G - T C CT + BS00012382_51 chr2B 740314948 A/G + A G AG + Kukri_c30659_91 chr2B 740315248 A/G + G A CT - IAAV3648 chr2B 740315587 T/C + C T CT + RAC875_c35778_201 chr2B 740733860 A/G - C T AG - tplb0053n06_606 chr2B 740735361 A/G - C T CT + BobWhite_c15453_1010 chr2B 740801854 A/C - G T AC - BS00092031_51 chr2B 740805231 T/C - A G CT - Excalibur_c48295_249 chr2B 740805315 T/G + T G GT + BobWhite_c13295_69 chr2B 741860245 T/C + C T CT + Excalibur_c18165_395 chr2B 741860392 T/C + T C CT + BobWhite_c13295_407 chr2B 741860583 T/C + C T CT + Excalibur_c7119_1369 chr2B 742081886 T/C + T C CT + BS00086180_51 chr2B 742465945 A/G - T C CT + Excalibur_c13046_166 chr2B 742466225 T/C + T C CT + Excalibur_c13046_700 chr2B 742466762 A/G + A G AG + RAC875_rep_c109891_156 chr2B 742466840 A/G - T C CT + GENE-0769_164 chr2B 742467212 A/C NA NA NA GT NA flanks do not match reference at this position BobWhite_rep_c65414_271 chr2B 742471902 T/C + T C AG - BobWhite_rep_c65414_318 chr2B 742471949 T/C + T C AG - BobWhite_c7888_145 chr2B 742524112 A/G + G A AG + Kukri_c6944_1636 chr2B 742814233 T/C - A G AG + IAAV1776 chr2B 742814954 T/C + T C CT + Kukri_c6944_714 chr2B 742815469 T/C - A G CT - BobWhite_c43399_64 chr2B 742893389 T/C + T C AG - Ku_c3479_1035 chr2B 743331273 T/C + C T CT + GENE-1232_258 chr2B 743693304 A/C NA NA NA GT NA flanks do not match reference at this position RAC875_c40992_113 chr2B 743745123 T/G NA NA NA GT NA flanks do not match reference at this position Excalibur_c37753_655 chr2B 743746042 T/C + T C CT + Excalibur_c37753_754 chr2B 743746278 A/G + A G CT - Tdurum_contig28795_381 chr2B 743746278 T/C - A G CT - Tdurum_contig28795_322 chr2B 743746337 T/C - G A AG + Tdurum_contig28795_273 chr2B 743746386 T/C - G A CT - Excalibur_c2157_173 chr2B 743746506 A/G - T C CT + Excalibur_c1940_359 chr2B 745579696 A/G + G A CT - Excalibur_c1940_396 chr2B 745579733 T/G + G T AC - RAC875_c1734_703 chr2B 745580732 T/C + C T CT + Kukri_c10138_598 chr2B 745700113 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c16752_283 chr2B 745717047 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig59546_695 chr2B 745717047 A/G NA NA NA CT NA flanks do not match reference at this position BS00022805_51 chr2B 745719282 A/G - C T CT + RAC875_c66695_560 chr2B 746037361 T/C - A G CT - Kukri_c27285_530 chr2B 746037953 T/C - G A AG + BobWhite_c7050_792 chr2B 746101501 T/C - A G CT - Tdurum_contig9214_279 chr2B 746101729 A/G + G A AG + Kukri_c89993_379 chr2B 746321149 A/G + A G AG + BS00043338_51 chr2B 747125491 A/G + G A CT - RFL_Contig2460_547 chr2B 747178307 A/G NA NA NA CT NA flanks do not match reference at this position IACX6324 chr2B 747179878 C/G - C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c35399_497 chr2B 747602868 A/C - T G AC - BS00100981_51 chr2B 747602904 A/G - C T CT + BS00009060_51 chr2B 747821525 A/C - G T AC - IAAV6288 chr2B 748152603 T/G + NA NA GT NA reference base A not among SNP alleles RAC875_c24546_866 chr2B 748700821 T/C - G A AG + RFL_Contig955_1021 chr2B 748725004 T/C + T C AG - Ra_c19225_591 chr2B 748973857 T/C NA NA NA CT NA flanks do not match reference at this position BS00010988_51 chr2B 748974423 A/C + C A AC + Excalibur_c18966_1008 chr2B 748980201 A/G NA NA NA AG NA flanks do not match reference at this position Jagger_c7991_160 chr2B 749139076 A/G - T C AG - Jagger_c7991_95 chr2B 749139141 T/C - A G CT - Kukri_c40146_126 chr2B 749419018 A/G - T C CT + Excalibur_c3727_382 chr2B 749419891 T/C - A G CT - Excalibur_c98275_372 chr2B 749420154 A/G - T C AG - Kukri_c44368_240 chr2B 749572812 T/C - A G AG + BS00022064_51 chr2B 749972453 T/C - G A AG + BS00030361_51 chr2B 750013199 T/C + C T CT + BS00030364_51 chr2B 750013548 T/C + T C CT + BS00068181_51 chr2B 751183085 A/G - T C AG - BobWhite_c18678_95 chr2B 751257597 T/G + T G AC - Ku_c48694_1284 chr2B 751262519 T/G + G T GT + Excalibur_rep_c103064_1279 chr2B 751262543 A/G + G A CT - BS00068203_51 chr2B 751264787 A/G - C T CT + GENE-1280_188 chr2B 751532660 T/C - A G CT - Ku_c102096_268 chr2B 751580675 T/C + T C CT + Excalibur_rep_c102526_112 chr2B 751581184 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c42146_266 chr2B 752485079 A/G + G A CT - Excalibur_c42146_338 chr2B 752485222 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c29259_751 chr2B 752491279 T/C + C T AG - IACX3246 chr2B 752785129 T/G + T G GT + CAP12_c6281_285 chr2B 752787940 T/C + C T AG - Kukri_c4824_239 chr2B 754547476 A/G - T C AG - BS00067828_51 chr2B 754661080 T/C - A G AG + IACX2222 chr2B 754663607 A/G - T C AG - RFL_Contig3761_791 chr2B 758592618 T/C - G A AG + GENE-0526_733 chr2B 758594502 T/C - A G CT - BS00028063_51 chr2B 759172998 A/C - G T GT + BS00023202_51 chr2B 759491095 T/G + NA NA GT NA reference base A not among SNP alleles BobWhite_c31708_99 chr2B 759818127 A/G - C T AG - BobWhite_c30140_119 chr2B 760119391 A/G + G A CT - CAP7_c4056_108 chr2B 760890405 T/C - A G CT - GENE-0777_105 chr2B 760890925 A/G + A G AG + Tdurum_contig49532_368 chr2B 760950039 T/C + C T CT + Excalibur_c9752_619 chr2B 760950576 T/C - G A AG + Excalibur_c9752_208 chr2B 760950987 T/C - G A CT - Excalibur_c9752_73 chr2B 760951122 T/G - A C GT - RAC875_c5949_2011 chr2B 760951241 T/G + G T GT + BobWhite_rep_c50285_616 chr2B 761990643 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_rep_c50285_700 chr2B 761990949 A/C + A C AC + Excalibur_c16679_215 chr2B 762503265 A/G - C T CT + RAC875_c25271_138 chr2B 762518972 T/C - G A CT - Excalibur_c10441_984 chr2B 763630822 A/G - C T AG - BobWhite_c10864_436 chr2B 763631878 A/G + G A CT - BS00084417_51 chr2B 763633070 A/C - T G AC - BS00080318_51 chr2B 763842555 T/G - A C GT - Ku_c30027_394 chr2B 764073108 A/C NA NA NA AC NA flanks do not match reference at this position IACX8298 chr2B 764074058 T/C - A G AG + Kukri_c12117_134 chr2B 764822961 T/G + T G GT + Kukri_c21087_79 chr2B 764902392 A/G - T C AG - IACX8202 chr2B 765061606 T/C - A G CT - Jagger_c7688_98 chr2B 765072211 A/G + A G AG + BS00011047_51 chr2B 765278696 A/G + G A AG + RAC875_c30797_179 chr2B 765279313 A/G - T C CT + BS00074091_51 chr2B 765897855 A/G - T C AG - RAC875_c98387_145 chr2B 766233774 A/G - C T CT + Kukri_c34553_110 chr2B 766234269 T/C + T C CT + Kukri_c15985_1277 chr2B 766566233 T/C + C T CT + RAC875_c16064_217 chr2B 767016371 T/G + T G AC - Kukri_c27631_1329 chr2B 767018159 T/C + T C CT + CAP12_c1817_77 chr2B 767018286 A/G + A G CT - RFL_Contig3713_538 chr2B 767021595 T/C + T C AG - BobWhite_c23950_145 chr2B 767021628 A/G - T C CT + BS00051965_51 chr2B 767021904 T/G + T G AC - Excalibur_c30744_181 chr2B 767132203 A/G - T C CT + CAP12_s9114_61 chr2B 767132251 T/C + C T AG - RFL_Contig385_761 chr2B 767169958 T/G + T G GT + RAC875_c22463_494 chr2B 767170221 A/G - T C CT + BS00106695_51 chr2B 767171587 A/C + A C GT - BobWhite_c33464_133 chr2B 767176664 A/G NA NA NA AG NA flanks do not match reference at this position BS00009882_51 chr2B 767651618 A/G + G A AG + Kukri_c24939_378 chr2B 768292033 T/C + T C CT + BS00010438_51 chr2B 768292420 A/G - T C CT + IACX7803 chr2B 768548091 T/C + C T AG - Excalibur_c1883_340 chr2B 768548794 A/G NA NA NA AG NA flanks do not match reference at this position BS00011276_51 chr2B 768548839 A/G + A G AG + Excalibur_c65466_714 chr2B 769072216 T/C + C T CT + RAC875_c24205_110 chr2B 769077646 T/C NA NA NA AG NA flanks do not match reference at this position BS00069756_51 chr2B 769079547 A/G - T C CT + BS00069754_51 chr2B 769079556 A/C - G T GT + IACX5726 chr2B 769428475 T/C + C T CT + IAAV1502 chr2B 769949884 T/C + T C CT + BS00063589_51 chr2B 770070240 T/G - A C GT - Kukri_c55909_1109 chr2B 770681399 T/C + T C AG - Kukri_c11040_787 chr2B 770684873 T/C + T C AG - BS00030172_51 chr2B 770715297 A/G - T C CT + RAC875_c21358_62 chr2B 772027185 T/C + C T CT + RFL_Contig4423_795 chr2B 772027221 A/G + A G CT - Tdurum_contig12159_468 chr2B 772053242 T/C - G A AG + BS00022222_51 chr2B 773140975 T/C + C T AG - Kukri_c657_1607 chr2B 773141126 T/G - A C AC + Kukri_c657_1514 chr2B 773141219 A/G - C T AG - Ex_c52711_584 chr2B 773142143 T/C + C T CT + Tdurum_contig42282_10323 chr2B 773145430 T/C - A G CT - Kukri_c4117_2610 chr2B 773147389 A/G + A G AG + Excalibur_c42561_571 chr2B 773151756 T/C + T C CT + RAC875_c1696_991 chr2B 773348786 A/C + A C AC + Kukri_c7146_870 chr2B 773349148 T/C - A G CT - Excalibur_c2174_1681 chr2B 773349577 A/G + G A CT - BS00064465_51 chr2B 774831041 T/C + T C AG - BS00064836_51 chr2B 774831066 T/C + T C AG - RFL_Contig2751_1562 chr2B 774945112 A/G - T C AG - Excalibur_c5438_1021 chr2B 774954920 T/C - A G CT - Excalibur_c56550_71 chr2B 775169387 A/G + A G CT - Kukri_c10869_1366 chr2B 775169574 A/C - T G GT + Excalibur_c56550_425 chr2B 775169740 A/C + C A AC + Kukri_c44231_1576 chr2B 775170824 T/C + C T AG - Excalibur_rep_c109577_191 chr2B 775369065 A/G - T C AG - BobWhite_c10520_1517 chr2B 775371493 A/G + A G AG + RFL_Contig5122_974 chr2B 776213706 T/C + C T CT + Kukri_c21008_657 chr2B 776747473 T/C - A G CT - BS00000012_51 chr2B 776815292 A/G - T C AG - Kukri_c26697_366 chr2B 776975976 T/C - A G CT - Tdurum_contig14482_423 chr2B 777114785 A/G + A G CT - Tdurum_contig14482_1013 chr2B 777115675 T/C + C T CT + IAAV7086 chr2B 777363062 A/G NA NA NA CT NA flanks do not match reference at this position CAP7_c16_567 chr2B 777384818 T/C - G A AG + Ku_c67680_195 chr2B 777513944 T/C + C T CT + Ex_c27573_778 chr2B 777514658 T/C - G A AG + RAC875_c56649_541 chr2B 777515687 A/G + A G CT - RAC875_rep_c108389_622 chr2B 777516728 T/C - A G CT - Excalibur_rep_c83640_791 chr2B 779251503 T/C - A G AG + Tdurum_contig10048_61 chr2B 779341273 T/C + C T AG - Tdurum_contig10048_207 chr2B 779341519 A/G + A G AG + BobWhite_c7274_333 chr2B 779344647 T/C - G A CT - IAAV1535 chr2B 779345848 T/G + NA NA AC NA reference base C not among SNP alleles BS00003593_51 chr2B 780782703 T/C + C T AG - tplb0043n06_1748 chr2B 780786186 A/C - T G GT + Excalibur_c23857_594 chr2B 780788118 T/C + C T CT + Ku_c738_453 chr2B 781536102 T/C + T C AG - BS00039187_51 chr2B 781584299 A/G - T C AG - BS00083329_51 chr2B 781830247 A/G - T C AG - BobWhite_c28685_381 chr2B 782145946 T/G - A C GT - Excalibur_c66045_388 chr2B 782152589 T/C - A G AG + RAC875_c7735_338 chr2B 782154215 T/C + C T AG - Ku_c2936_1987 chr2B 782154354 T/C + T C CT + CAP11_c1820_244 chr2B 782534064 A/C + A C GT - RAC875_rep_c119322_54 chr2B 782534412 T/C - G A AG + BS00022478_51 chr2B 783226978 A/G + G A AG + BS00004413_51 chr2B 784551365 A/G - C T AG - BobWhite_c928_311 chr2B 784553492 A/C NA NA NA GT NA flanks do not match reference at this position BS00067878_51 chr2B 784621083 A/G + G A AG + GENE-1136_260 chr2B 785136132 T/G + G T AC - Kukri_c94792_69 chr2B 785890205 A/G + A G AG + Kukri_c94792_127 chr2B 785890263 A/G + G A AG + BS00097147_51 chr2B 786033209 T/C - A G CT - BobWhite_c20158_834 chr2B 786035733 T/C + C T AG - RAC875_c16993_196 chr2B 786105954 A/G - T C AG - Tdurum_contig27848_179 chr2B 786225768 T/C - A G AG + Excalibur_c2993_457 chr2B 786226967 A/G + A G AG + RAC875_c12741_101 chr2B 786229394 A/G + G A CT - Excalibur_c5193_64 chr2B 786230010 A/G + G A AG + Excalibur_c21117_99 chr2B 788524254 A/G + A G CT - BS00100117_51 chr2B 788524814 A/G + G A CT - Excalibur_c12675_1395 chr2B 788656076 T/G NA NA NA AC NA flanks do not match reference at this position Excalibur_c12675_1147 chr2B 788656700 T/C - A G AG + IAAV1798 chr2B 788658756 T/C - A G CT - GENE-1304_735 chr2B 788661613 T/G + T G GT + Kukri_c49647_151 chr2B 788804866 A/G + A G AG + Kukri_c3501_1175 chr2B 789437020 T/C - A G CT - Excalibur_c8919_345 chr2B 789437154 A/G + A G CT - Excalibur_c94383_157 chr2B 789438902 A/G + G A AG + RFL_Contig1115_407 chr2B 789601631 T/C - G A AG + BS00072840_51 chr2B 789605603 A/G + A G AG + BS00072839_51 chr2B 789605639 A/G + G A CT - Kukri_c52900_280 chr2B 790228772 T/C + T C CT + BS00065302_51 chr2B 790274439 A/G - C T AG - BS00083998_51 chr2B 790751851 A/G + G A CT - RFL_Contig5495_464 chr2B 790752036 A/C + C A AC + RFL_Contig5495_682 chr2B 790752254 A/G + G A CT - Ra_c105904_187 chr2B 790753463 T/C + T C CT + Ra_c105904_1191 chr2B 790754699 A/G + A G CT - Excalibur_rep_c106048_800 chr2B 790755087 T/C + C T CT + tplb0042a21_1091 chr2B 791479476 A/G - T C CT + RAC875_c17798_66 chr2B 791704600 T/C + C T CT + BS00106606_51 chr2B 793130022 A/G - T C CT + Excalibur_c47996_509 chr2B 793150837 A/G + A G AG + BS00026037_51 chr2B 793151178 A/G - C T CT + BobWhite_c5756_532 chr2B 794501126 A/C - G T AC - tplb0035c15_1393 chr2B 794893214 A/C + C A AC + BS00022863_51 chr2B 795045996 T/C - A G CT - BS00083626_51 chr2B 795065614 T/C - A G CT - RAC875_c7602_1205 chr2B 795067068 A/G - C T CT + Excalibur_c6937_1065 chr2B 796344864 T/C - G A CT - BS00110814_51 chr2B 796801998 T/C - G A CT - RAC875_c19042_2102 chr2B 796803336 T/C - A G CT - Kukri_c900_1376 chr2B 796806856 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c900_1334 chr2B 796807546 T/C - A G CT - RAC875_c19042_443 chr2B 796808237 T/C - A G AG + Excalibur_c25043_357 chr2B 797328204 A/G + A G AG + GENE-0686_186 chr2B 797328414 A/G - C T CT + Excalibur_c25043_1221 chr2B 797332522 A/G + A G CT - BobWhite_c1105_745 chr2B 797625995 A/G + A G AG + Kukri_c52608_142 chr2B 797627240 T/C + C T AG - Kukri_c16621_417 chr2B 798213263 A/G - T C CT + Kukri_c39136_675 chr2B 798306089 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c20793_249 chr2B 798308359 A/G + G A AG + Kukri_c49784_86 chr2B 800031404 A/G - T C CT + Kukri_c12693_396 chr2B 800125065 T/C - A G CT - Excalibur_rep_c106698_235 chr2B 801217354 A/G + A G AG + Kukri_rep_c78353_161 chr2B 801219489 T/C + T C CT + GENE-0676_715 chr2B 801222223 T/C - A G AG + GENE-0676_322 chr2B 801222345 T/C - G A AG + BS00065264_51 chr2B 801253554 T/G - C A GT - RAC875_rep_c73605_271 chr2D 280916 T/G - A C GT - IAAV8205 chr2D 678809 T/C - A G CT - Kukri_c19266_779 chr2D 2470447 A/C - G T AC - IACX11138 chr2D 3756310 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles IAAV4862 chr2D 4463953 A/G - T C AG - Excalibur_c42248_211 chr2D 4464008 A/G - T C AG - RAC875_c34512_685 chr2D 5234943 A/C + C A AC + Excalibur_c61319_274 chr2D 5235851 A/G + A G CT - TA002227-1090 chr2D 5642971 A/G NA NA NA AG NA flanks do not match reference at this position IAAV1807 chr2D 5771475 A/C - G T AC - Kukri_c7339_113 chr2D 6642700 A/G - C T AG - Kukri_c46542_414 chr2D 7168901 A/G + A G AG + IAAV3684 chr2D 7169103 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Excalibur_c18324_390 chr2D 7972711 A/G + A G CT - Excalibur_c25599_358 chr2D 8295045 A/G - T C CT + BS00068050_51 chr2D 8478664 T/C - G A AG + Kukri_c1175_1577 chr2D 8499833 T/C + T C AG - Excalibur_rep_c109101_94 chr2D 9623759 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c10442_1911 chr2D 10334745 A/C - T G AC - RAC875_c20989_348 chr2D 10334965 A/G + A G CT - RAC875_c20989_1049 chr2D 10335666 A/G + A G CT - BS00108451_51 chr2D 11094480 T/C - A G AG + BS00108448_51 chr2D 11094608 A/G - C T CT + BS00023099_51 chr2D 11477071 A/C - G T GT + Kukri_c30439_2407 chr2D 12329606 A/G - T C CT + BS00012313_51 chr2D 12689184 T/G + T G AC - IAAV7407 chr2D 12690486 T/G - A C GT - Tdurum_contig77522_310 chr2D 12697325 A/G + G A AG + BS00022957_51 chr2D 12786080 A/G + G A CT - BS00064216_51 chr2D 12907942 T/C - G A AG + BS00049370_51 chr2D 12978032 A/G - T C AG - BS00063632_51 chr2D 13427835 T/G + G T GT + IACX8451 chr2D 13440469 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles GENE-1343_886 chr2D 13440952 T/C + T C AG - BS00095512_51 chr2D 13680056 A/G - C T CT + BS00002660_51 chr2D 13838381 T/C - G A AG + BS00018532_51 chr2D 13885025 A/G - C T CT + Kukri_c45103_371 chr2D 13906510 T/G + G T GT + RFL_Contig772_1037 chr2D 13911386 A/G - T C AG - Jagger_c5341_126 chr2D 14254326 A/G - T C CT + BS00110224_51 chr2D 14254638 T/C + C T CT + Kukri_c5282_726 chr2D 14402794 A/G - T C AG - Kukri_c19434_1170 chr2D 14413782 A/G - T C AG - Kukri_c102346_668 chr2D 14414716 T/C NA NA NA AG NA flanks do not match reference at this position D_F1BEJMU01A0OMY_356 chr2D 14636322 A/G + A G AG + CAP11_c464_72 chr2D 14778524 T/C + T C CT + D_contig16084_234 chr2D 14779053 A/C - G T GT + BS00067698_51 chr2D 14860398 T/C - A G CT - D_F1BEJMU02GB94Z_188 chr2D 15194290 A/G - T C CT + RAC875_c22368_641 chr2D 15728939 T/C + C T CT + BS00047901_51 chr2D 15967398 A/G + A G AG + BS00063645_51 chr2D 16344389 A/G - T C CT + Kukri_c4949_201 chr2D 16493001 T/C + C T CT + Kukri_c4949_261 chr2D 16493061 T/C + C T CT + TA004158-0971 chr2D 17814026 A/G + A G AG + RAC875_c16897_367 chr2D 17814828 T/C + T C CT + Kukri_c3882_2021 chr2D 17815713 T/G + T G AC - Kukri_c12648_434 chr2D 17955970 T/C + T C CT + Excalibur_c1408_1577 chr2D 18232136 A/G - C T AG - JD_c63957_1176 chr2D 20769354 T/C + T C CT + Ex_c14755_1362 chr2D 20769531 T/G + G T GT + tplb0053n05_793 chr2D 22449284 T/C - A G CT - BS00064194_51 chr2D 22499961 T/C + T C CT + RAC875_c58089_105 chr2D 22818378 A/G - T C CT + RAC875_c1755_971 chr2D 25170701 T/C - G A CT - Tdurum_contig42153_5214 chr2D 25645886 T/G + G T GT + Tdurum_contig42153_6232 chr2D 25652306 A/G + G A AG + BS00093760_51 chr2D 27924761 T/C - A G CT - BS00093757_51 chr2D 27924953 T/C - A G AG + tplb0030j08_1960 chr2D 27928724 T/C + T C CT + GENE-1417_89 chr2D 28627348 T/C - A G CT - Excalibur_rep_c113724_109 chr2D 28628355 T/C - A G CT - Excalibur_c59287_531 chr2D 28629667 A/G + A G CT - Excalibur_c59287_876 chr2D 28630164 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c53516_119 chr2D 28633670 T/C NA NA NA AG NA flanks do not match reference at this position BobWhite_c24495_282 chr2D 28731594 A/G + A G AG + D_GDS7LZN01C04AG_36 chr2D 28756622 T/G - A C AC + GENE-0137_1290 chr2D 29162000 T/C + C T CT + Excalibur_c7963_1722 chr2D 29165900 A/G - T C AG - BobWhite_c8085_498 chr2D 29167070 T/C + T C CT + BS00010087_51 chr2D 29167079 A/C + A C AC + BS00022276_51 chr2D 29454322 T/G - A C GT - IAAV1634 chr2D 29495371 A/C - T G GT + Excalibur_c20196_503 chr2D 29844485 A/G + A G CT - Excalibur_c19260_105 chr2D 30747062 A/G + G A CT - RAC875_c4314_993 chr2D 30748567 T/C + C T CT + Kukri_c108931_87 chr2D 32029757 A/G - T C CT + BobWhite_c11059_169 chr2D 32054673 A/C - G T AC - RAC875_rep_c105135_247 chr2D 32799834 A/G + G A CT - RAC875_c7319_195 chr2D 34231554 A/G - C T CT + Kukri_c34861_523 chr2D 35510567 A/G - T C CT + D_F1BEJMU01EISTM_67 chr2D 37302738 A/G + A G CT - Excalibur_c21752_768 chr2D 44077785 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig62138_414 chr2D 45800506 A/G + A G CT - Kukri_c67627_393 chr2D 48566001 T/C - G A CT - GENE-0581_156 chr2D 49881785 A/G - C T AG - Kukri_c12627_150 chr2D 54673654 T/C - A G AG + RAC875_c19409_300 chr2D 56582349 T/C NA NA NA CT NA flanks do not match reference at this position GENE-1741_103 chr2D 58655424 A/G - C T AG - IACX6239 chr2D 59008004 A/G + A G CT - Excalibur_c15048_488 chr2D 60946925 T/C - G A CT - Kukri_c36343_315 chr2D 61315653 A/G - C T AG - BobWhite_c16439_1143 chr2D 62401901 T/C - A G CT - BobWhite_c16439_1102 chr2D 62401942 T/C - A G CT - BobWhite_c16655_421 chr2D 62593536 A/G + G A AG + IAAV666 chr2D 62958775 T/G + G T GT + D_contig31797_313 chr2D 63555521 A/G - T C CT + tplb0045o20_1168 chr2D 63693637 T/C - A G CT - BS00011313_51 chr2D 64733132 A/G + A G AG + BS00073229_51 chr2D 64981233 A/G - T C AG - RAC875_c45366_729 chr2D 65264854 T/C - A G CT - BS00009540_51 chr2D 65563563 T/G - C A GT - RFL_Contig4542_1281 chr2D 66761344 A/G - T C AG - BS00022143_51 chr2D 66868572 A/G + G A AG + IACX9152 chr2D 66869519 T/C - A G CT - Excalibur_c6136_312 chr2D 67226133 A/G + A G AG + GENE-0787_85 chr2D 67231672 T/G + G T AC - BS00081578_51 chr2D 67552821 T/G - A C AC + RAC875_c61885_58 chr2D 67553519 A/G + A G AG + BS00067820_51 chr2D 67557198 T/C - G A CT - Kukri_rep_c114322_506 chr2D 67967527 A/C + A C AC + BS00106937_51 chr2D 68733925 A/G + A G CT - BS00062865_51 chr2D 69251614 T/G - A C GT - BS00062864_51 chr2D 69251622 T/C - G A AG + BS00032252_51 chr2D 69504609 A/G - C T AG - Kukri_c4790_1174 chr2D 69504871 T/C - G A AG + BobWhite_c47086_539 chr2D 69508990 A/G + A G CT - RAC875_rep_c69728_528 chr2D 69536272 T/C + C T CT + Excalibur_c11947_746 chr2D 70951678 T/C + C T CT + IAAV3173 chr2D 71208551 A/G - T C AG - Excalibur_c20376_615 chr2D 71761013 T/C - A G CT - Kukri_c39227_310 chr2D 71761184 A/G + A G AG + Excalibur_c2887_131 chr2D 73019422 T/C + C T CT + Kukri_c9102_84 chr2D 73021542 T/C + T C CT + BS00022211_51 chr2D 73023918 T/G + G T AC - RAC875_rep_c114236_188 chr2D 73572961 A/G + A G AG + Kukri_c60627_74 chr2D 74279469 T/G - A C AC + BobWhite_c8650_382 chr2D 74935351 T/C NA NA NA AG NA flanks do not match reference at this position BS00063517_51 chr2D 74938353 A/G + G A CT - Kukri_c59403_339 chr2D 75001895 A/G - C T CT + RAC875_c53308_1030 chr2D 75003849 A/G + A G CT - Kukri_c63505_174 chr2D 75097166 A/G + G A AG + Excalibur_c15505_87 chr2D 75251458 T/C + T C AG - Kukri_c9636_947 chr2D 75256116 T/C - A G CT - Excalibur_c17456_428 chr2D 75257764 T/C + C T AG - Kukri_rep_c71152_906 chr2D 75393758 T/G - A C AC + BobWhite_c6055_185 chr2D 75395203 T/G - A C GT - Excalibur_c22877_1990 chr2D 75396131 T/C + T C CT + RAC875_c14561_264 chr2D 75504509 T/C - A G AG + Kukri_c16557_855 chr2D 76007955 A/C + C A AC + Kukri_rep_c70504_1385 chr2D 76541622 T/C + T C AG - BS00076261_51 chr2D 76580054 A/C + A C AC + BobWhite_c38833_197 chr2D 76653013 A/G + A G AG + RAC875_c31560_141 chr2D 76761267 A/G + A G AG + IAAV1002 chr2D 76761425 C/G - C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_rep_c103893_601 chr2D 76860548 T/C + T C CT + RAC875_c26896_339 chr2D 76899647 A/G - T C AG - IAAV2480 chr2D 77131618 A/G - C T CT + BobWhite_rep_c51612_864 chr2D 77132677 T/G + T G GT + BobWhite_c27044_149 chr2D 78383782 A/G NA NA NA CT NA flanks do not match reference at this position BS00082604_51 chr2D 78392291 A/G - T C CT + BS00082605_51 chr2D 78392670 T/C - A G CT - RAC875_rep_c72220_143 chr2D 78562339 A/G + A G AG + D_contig77859_59 chr2D 78692295 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c31493_120 chr2D 78692489 A/C + C A GT - BS00044720_51 chr2D 78793706 A/G + A G CT - BS00067584_51 chr2D 79416639 T/C - A G AG + BS00079440_51 chr2D 79421706 T/C + T C AG - RAC875_rep_c71350_1712 chr2D 79421800 A/G + G A AG + BS00083080_51 chr2D 79541210 A/G + A G CT - Excalibur_c2127_863 chr2D 79692303 T/C + T C AG - GENE-1010_148 chr2D 79877812 T/C + T C CT + BS00046890_51 chr2D 79941364 T/C - G A CT - BobWhite_c25482_176 chr2D 79984914 T/C + T C AG - Kukri_rep_c69214_641 chr2D 79985364 T/C + T C CT + CAP11_c3942_361 chr2D 79987027 T/C - A G AG + Kukri_c26576_329 chr2D 79987846 A/G + A G AG + GENE-0791_244 chr2D 80038515 A/G NA NA NA AG NA flanks do not match reference at this position GENE-1353_120 chr2D 80730316 T/G + T G GT + GENE-1353_136 chr2D 80730328 T/C + T C AG - BS00021940_51 chr2D 80820393 A/G + A G AG + Kukri_c49670_857 chr2D 81299077 A/G + G A AG + RAC875_c46007_340 chr2D 81305621 A/G + G A AG + GENE-1409_76 chr2D 81311138 A/G + A G CT - BobWhite_c890_199 chr2D 81326095 A/C + A C GT - BS00083504_51 chr2D 81327490 T/C - A G CT - Excalibur_c99485_336 chr2D 81470581 A/C - T G GT + BS00021865_51 chr2D 81651714 T/C - A G CT - BS00109570_51 chr2D 81836872 A/G + A G AG + IAAV4282 chr2D 82108241 T/C - G A CT - BS00080239_51 chr2D 82185677 T/C + C T AG - IACX5670 chr2D 83142083 T/C - G A AG + RFL_Contig5917_3026 chr2D 83161935 A/G NA NA NA CT NA flanks do not match reference at this position BS00021718_51 chr2D 83854169 T/C - A G CT - RAC875_rep_c72435_90 chr2D 84342583 A/G - C T AG - GENE-1015_49 chr2D 93055259 T/G + T G AC - RAC875_c2571_1233 chr2D 93085906 A/G - T C CT + Kukri_rep_c101016_905 chr2D 97222392 T/C + T C AG - Kukri_rep_c112585_518 chr2D 97223229 A/G + A G AG + Kukri_rep_c110868_147 chr2D 97275572 T/C + C T CT + IAAV7129 chr2D 98268204 T/C + C T AG - Jagger_c9129_252 chr2D 98269195 A/C NA NA NA AC NA flanks do not match reference at this position BobWhite_c30826_779 chr2D 98907043 T/C NA NA NA AG NA flanks do not match reference at this position BobWhite_rep_c55691_302 chr2D 100318131 T/C - G A CT - Excalibur_c13676_266 chr2D 102880505 T/C + C T AG - RAC875_c77938_731 chr2D 108770368 A/G - T C AG - GENE-1389_396 chr2D 109700911 T/G + T G AC - Kukri_c22200_1171 chr2D 109702523 T/C + C T AG - BobWhite_c28404_121 chr2D 109702560 T/C NA NA NA CT NA flanks do not match reference at this position RFL_Contig1339_589 chr2D 114142420 T/C + C T AG - Tdurum_contig10750_130 chr2D 117839152 A/G + A G AG + Kukri_c17515_353 chr2D 122863322 T/C + T C CT + Excalibur_c8959_403 chr2D 123508388 A/C + C A GT - Excalibur_c18901_292 chr2D 123806112 T/C - G A CT - Excalibur_c18901_246 chr2D 123806158 A/G - T C AG - Excalibur_c43358_1063 chr2D 124874414 T/C - G A AG + GENE-1423_81 chr2D 126737146 T/G - C A GT - BobWhite_c7786_376 chr2D 126950305 T/C + C T CT + tplb0058k01_1177 chr2D 126969548 A/G + A G AG + Kukri_rep_c103649_475 chr2D 127085714 A/G - C T CT + Kukri_c10054_567 chr2D 128399221 A/C - G T AC - RAC875_rep_c72897_262 chr2D 129961078 T/C - A G CT - RAC875_c44703_199 chr2D 133235199 T/C + T C AG - Excalibur_rep_c107558_300 chr2D 133752196 A/G + A G CT - Excalibur_rep_c107558_367 chr2D 133752263 A/C + C A AC + Excalibur_c8832_711 chr2D 133753414 A/G - T C AG - RAC875_c5080_312 chr2D 145892684 T/C - A G AG + Kukri_c6546_255 chr2D 147230854 T/C - A G AG + tplb0059a11_1514 chr2D 147966977 A/G - T C AG - RAC875_c5077_313 chr2D 150379591 T/C + T C AG - BobWhite_c19742_105 chr2D 152627562 A/G - T C CT + RAC875_rep_c72417_104 chr2D 154099719 T/C + T C CT + Kukri_c19857_547 chr2D 155735973 A/G + A G CT - RFL_Contig1533_819 chr2D 156825059 T/C - A G CT - BS00065690_51 chr2D 157138592 A/C + A C AC + Excalibur_rep_c69421_986 chr2D 157891668 A/C + C A GT - RAC875_c13922_303 chr2D 157892092 T/C + C T CT + Excalibur_rep_c102405_141 chr2D 157892271 A/G + A G AG + GENE-1313_319 chr2D 159687400 T/C - G A CT - RAC875_c20987_92 chr2D 166109394 A/G + A G AG + Excalibur_c15166_112 chr2D 170407422 A/C - T G GT + BobWhite_c3664_81 chr2D 170451213 A/G - T C AG - Excalibur_c30286_467 chr2D 179134863 T/C + T C AG - Kukri_c22419_172 chr2D 186696872 T/C + T C AG - Excalibur_rep_c70398_484 chr2D 187530730 T/C - A G CT - Excalibur_rep_c80772_128 chr2D 189673163 T/C - A G AG + RAC875_c67683_403 chr2D 193119560 T/C - A G CT - GENE-0753_342 chr2D 193400277 T/C - A G CT - Jagger_c699_353 chr2D 194191297 T/C - A G AG + Kukri_c36956_401 chr2D 194191297 A/G + A G AG + Excalibur_c16184_1201 chr2D 194757493 A/G - T C AG - Excalibur_c60255_727 chr2D 195292890 A/G - T C CT + RAC875_c50475_270 chr2D 204140412 T/C - G A CT - BS00068029_51 chr2D 209508810 T/C + T C CT + Excalibur_c10609_256 chr2D 218048557 T/C + T C AG - Excalibur_rep_c102654_375 chr2D 247848449 A/G + G A CT - D_contig01615_264 chr2D 254978365 T/C - G A CT - Kukri_c8562_1146 chr2D 256669457 T/C - A G AG + IAAV233 chr2D 261735153 A/G + A G AG + IAAV6642 chr2D 261735153 T/C - A G AG + RAC875_c17874_1344 chr2D 261741872 A/C - T G GT + Kukri_c47140_128 chr2D 267702553 T/C - G A CT - GENE-1326_350 chr2D 282933779 T/C + C T CT + Kukri_c9197_1341 chr2D 293656078 T/C - A G CT - CAP11_c5434_172 chr2D 301817091 A/G - T C AG - Kukri_c12194_1322 chr2D 304659201 A/G - C T AG - RAC875_rep_c77067_347 chr2D 304967305 T/C + C T AG - Kukri_s117812_125 chr2D 304967572 A/C + C A AC + RAC875_c2923_1201 chr2D 304997227 A/G + A G AG + Ra_c105962_177 chr2D 305905860 A/G + A G AG + RAC875_c23476_88 chr2D 305909158 T/C + T C CT + Ra_c40751_1203 chr2D 306251464 T/C + C T CT + RAC875_c43835_231 chr2D 306531266 A/C + A C AC + Kukri_c4432_188 chr2D 308480258 T/C NA NA NA AG NA flanks do not match reference at this position BS00067102_51 chr2D 310087162 T/C + C T CT + TA002695-2341 chr2D 314078848 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c43780_140 chr2D 314498155 T/C + T C CT + BobWhite_rep_c61114_267 chr2D 316653749 T/C - G A CT - RAC875_c46245_569 chr2D 317946339 A/G + A G CT - RAC875_c30440_448 chr2D 318337882 T/C + C T CT + Kukri_c2094_749 chr2D 320160163 T/C + T C CT + Kukri_c67664_160 chr2D 326220583 A/G + A G AG + Excalibur_c46864_118 chr2D 332332233 A/C + C A GT - Excalibur_c10122_789 chr2D 352705674 T/C + T C AG - D_GB5Y7FA01EHPZX_186 chr2D 353058238 T/C - G A AG + BobWhite_c13066_776 chr2D 355986868 A/G - T C AG - RAC875_c9122_395 chr2D 360488600 T/C - A G CT - Excalibur_c33079_199 chr2D 361396819 A/C - G T AC - CAP12_c2215_260 chr2D 364166814 T/G NA NA NA AC NA flanks do not match reference at this position BS00000905_51 chr2D 369762241 T/C - A G CT - BobWhite_c23958_102 chr2D 372701962 T/C - A G AG + RAC875_c11272_443 chr2D 372928895 A/G + A G AG + BobWhite_c12732_205 chr2D 373224433 T/C - A G CT - Kukri_rep_c91092_204 chr2D 373225786 T/C - A G CT - RAC875_rep_c108797_110 chr2D 373225795 T/C - A G AG + RAC875_c17677_1850 chr2D 373226988 A/G + G A AG + D_GCE8AKX01AOZXN_340 chr2D 375366422 T/G + G T GT + RFL_Contig96_137 chr2D 377503856 A/C - G T AC - BobWhite_c46028_206 chr2D 385173293 T/C + C T CT + Excalibur_rep_c67360_303 chr2D 385269712 T/G + T G AC - Kukri_c52754_149 chr2D 386585365 T/C - G A CT - Excalibur_c45745_450 chr2D 392687828 T/C - A G CT - Excalibur_c21538_175 chr2D 394521704 T/G - C A AC + Excalibur_c54445_803 chr2D 394788404 A/G - C T CT + BobWhite_c35458_206 chr2D 399353355 A/G - T C CT + Kukri_c53250_497 chr2D 402711008 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c13225_696 chr2D 402711899 A/G + A G AG + Kukri_c28941_403 chr2D 405274106 A/G + A G CT - Excalibur_c29121_68 chr2D 405418257 A/G + A G AG + BobWhite_c27715_321 chr2D 412472694 T/C - A G CT - Tdurum_contig30648_210 chr2D 413352404 A/C - T G AC - BobWhite_rep_c56510_164 chr2D 414956648 T/C - G A AG + Kukri_c11491_275 chr2D 420175048 T/C + C T CT + Excalibur_c60933_318 chr2D 422325602 A/G + G A AG + Excalibur_c60933_632 chr2D 422325995 T/C + T C AG - BS00067806_51 chr2D 423853576 T/C + T C CT + Excalibur_c6699_439 chr2D 423873382 T/C + T C CT + Excalibur_c54282_1143 chr2D 424853902 A/G - C T AG - Kukri_c12593_1243 chr2D 424855426 A/G - T C CT + GENE-1213_138 chr2D 425743445 A/C - G T GT + RAC875_rep_c70305_65 chr2D 428562267 T/C - A G AG + Excalibur_c18673_577 chr2D 429085894 A/G + G A AG + IAAV8552 chr2D 429086186 C/G NA NA NA CG NA flanks do not match reference at this position BobWhite_c42560_403 chr2D 430433711 A/G - T C CT + BobWhite_c1225_376 chr2D 436370191 A/G + A G CT - RAC875_c6156_428 chr2D 439442024 A/C - T G AC - BobWhite_c12892_140 chr2D 445397186 T/C + C T AG - BobWhite_c20126_546 chr2D 446850967 T/C - G A AG + Ra_c9190_1384 chr2D 449516559 A/G - T C AG - Kukri_c11566_386 chr2D 450529872 T/C + T C CT + Kukri_c16024_785 chr2D 451972150 T/C + T C CT + Excalibur_c24307_739 chr2D 455336516 A/G - C T CT + GENE-4086_115 chr2D 455338955 T/C - A G AG + D_GBUVHFX01DW8LN_198 chr2D 455354385 T/G - A C AC + Kukri_c46100_246 chr2D 457407451 T/C + T C CT + RAC875_rep_c114294_55 chr2D 458734369 A/G + A G CT - D_GCE8AKX02JL8RM_184 chr2D 459853211 A/G + A G AG + Ku_c19185_1569 chr2D 461301262 T/C - G A AG + Kukri_rep_c103525_361 chr2D 467241046 T/C + C T AG - GENE-0763_212 chr2D 469734483 T/C NA NA NA CT NA flanks do not match reference at this position Ra_c34214_1320 chr2D 469985324 A/G + A G CT - RAC875_c24668_306 chr2D 470224122 T/C + T C AG - RAC875_c16162_546 chr2D 474748927 T/C - A G CT - RAC875_c16162_519 chr2D 474748954 A/C - G T GT + Kukri_c24754_118 chr2D 480769067 T/C + T C AG - Tdurum_contig13653_255 chr2D 481053658 T/C + T C AG - Excalibur_c34712_295 chr2D 481690473 T/G + G T GT + RFL_Contig4683_1614 chr2D 482656712 T/C - A G AG + RAC875_c109690_419 chr2D 482804841 T/C + T C CT + RAC875_c16254_105 chr2D 485992234 T/C - A G CT - GENE-1271_14 chr2D 492662767 A/G - C T CT + Excalibur_c54005_537 chr2D 493005012 A/G - T C CT + RAC875_c9591_607 chr2D 493522014 A/C + A C AC + RAC875_c11459_655 chr2D 493882897 T/C - G A AG + GENE-1100_127 chr2D 494641738 A/C + A C GT - BobWhite_c3444_750 chr2D 497363274 A/G + G A AG + GENE-1351_273 chr2D 498228655 A/G + G A AG + Excalibur_rep_c103675_93 chr2D 503444852 T/C + T C CT + BobWhite_c34273_67 chr2D 503583029 A/C - T G AC - BobWhite_c4697_110 chr2D 506795065 T/C - A G AG + GENE-0925_250 chr2D 513008963 A/G + A G AG + GENE-0872_133 chr2D 513462154 A/G + G A CT - Kukri_rep_c70870_919 chr2D 514341623 T/C - A G CT - BobWhite_c37490_75 chr2D 516121665 T/G - A C AC + RAC875_c46045_279 chr2D 518029630 A/G - T C AG - Excalibur_c36291_215 chr2D 518808297 T/C - A G CT - Kukri_c26150_331 chr2D 518808565 T/C - A G AG + Kukri_c1296_2801 chr2D 519124552 A/G - T C AG - Ex_c2510_477 chr2D 520040744 A/G - T C AG - BobWhite_c7649_248 chr2D 520508670 T/C + T C AG - Ex_c68194_1994 chr2D 523153776 T/C - A G CT - Kukri_c24669_51 chr2D 523310347 A/C - T G GT + RAC875_c45951_123 chr2D 523738084 T/C - G A CT - Excalibur_c9477_3187 chr2D 527916425 A/C + C A AC + BobWhite_c1719_416 chr2D 528083341 A/G - T C AG - Kukri_c19664_846 chr2D 531677246 T/C - G A CT - Kukri_s118386_107 chr2D 532181840 A/C - T G GT + Kukri_c29225_84 chr2D 532428435 T/C - A G CT - Kukri_c58267_713 chr2D 534950740 T/C + T C CT + GENE-0609_166 chr2D 537217619 T/C - A G AG + Kukri_c40621_513 chr2D 538281347 A/G + A G CT - Kukri_c9785_1472 chr2D 539428842 A/G + A G AG + Ex_c9729_243 chr2D 539429209 A/G - T C AG - Excalibur_c73922_109 chr2D 539872627 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c73922_55 chr2D 539872681 A/G - T C CT + CAP12_c5981_595 chr2D 540824860 A/G - C T AG - Kukri_c32234_413 chr2D 541473362 A/G - C T AG - Kukri_c48622_737 chr2D 541474315 A/G + G A AG + Excalibur_rep_c71791_1114 chr2D 541474570 A/G + A G CT - Kukri_c63908_1076 chr2D 543200546 A/C + C A AC + Kukri_rep_c70454_248 chr2D 544653265 A/G + A G CT - IACX7718 chr2D 546870008 C/G + NA NA CG NA reference base A not among SNP alleles Kukri_c7193_5892 chr2D 547678658 A/G - C T AG - D_GDS7LZN02H2ID6_146 chr2D 548080781 A/G - T C CT + Kukri_c3024_1163 chr2D 552141353 A/C - G T AC - Kukri_c7666_1389 chr2D 552186632 T/C + T C AG - Kukri_c7666_2637 chr2D 552187879 A/G + A G CT - RAC875_rep_c91134_949 chr2D 552194567 A/G + A G CT - RFL_Contig3522_1336 chr2D 554306778 T/C - A G AG + Excalibur_c66139_1663 chr2D 556950433 A/G + A G CT - RAC875_rep_c109853_97 chr2D 556950501 T/C - A G CT - GENE-1182_133 chr2D 563798654 T/C + C T AG - Kukri_c50736_53 chr2D 564092444 A/G - T C CT + BS00067336_51 chr2D 564384975 T/C + T C CT + D_contig05885_42 chr2D 564679396 T/C + T C AG - Kukri_c8768_652 chr2D 565476315 A/C + A C AC + RAC875_c2302_496 chr2D 567045827 T/C + T C CT + BS00011825_51 chr2D 568943578 A/C - NA NA GT NA reference base C not among SNP alleles BobWhite_c10627_354 chr2D 569949092 A/G - C T CT + BobWhite_c18540_435 chr2D 570948565 T/C + T C CT + Ra_c69210_724 chr2D 570949916 T/G - C A AC + Ra_c69210_713 chr2D 570949927 T/C - G A AG + Kukri_c20646_2845 chr2D 570959478 T/C + C T CT + RAC875_c18309_605 chr2D 571057672 T/C + C T CT + Kukri_c38510_111 chr2D 571059044 A/G + G A CT - Excalibur_c40976_87 chr2D 571077878 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c40976_111 chr2D 571077902 A/C + A C AC + IACX5919 chr2D 571080527 T/G - NA NA AC NA reference base G not among SNP alleles BobWhite_c9705_429 chr2D 571080848 A/G - T C AG - RAC875_rep_c77617_239 chr2D 571080976 T/C - A G CT - Excalibur_c93588_271 chr2D 571081881 A/G - T C AG - RAC875_rep_c85788_126 chr2D 572074583 A/G + A G CT - RAC875_rep_c85788_282 chr2D 572074739 A/G + A G CT - BobWhite_c3871_210 chr2D 572079797 T/C + C T CT + BobWhite_c3871_615 chr2D 572080202 A/C + C A GT - BobWhite_c38713_202 chr2D 572080403 T/C - G A AG + BobWhite_c3871_903 chr2D 572081260 A/G NA NA NA CT NA flanks do not match reference at this position BobWhite_c3871_1170 chr2D 572081527 A/G + A G CT - BobWhite_c3871_1596 chr2D 572082047 A/G + G A AG + IAAV3238 chr2D 572786242 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Excalibur_c907_1643 chr2D 573970266 T/C - G A CT - CAP11_c5658_270 chr2D 574104192 A/C - T G GT + Excalibur_rep_c69692_342 chr2D 574104463 T/C + T C CT + CAP11_c1070_54 chr2D 574109039 A/G + A G AG + Excalibur_rep_c67221_153 chr2D 574109537 A/C - T G AC - RAC875_rep_c102601_204 chr2D 574345719 A/G - C T AG - IAAV7678 chr2D 574351308 T/C + C T CT + RAC875_c110838_499 chr2D 574351525 A/G + A G AG + Excalibur_rep_c103649_61 chr2D 574351671 A/C + A C GT - Kukri_c36639_186 chr2D 574351998 A/G - T C CT + RAC875_c43244_404 chr2D 574387224 T/C + C T AG - Kukri_c58969_980 chr2D 576280490 T/G - A C GT - Kukri_c52356_96 chr2D 577077223 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c488_4121 chr2D 577126761 A/G - C T AG - IACX6231 chr2D 577126804 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles GENE-1316_443 chr2D 577152939 A/C + A C AC + RFL_Contig3172_444 chr2D 577158511 T/C - A G AG + IACX10993 chr2D 577337854 A/C + A C GT - Excalibur_c4386_429 chr2D 578929042 A/G - T C AG - RAC875_c29700_198 chr2D 578929290 A/G + A G AG + BS00066350_51 chr2D 578931171 A/G + A G AG + Kukri_c3183_1959 chr2D 578932334 A/G + G A AG + CAP7_c9226_239 chr2D 579201862 A/C - G T AC - RAC875_c14885_1147 chr2D 579202008 T/C - A G AG + Excalibur_c8573_291 chr2D 579203890 A/G - T C CT + BobWhite_c31108_66 chr2D 579394002 A/G - C T CT + Kukri_c4319_2410 chr2D 579394140 T/G - A C GT - Excalibur_c14921_298 chr2D 579395753 T/C - A G CT - Excalibur_c62255_986 chr2D 579535661 T/G - A C GT - RAC875_c48856_177 chr2D 580005127 T/C + T C AG - Excalibur_c21486_352 chr2D 580011582 T/C - A G AG + RAC875_c20093_318 chr2D 580193706 A/C + A C AC + RAC875_c17459_566 chr2D 580238728 A/G + NA NA AG NA reference base C not among SNP alleles RAC875_rep_c69388_778 chr2D 580386052 T/C - A G AG + RAC875_rep_c69388_512 chr2D 580386318 A/G - C T CT + RAC875_rep_c69388_413 chr2D 580386417 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_rep_c69388_134 chr2D 580387061 T/C - A G AG + BS00065717_51 chr2D 582490175 A/G - T C CT + BS00065515_51 chr2D 582490197 A/G - T C CT + BS00092666_51 chr2D 583233146 A/G - T C CT + RAC875_c14797_658 chr2D 584607738 T/C - A G AG + tplb0062d15_1382 chr2D 584864028 T/C + T C CT + D_contig80448_280 chr2D 585720681 A/C + C A AC + RAC875_c21300_131 chr2D 586288801 A/G + A G AG + GENE-0664_64 chr2D 587164295 T/G + G T GT + GENE-1016_565 chr2D 587292505 T/C + C T CT + Excalibur_c74714_108 chr2D 587699172 A/G + A G AG + Excalibur_c77484_60 chr2D 587702124 A/G - C T AG - BobWhite_c38001_528 chr2D 589496498 A/G - T C CT + BS00009511_51 chr2D 590070061 T/C + T C CT + BobWhite_c4704_351 chr2D 590071465 T/G - A C AC + Kukri_c22585_626 chr2D 590161920 A/C - T G AC - RAC875_rep_c72115_351 chr2D 590240825 A/G + A G CT - Kukri_c28674_262 chr2D 590241234 T/G + T G GT + RAC875_c21305_118 chr2D 590410094 T/C - A G CT - Excalibur_c1027_655 chr2D 590678245 T/C + T C CT + BS00044983_51 chr2D 590929944 A/C - G T AC - Excalibur_c16438_318 chr2D 591031321 T/G + T G GT + Kukri_c32355_1027 chr2D 592787542 A/G + A G AG + GENE-0638_732 chr2D 593274763 A/G NA NA NA AG NA flanks do not match reference at this position GENE-0638_677 chr2D 593274814 A/G - T C CT + GENE-0684_1473 chr2D 593513251 T/G + G T GT + GENE-0684_1550 chr2D 593513304 A/G + A G CT - BobWhite_c8899_200 chr2D 593734149 T/C + T C CT + Kukri_rep_c72959_145 chr2D 594102095 T/G - A C AC + D_contig01089_344 chr2D 594192344 T/C - G A AG + GENE-1908_742 chr2D 594546705 A/G + G A AG + GENE-1908_884 chr2D 594546815 T/C + T C AG - GENE-1908_97 chr2D 594546895 A/G - C T AG - Kukri_c26015_510 chr2D 594546982 T/C + T C CT + RAC875_c24876_388 chr2D 594581418 A/G - C T AG - BobWhite_c1841_733 chr2D 595148741 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c16967_68 chr2D 595149297 T/C + T C AG - BobWhite_c38419_677 chr2D 595162958 T/C - A G CT - Kukri_c34647_218 chr2D 595439801 A/G + A G AG + BobWhite_c28250_220 chr2D 596911721 T/G - A C GT - Excalibur_c30328_713 chr2D 596912194 A/C + A C GT - Excalibur_c4775_71 chr2D 596914766 T/C - A G CT - RAC875_c23769_577 chr2D 597894311 A/G - C T AG - RAC875_c23769_347 chr2D 597894541 T/C - G A CT - Kukri_c98474_481 chr2D 598639716 A/C - T G AC - Kukri_rep_c73433_61 chr2D 598714669 A/G - T C CT + GENE-1176_655 chr2D 598717535 T/G - C A GT - tplb0021c10_951 chr2D 600131691 T/C - A G CT - Excalibur_rep_c102310_1429 chr2D 600295779 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c14696_214 chr2D 600298361 T/C - G A AG + CAP7_rep_c13224_320 chr2D 600406668 T/C - A G AG + Excalibur_c45366_1019 chr2D 601182368 T/C + T C CT + Excalibur_c45366_1788 chr2D 601184103 T/C + T C AG - RAC875_c78404_242 chr2D 601212782 A/C - T G AC - D_contig13626_260 chr2D 601256572 T/C - G A AG + GENE-1236_62 chr2D 601414452 T/G + T G AC - RAC875_c2176_3046 chr2D 601597907 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c2176_2416 chr2D 601600667 T/G - C A GT - CAP12_rep_c5547_123 chr2D 601601854 T/C + T C CT + BS00065366_51 chr2D 602507559 A/G - C T AG - Excalibur_c23239_718 chr2D 602513709 A/G - T C CT + RAC875_c29913_139 chr2D 602515132 A/G + G A CT - BobWhite_c32336_198 chr2D 605711406 T/G + T G AC - RAC875_rep_c107542_828 chr2D 605713516 A/G + G A AG + RAC875_rep_c72155_1009 chr2D 605713657 A/G + G A CT - BobWhite_c22273_227 chr2D 606752891 T/C - A G CT - Kukri_rep_c70958_1044 chr2D 607418730 A/G - T C CT + Kukri_c31121_608 chr2D 607422568 A/G + G A AG + BS00011478_51 chr2D 607422739 T/G + G T AC - Kukri_c31121_1011 chr2D 607422971 A/G + A G CT - BobWhite_c13924_707 chr2D 607423030 A/G + G A AG + Kukri_c31121_1460 chr2D 607423420 T/C + T C CT + Excalibur_c44325_92 chr2D 608198626 T/C + T C AG - Excalibur_c44325_339 chr2D 608198957 A/C + A C GT - Excalibur_c44325_392 chr2D 608199010 T/C + T C CT + BS00110128_51 chr2D 608540121 A/G - T C AG - Excalibur_c18353_55 chr2D 608755604 T/G - C A AC + BS00086228_51 chr2D 608756250 A/G - T C AG - RAC875_c14766_952 chr2D 608772232 A/G - T C AG - Excalibur_c11031_129 chr2D 609420352 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c39690_264 chr2D 609423246 A/G + A G CT - RAC875_c51420_117 chr2D 609433848 T/C - A G CT - RFL_Contig3273_298 chr2D 609485948 A/G - T C AG - tplb0021e03_713 chr2D 609775957 A/G + A G CT - Excalibur_c8720_297 chr2D 610277824 A/G NA NA NA CT NA flanks do not match reference at this position Ra_c6782_717 chr2D 610291266 A/C + A C GT - Kukri_rep_c101148_401 chr2D 611159777 A/G + A G CT - RAC875_c17722_1704 chr2D 611159777 T/C - A G CT - D_contig14237_449 chr2D 611223072 A/G + G A AG + Excalibur_c18644_566 chr2D 611529375 T/C + C T CT + Excalibur_c1451_660 chr2D 612342729 A/G - T C AG - Kukri_c81384_166 chr2D 612740278 A/C + C A GT - Excalibur_c21749_470 chr2D 613322353 A/G + G A CT - Kukri_c64373_99 chr2D 613322366 T/C + C T AG - BS00084880_51 chr2D 613435544 T/C + C T AG - Excalibur_c39207_880 chr2D 613435821 A/G + A G AG + RAC875_c37639_94 chr2D 613444585 T/C - A G AG + BobWhite_c1275_304 chr2D 614644339 A/G - C T CT + D_GDS7LZN02G73QS_245 chr2D 614750963 T/C - A G CT - BS00066527_51 chr2D 615715069 A/G - T C AG - BS00066526_51 chr2D 615715101 T/C - A G AG + BS00110411_51 chr2D 616073566 T/C + C T AG - BS00110412_51 chr2D 616073576 A/G + A G AG + Excalibur_c81356_316 chr2D 616570247 A/G - T C AG - RAC875_c10807_274 chr2D 616570508 A/G + A G AG + Kukri_c15669_406 chr2D 616570821 A/G + A G AG + IACX6200 chr2D 616571137 A/G + G A CT - Kukri_rep_c71629_554 chr2D 616609039 T/G + G T GT + Excalibur_c4248_1752 chr2D 616927444 T/G - A C GT - Excalibur_c4248_1411 chr2D 616928354 A/G - T C CT + BS00024884_51 chr2D 617089339 A/G - T C AG - BS00100539_51 chr2D 617092900 T/C + T C AG - Kukri_c61575_80 chr2D 617390548 A/C + A C GT - BS00100106_51 chr2D 617409407 T/C + C T CT + TA006113-0823 chr2D 617893014 T/C NA NA NA AG NA flanks do not match reference at this position BS00097302_51 chr2D 618149739 A/G - C T CT + BS00097299_51 chr2D 618149775 T/C - G A AG + RAC875_c30919_311 chr2D 618149805 A/G + A G AG + RAC875_c30919_401 chr2D 618149895 A/G + A G CT - Kukri_c9274_1004 chr2D 618151715 T/C - G A CT - GENE-1388_216 chr2D 618152283 A/G - T C CT + GENE-1388_98 chr2D 618152377 T/C - G A CT - BS00111296_51 chr2D 618153007 A/G - C T CT + TA005542-0450 chr2D 618701271 T/C - A G AG + RAC875_c29079_177 chr2D 619576316 A/G NA NA NA CT NA flanks do not match reference at this position BS00074216_51 chr2D 619576754 T/C - G A CT - BS00031259_51 chr2D 620224895 A/G + G A CT - Kukri_c16965_1077 chr2D 620323423 T/C - A G CT - Kukri_c11915_313 chr2D 620540966 T/C - A G AG + GENE-1355_130 chr2D 621845138 T/C + C T AG - GENE-1355_265 chr2D 621845269 T/C + T C CT + RAC875_c31606_234 chr2D 621950721 A/G - T C CT + RAC875_c5673_1209 chr2D 622382798 T/G + G T AC - BobWhite_c43279_341 chr2D 622915512 A/G + G A AG + BobWhite_c32319_268 chr2D 622923341 A/G NA NA NA CT NA flanks do not match reference at this position BobWhite_c32319_313 chr2D 622923386 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_rep_c102228_810 chr2D 622925355 A/G + A G CT - Excalibur_c7051_537 chr2D 624553155 T/C + T C AG - Excalibur_c7051_590 chr2D 624553208 A/G + A G AG + BobWhite_c11917_124 chr2D 626807985 T/C - A G CT - RAC875_c1043_258 chr2D 627918495 A/G + G A CT - IACX7683 chr2D 627919734 A/C + A C AC + Tdurum_contig56321_232 chr2D 627978338 T/C - A G CT - Excalibur_c6681_580 chr2D 628937584 A/G + A G AG + Ku_c22718_1072 chr2D 629201415 A/G - T C CT + Excalibur_c91176_326 chr2D 629203237 A/G - T C CT + BS00010477_51 chr2D 629207538 T/C - G A AG + RAC875_c17620_1013 chr2D 630390532 A/G + G A CT - Tdurum_contig42282_11463 chr2D 630390644 T/C - A G AG + Kukri_c4117_160 chr2D 630392184 A/G + A G CT - RAC875_c27530_860 chr2D 630395071 A/G - C T CT + D_GB5Y7FA01CSIXD_305 chr2D 630838697 A/G + A G CT - Kukri_c24081_1605 chr2D 631244491 T/G + T G AC - Ex_c5327_597 chr2D 634055356 A/C NA NA NA AC NA flanks do not match reference at this position RAC875_c19685_944 chr2D 634296165 T/C - A G CT - Excalibur_c16329_493 chr2D 634296684 A/G - C T CT + Excalibur_c15905_745 chr2D 634411505 T/C + C T CT + RAC875_c9897_638 chr2D 634433553 T/G - C A AC + GENE-2324_85 chr2D 634471413 T/C - NA NA CT NA reference base C not among SNP alleles RAC875_c35200_230 chr2D 634472103 A/G - T C AG - BobWhite_c40015_213 chr2D 634472278 T/G - A C AC + Ex_c27573_760 chr2D 634472526 A/G - T C CT + RAC875_rep_c108389_937 chr2D 634473521 T/C - G A CT - RAC875_c56649_1293 chr2D 634475375 A/G + A G CT - Tdurum_contig10048_447 chr2D 635229168 A/G + A G CT - RAC875_c10408_188 chr2D 635595175 A/G - C T CT + RAC875_c10408_90 chr2D 635595273 T/C - G A CT - Excalibur_c42413_442 chr2D 635950217 T/C - G A AG + Kukri_c365_345 chr2D 635950371 A/G - C T AG - BS00086534_51 chr2D 635950428 A/G - T C AG - BS00010685_51 chr2D 635950619 T/G - C A AC + BobWhite_c5756_633 chr2D 636600090 A/G - T C CT + BS00009458_51 chr2D 637650866 A/G + A G CT - IAAV5315 chr2D 638140267 A/C NA NA NA GT NA flanks do not match reference at this position RAC875_c50347_258 chr2D 638141003 T/C - G A AG + RAC875_c11879_1042 chr2D 638367887 T/C - G A CT - GENE-0676_649 chr2D 640211042 A/G + A G AG + Excalibur_c2311_1190 chr2D 640214413 T/C + T C AG - Excalibur_c2311_2260 chr2D 640216210 T/C + C T AG - Excalibur_c48871_625 chr2D 641232551 A/G + A G AG + Excalibur_c48871_1330 chr2D 641233256 A/G + G A AG + Excalibur_rep_c89066_287 chr2D 641234421 T/C - G A AG + RAC875_c23815_545 chr2D 641963416 A/G + A G CT - RAC875_c64504_417 chr2D 642871634 A/G - T C AG - Excalibur_c8768_1163 chr2D 642871833 A/C - T G AC - tplb0042o21_938 chr2D 642990324 A/C + C A GT - D_GBUVHFX02HUXG0_432 chr2D 643854485 A/C NA NA NA AC NA flanks do not match reference at this position D_wsnpbg608313_Contig1_1 chr2D 644095518 T/C - A G AG + tplb0030l01_1677 chr2D 644095872 T/C + T C AG - RAC875_c29056_120 chr2D 644331894 A/G + A G AG + Excalibur_c14639_684 chr2D 644719060 T/G + T G GT + D_GDS7LZN01C5JBV_39 chr2D 644876870 T/C + C T AG - RAC875_c35807_595 chr2D 645046650 A/G + A G CT - D_contig03185_174 chr2D 645047287 A/G - T C AG - RAC875_c319_582 chr2D 645723180 A/C + A C GT - Excalibur_rep_c108819_157 chr2D 645797600 A/G - T C AG - RFL_Contig4583_1909 chr2D 646032267 T/C + T C AG - GENE-1304_646 chr2D 647280410 T/G - A C AC + RAC875_c47965_111 chr2D 647968531 T/G + T G GT + IAAV9128 chr2D 647970525 T/C + T C AG - RAC875_c4851_1600 chr2D 648112753 A/G - T C CT + RAC875_c4851_1367 chr2D 648112986 T/C - A G AG + BobWhite_c1971_839 chr2D 648211743 A/G - T C AG - RFL_Contig2862_1174 chr2D 648284498 A/G + A G CT - IAAV4307 chr2D 648387747 A/G + A G AG + RFL_Contig3121_1979 chr2D 648470008 T/C + C T CT + D_F5MV3MU01EDEO3_100 chr2D 649047594 A/G - C T AG - Excalibur_c31806_491 chr2D 649815809 T/C - G A CT - Kukri_c38203_354 chr2D 650060622 A/C - T G GT + Kukri_c17_943 chr2D 650062118 A/G + A G AG + CAP8_c2833_325 chr2D 650321997 T/C - A G AG + Jagger_c7882_154 chr2D 650322164 A/G - C T AG - BS00015680_51 chr2D 650322679 T/C - G A CT - Excalibur_rep_c67599_2154 chr2D 650325224 T/G - A C AC + Excalibur_rep_c67599_242 chr2D 650327136 T/C - A G CT - RAC875_c5998_913 chr2D 650327579 T/C - G A CT - Excalibur_c48759_67 chr2D 650859465 T/C + T C AG - D_contig36097_218 chr2D 650862540 A/G - C T AG - RFL_Contig5251_896 chr2D 650862577 T/C - A G CT - Kukri_rep_c104451_213 chr2D 651611246 A/G - T C AG - RAC875_c46403_233 chr3A 1031141 A/G + G A AG + IACX9278 chr3A 1031348 T/C - G A AG + RAC875_rep_c111781_179 chr3A 1307546 A/G + A G AG + BS00092728_51 chr3A 1309010 T/C + T C AG - Excalibur_c34889_526 chr3A 1922747 T/C + C T CT + RAC875_c76948_970 chr3A 7259878 T/C + C T CT + BS00094057_51 chr3A 7437153 A/C + A C AC + BS00037189_51 chr3A 7782448 A/C + A C AC + tplb0050o09_968 chr3A 8211587 A/G - C T CT + tplb0053a24_1247 chr3A 8590685 T/C + T C AG - tplb0053a24_2232 chr3A 8593575 A/G + A G AG + Kukri_rep_c89183_282 chr3A 8686047 A/G + A G CT - Excalibur_c1529_1644 chr3A 8686482 T/C + C T AG - RAC875_c12071_413 chr3A 8686777 A/C - G T AC - CAP12_c1860_280 chr3A 8687027 T/G + G T GT + Excalibur_c9485_707 chr3A 8864552 A/G NA NA NA AG NA flanks do not match reference at this position IAAV2980 chr3A 8865316 T/G - C A GT - RFL_Contig1488_671 chr3A 8866683 T/C - G A AG + Kukri_rep_c69028_139 chr3A 10300648 A/G + G A AG + Ra_c73278_1234 chr3A 10301063 T/G - C A GT - Excalibur_c12875_864 chr3A 10305254 A/G + G A AG + BobWhite_c30930_192 chr3A 11235368 T/C - G A CT - BS00036089_51 chr3A 11411963 T/C - G A AG + BS00022798_51 chr3A 11941212 T/C + C T CT + BobWhite_c5461_338 chr3A 11941610 A/G + G A AG + BS00093975_51 chr3A 11941986 A/G + A G CT - BS00048489_51 chr3A 12253770 A/G + A G CT - BS00084661_51 chr3A 12812091 A/G - C T CT + CAP11_c570_73 chr3A 12812091 A/G - C T CT + BS00022279_51 chr3A 12814022 T/C + T C CT + BS00022347_51 chr3A 12838991 T/C - G A CT - BS00079521_51 chr3A 12840245 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_rep_c107888_617 chr3A 12975473 T/C - A G CT - Ku_c17560_162 chr3A 12980673 A/G - C T AG - Ku_c17560_146 chr3A 12980689 T/G - C A AC + BS00073062_51 chr3A 12997722 A/G - C T AG - BS00055211_51 chr3A 12998811 T/C + T C CT + Jagger_c8039_67 chr3A 13035944 T/C - A G CT - RAC875_c787_431 chr3A 13037791 A/C - T G AC - RAC875_c787_395 chr3A 13037827 A/G - T C CT + BS00004158_51 chr3A 13354442 T/C - G A AG + Kukri_c54593_543 chr3A 13354470 A/G - C T CT + BS00104401_51 chr3A 13405119 T/C + C T CT + BobWhite_c23392_496 chr3A 13496782 A/C - G T GT + RAC875_c82493_67 chr3A 13497049 T/C - G A CT - Kukri_s117068_130 chr3A 13500799 T/C - G A AG + BobWhite_c17021_297 chr3A 13517620 A/G + A G CT - Kukri_rep_c84820_251 chr3A 13740094 T/C + C T CT + Kukri_c3982_192 chr3A 13902645 T/C - G A AG + BS00101363_51 chr3A 14045732 A/G + A G CT - RAC875_c20134_535 chr3A 14851011 A/G - C T CT + tplb0059m03_622 chr3A 14851104 T/C - A G AG + IAAV1155 chr3A 14851251 A/G + G A AG + CAP11_c6193_232 chr3A 15090085 T/C + T C CT + Kukri_c34793_360 chr3A 15690752 T/G - C A GT - BS00064422_51 chr3A 16809296 T/G + G T GT + Ra_c6118_350 chr3A 19485906 A/G - T C CT + Excalibur_c8483_1308 chr3A 20019896 T/C - A G CT - IACX2831 chr3A 20020918 A/G + G A CT - Kukri_c17099_871 chr3A 20037682 T/C + T C CT + Kukri_c49280_230 chr3A 20134785 A/G + A G CT - TA001702-0608 chr3A 20328724 T/C + T C CT + Kukri_c13830_556 chr3A 20329322 A/G - T C CT + RAC875_c60169_200 chr3A 20714090 A/G - T C CT + Tdurum_contig52302_649 chr3A 21788031 T/G - C A GT - Tdurum_contig52302_92 chr3A 21788603 A/G - C T CT + Ku_c7572_802 chr3A 23275902 A/C + C A AC + Excalibur_c4548_2697 chr3A 23651282 T/G - C A GT - Excalibur_c4548_2505 chr3A 23651474 A/G - T C CT + BobWhite_c9249_564 chr3A 23831893 T/C - G A CT - RFL_Contig1896_1236 chr3A 25000429 T/C + T C CT + Excalibur_rep_c104532_80 chr3A 25358045 T/C - G A CT - Kukri_rep_c101341_425 chr3A 25360354 T/C - A G AG + BS00057444_51 chr3A 25387996 A/C + A C AC + BS00057445_51 chr3A 25388020 T/C + T C AG - Excalibur_c98205_83 chr3A 25493701 A/G + G A CT - BobWhite_s67516_159 chr3A 25932560 A/G + A G AG + Excalibur_rep_c112985_337 chr3A 25933112 T/C - G A AG + Kukri_c3289_932 chr3A 27007732 T/C - G A AG + Kukri_c7508_805 chr3A 27428730 T/C - G A CT - BobWhite_c22370_352 chr3A 31953141 T/C + T C AG - Kukri_c908_584 chr3A 32118749 A/G + G A CT - Excalibur_c55759_282 chr3A 32119931 T/G - C A GT - Tdurum_contig31379_183 chr3A 36228940 T/G + G T AC - Kukri_c30370_79 chr3A 36229188 T/C - A G CT - BS00025191_51 chr3A 36474903 T/G + T G GT + IAAV5729 chr3A 36921508 T/C + T C CT + RAC875_c47976_291 chr3A 36921508 A/G - T C AG - Excalibur_c25239_283 chr3A 36921940 A/G + G A CT - BS00065956_51 chr3A 37826047 A/G - T C CT + BS00048757_51 chr3A 38037262 A/C + C A GT - Tdurum_contig91865_242 chr3A 41068049 T/C + T C AG - Kukri_c46948_558 chr3A 44629466 A/G - C T AG - Ku_c9092_1164 chr3A 44630645 A/G - C T CT + Ku_c8627_745 chr3A 44631961 A/G - C T CT + Kukri_c8627_552 chr3A 44632245 T/C - G A CT - Ex_c6864_677 chr3A 44632686 T/C - G A CT - Ku_c18096_552 chr3A 45598422 A/G - T C CT + GENE-1533_226 chr3A 45598509 T/C + T C CT + Kukri_rep_c71916_1548 chr3A 46165060 T/C - G A CT - TA003760-0970 chr3A 46165779 T/C - A G AG + RAC875_c99286_60 chr3A 46425326 A/G + A G AG + RAC875_c19534_68 chr3A 46667905 A/G - C T CT + RAC875_c14060_1935 chr3A 46993862 A/G - T C CT + BobWhite_c13210_115 chr3A 47084187 T/C - G A AG + Excalibur_c16197_748 chr3A 47549530 A/G - T C CT + RAC875_c10246_839 chr3A 47823906 T/G + T G AC - Excalibur_c11594_497 chr3A 47824787 T/C + T C AG - Tdurum_contig12371_132 chr3A 47825432 A/G + A G AG + Tdurum_contig45380_92 chr3A 49478004 T/C + C T AG - IAAV1405 chr3A 49481270 A/C + C A AC + RAC875_c584_303 chr3A 50889699 T/G + G T AC - Excalibur_c1806_1285 chr3A 51288048 T/C - A G AG + Excalibur_c6264_249 chr3A 53180783 A/G + A G CT - Excalibur_c6264_1054 chr3A 53181735 T/C + T C CT + CAP8_rep_c3652_80 chr3A 53553884 A/G + G A AG + Kukri_c3673_2442 chr3A 53569343 T/C - A G CT - Kukri_c14029_117 chr3A 53570963 T/C + C T CT + Kukri_c62467_362 chr3A 53572586 T/C + T C AG - CAP8_rep_c6382_237 chr3A 53832154 A/C + A C GT - Kukri_rep_c73936_154 chr3A 53838329 A/G - T C CT + BobWhite_c17852_511 chr3A 54662933 T/C - A G CT - BobWhite_c9704_273 chr3A 54879120 A/G - C T CT + Excalibur_c1905_1117 chr3A 54940125 T/G - C A AC + RAC875_c10286_1247 chr3A 55045830 T/G - A C GT - JG_c3077_225 chr3A 55086245 A/G + G A CT - BS00036492_51 chr3A 56141694 T/C - A G CT - Excalibur_c24123_165 chr3A 56219939 T/C + C T CT + Excalibur_c24123_1597 chr3A 56222465 A/G + A G CT - BS00021694_51 chr3A 56397306 T/C - G A CT - BS00094366_51 chr3A 56397857 T/C + T C AG - BS00007502_51 chr3A 56399617 A/G - C T AG - RAC875_rep_c77148_311 chr3A 56399941 A/G + G A CT - GENE-4252_246 chr3A 56670747 A/G + G A AG + Excalibur_c10079_1585 chr3A 56675625 T/C + C T CT + RAC875_c2464_274 chr3A 56676091 A/G + G A CT - BobWhite_c11298_512 chr3A 56676186 A/G + G A AG + IAAV2646 chr3A 56676186 T/C - G A AG + Tdurum_contig86206_149 chr3A 57013009 A/C + C A AC + RAC875_c6445_275 chr3A 57856017 T/C - A G AG + BS00013584_51 chr3A 57857768 A/G - T C CT + TA003281-2379 chr3A 57857768 T/C + T C CT + Tdurum_contig25520_363 chr3A 57958219 T/C + C T AG - BS00065932_51 chr3A 58045656 T/G - A C AC + RAC875_c50864_1921 chr3A 59519533 A/G - T C AG - RAC875_c55313_89 chr3A 60005477 A/G + G A CT - BS00034334_51 chr3A 61219665 A/C - G T GT + Jagger_c791_62 chr3A 61308062 T/C + T C AG - Excalibur_rep_c102974_175 chr3A 61308955 A/G - T C AG - IAAV6676 chr3A 61348608 A/C + C A AC + BS00022516_51 chr3A 61348643 A/G + G A AG + Excalibur_rep_c116278_53 chr3A 62406668 A/G - T C AG - Kukri_c28165_906 chr3A 67425070 A/G + A G CT - Excalibur_c2578_1966 chr3A 69647605 T/C - A G AG + RAC875_rep_c109288_122 chr3A 71149373 T/C + C T AG - Tdurum_contig44029_621 chr3A 71795315 A/G - C T AG - Tdurum_contig44029_158 chr3A 71795778 A/G - T C CT + Tdurum_contig44029_144 chr3A 71795792 T/C - A G CT - RFL_Contig1170_1827 chr3A 71795870 T/C + T C AG - Tdurum_contig44029_66 chr3A 71795870 A/G - T C AG - BobWhite_c34866_232 chr3A 72488559 T/G - A C AC + RAC875_c10430_672 chr3A 72671116 T/C - A G AG + Excalibur_rep_c68583_689 chr3A 75957423 A/G - T C AG - TA004095-0446 chr3A 77912108 A/G + A G AG + BS00067216_51 chr3A 83722160 T/C - A G AG + BS00067215_51 chr3A 83722202 A/G - T C CT + TA003540-1083 chr3A 84187174 A/G NA NA NA CT NA flanks do not match reference at this position IAAV9068 chr3A 86369509 A/G - T C CT + Ku_c103671_362 chr3A 86369509 T/C + T C CT + TA013323-0732 chr3A 87366077 A/C + A C AC + CAP12_rep_c4638_80 chr3A 93041321 T/C + T C AG - IACX5844 chr3A 102685911 A/G - T C CT + BS00022148_51 chr3A 106435192 T/C + T C CT + Tdurum_contig10426_280 chr3A 107399433 A/G + A G AG + IAAV4781 chr3A 107738831 T/C + T C CT + RAC875_c22074_517 chr3A 112937675 A/G + A G AG + GENE-1997_169 chr3A 125484416 T/C + T C CT + BobWhite_c35303_192 chr3A 134245071 T/C - G A CT - RAC875_c16846_1247 chr3A 135988534 T/C - A G CT - Excalibur_c9811_131 chr3A 136568291 A/G + G A CT - BS00030876_51 chr3A 137582286 A/G - T C AG - BS00098840_51 chr3A 140043285 T/C + T C CT + TA005199-0585 chr3A 140043285 A/G - T C CT + Kukri_c51247_322 chr3A 140043543 T/C + T C CT + BS00073854_51 chr3A 144472115 T/C + C T CT + Tdurum_contig19415_271 chr3A 148603713 T/C + C T AG - RFL_Contig4403_1034 chr3A 176558290 T/G + G T GT + RAC875_c66892_58 chr3A 177862242 T/C - G A AG + GENE-1721_852 chr3A 178132423 A/C + A C GT - GENE-0357_96 chr3A 179536309 T/G + G T GT + BS00110129_51 chr3A 266691282 A/G + G A AG + Tdurum_contig28877_248 chr3A 269392807 A/C + C A GT - Kukri_rep_c114028_94 chr3A 269670959 A/G NA NA NA AG NA flanks do not match reference at this position BS00064214_51 chr3A 288606679 T/C - A G CT - BobWhite_c41725_430 chr3A 292178959 T/C - A G CT - RFL_Contig4109_571 chr3A 306870678 A/G + A G CT - Kukri_c17313_667 chr3A 351125842 A/G - C T AG - BobWhite_c11225_941 chr3A 368533810 T/C - A G CT - BS00078430_51 chr3A 374878909 A/G - C T AG - GENE-1532_226 chr3A 376785071 A/G - T C AG - GENE-1477_342 chr3A 416450428 T/C - A G CT - Kukri_c40909_784 chr3A 423958992 A/G - T C CT + BS00066585_51 chr3A 430317745 A/G + G A CT - BobWhite_rep_c55551_53 chr3A 431127864 T/C + C T CT + BobWhite_c28950_147 chr3A 431128248 A/G - C T CT + BS00066800_51 chr3A 431822454 A/G - C T CT + Kukri_c13793_1152 chr3A 432855554 T/C - G A AG + Tdurum_contig57753_138 chr3A 433410408 A/G - C T AG - Ex_c8871_1318 chr3A 433999148 A/G - T C AG - Tdurum_contig697_73 chr3A 434615887 A/G + A G CT - Ra_c27641_452 chr3A 438267000 A/G + A G CT - Excalibur_c15098_591 chr3A 449511065 T/C - A G CT - BS00022016_51 chr3A 471358821 T/G - A C GT - Excalibur_c27055_1326 chr3A 474965650 A/G - T C AG - Kukri_c46833_105 chr3A 477564151 T/G - A C GT - IAAV5166 chr3A 477602430 A/G - T C AG - BobWhite_c43213_184 chr3A 477793837 T/C - A G CT - Kukri_c54729_181 chr3A 477794812 A/G - T C CT + RAC875_c39728_187 chr3A 477795356 A/G + A G AG + Kukri_c23833_181 chr3A 478687821 A/C + C A AC + BS00022029_51 chr3A 478911459 A/G + G A AG + Ex_c45438_377 chr3A 479474002 T/C - G A AG + IAAV6934 chr3A 479477063 A/T + T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Excalibur_c64302_103 chr3A 480104404 T/G + T G GT + JD_c1187_1398 chr3A 480105504 T/C + T C AG - BS00041121_51 chr3A 480433970 T/G + G T GT + BS00010531_51 chr3A 480437531 T/C + T C AG - RAC875_c27323_867 chr3A 480438551 T/C + T C CT + BS00095423_51 chr3A 481018306 A/G - T C CT + Ku_c17569_905 chr3A 481019772 A/G + A G AG + IAAV6474 chr3A 481019786 A/G + A G AG + Kukri_rep_c109051_116 chr3A 481516053 T/C - A G AG + Excalibur_c91154_175 chr3A 481659452 A/C - T G GT + Excalibur_c91154_164 chr3A 481659463 T/C - A G AG + IAAV488 chr3A 482403280 A/G + A G AG + Kukri_c63361_97 chr3A 482403709 T/C - G A AG + Ku_c64839_240 chr3A 482976458 A/G - T C AG - RAC875_c19570_671 chr3A 483922767 T/C + T C CT + BS00045327_51 chr3A 485012145 A/G - T C AG - BS00093377_51 chr3A 485601646 A/G + A G CT - Ra_c14565_1056 chr3A 486360239 T/G - C A AC + Kukri_rep_c112061_617 chr3A 487438266 T/C NA NA NA CT NA flanks do not match reference at this position IACX5968 chr3A 487458140 T/C + T C CT + Ku_c34565_1576 chr3A 487461581 T/G + T G GT + BS00110452_51 chr3A 487854514 A/G - C T AG - Excalibur_c6040_762 chr3A 488309747 T/C - G A CT - Excalibur_c41557_147 chr3A 488720640 A/G + G A AG + CAP8_c1093_136 chr3A 488722510 A/G + A G CT - BS00031903_51 chr3A 490340671 T/C - A G CT - Tdurum_contig42234_6222 chr3A 490932528 A/G + A G AG + Tdurum_contig22253_104 chr3A 495024538 T/C - A G AG + RFL_Contig1798_1606 chr3A 495073247 T/C - G A CT - RFL_Contig102_119 chr3A 496637235 A/G - C T AG - RFL_Contig4399_956 chr3A 496704860 T/C - A G CT - Ku_c14982_168 chr3A 497649774 A/G - C T CT + BS00091769_51 chr3A 497710494 A/G - C T CT + Tdurum_contig31586_197 chr3A 500971452 T/C NA NA NA AG NA flanks do not match reference at this position Ex_c67794_487 chr3A 500977005 T/C + C T CT + Kukri_c1307_1223 chr3A 500977584 A/C + C A AC + Tdurum_contig10979_1523 chr3A 501224970 A/G - C T CT + RAC875_c19030_112 chr3A 504623985 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c93405_296 chr3A 506240416 A/G + G A CT - Excalibur_c6501_477 chr3A 507273477 A/G + G A CT - BS00028660_51 chr3A 507467861 A/G + A G AG + Kukri_c5459_334 chr3A 507469938 T/C + C T CT + BobWhite_s65081_93 chr3A 510690497 A/G - T C AG - BS00071823_51 chr3A 511754996 T/C - G A AG + BobWhite_rep_c61884_158 chr3A 513605113 A/C + A C AC + RAC875_c13895_763 chr3A 513608185 A/G + A G AG + RAC875_c30121_270 chr3A 513894827 T/C + T C CT + RAC875_c52345_1050 chr3A 514111178 T/C - A G CT - Ra_c5515_2396 chr3A 514111884 A/G + A G CT - Ra_c5515_2469 chr3A 514111957 T/C + T C AG - IACX8272 chr3A 514167714 A/C + C A AC + GENE-1787_339 chr3A 514311708 T/G - A C GT - Tdurum_contig61299_55 chr3A 514493982 A/G + A G CT - tplb0050h15_1287 chr3A 514493982 T/C - A G CT - IAAV4286 chr3A 514496227 T/G - C A AC + CAP7_c2141_129 chr3A 515827868 T/C + T C AG - Excalibur_rep_c76510_255 chr3A 515889969 T/C + T C CT + BobWhite_c48560_103 chr3A 516632058 A/C + C A AC + RAC875_rep_c75768_245 chr3A 516802279 A/G - C T CT + Tdurum_contig58326_467 chr3A 516802279 T/C + C T CT + Ku_c28597_514 chr3A 517074826 T/C - G A AG + Tdurum_contig59782_86 chr3A 517075038 T/C + C T CT + BobWhite_c9468_453 chr3A 517075151 A/G + G A CT - BobWhite_c9468_478 chr3A 517075176 A/C + C A AC + TA001068-0306-w chr3A 517095339 T/C + C T CT + CAP7_c3367_68 chr3A 517661833 A/G + G A CT - RAC875_c53864_310 chr3A 517662459 T/C + T C CT + RAC875_c11672_1240 chr3A 518489424 T/G + G T GT + RAC875_c37118_595 chr3A 519083103 T/C - A G CT - BobWhite_c42102_237 chr3A 519209987 A/G - T C AG - BS00082982_51 chr3A 521304691 A/C + A C AC + BS00110266_51 chr3A 521304691 T/G - A C AC + Jagger_c5842_90 chr3A 521308467 A/G - C T AG - BS00026189_51 chr3A 521631015 T/C - G A CT - Ku_c56370_1155 chr3A 521719100 A/G + G A CT - BobWhite_c34548_96 chr3A 522058989 A/C - G T AC - IAAV5821 chr3A 522060498 T/C + C T CT + Ku_c41007_116 chr3A 522187699 T/C - G A CT - TA002508-0190 chr3A 522272539 T/C - A G AG + tplb0055d10_1024 chr3A 523158872 A/G + A G CT - Kukri_rep_c70927_886 chr3A 523546452 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c6932_1229 chr3A 523548957 A/G + G A AG + Tdurum_contig57139_318 chr3A 523556237 T/G + T G GT + Tdurum_contig28699_54 chr3A 523557457 T/C - A G CT - IAAV8351 chr3A 523756045 T/C + T C AG - Ex_c18484_2048 chr3A 525200889 A/C - G T GT + Ex_c18484_2026 chr3A 525200911 T/C - G A AG + BobWhite_c1740_97 chr3A 525203703 A/G - T C AG - Excalibur_c7181_813 chr3A 526525029 A/C NA NA NA GT NA flanks do not match reference at this position BS00040798_51 chr3A 528555193 A/G - T C CT + Kukri_c82097_197 chr3A 528592763 A/G - T C AG - BobWhite_c43681_334 chr3A 529772784 T/G + T G AC - Kukri_c25564_185 chr3A 531451417 T/G + G T GT + Ex_c8999_129 chr3A 532324976 A/G - T C CT + Tdurum_contig11121_834 chr3A 532448409 T/G - A C GT - Tdurum_contig11121_739 chr3A 532448965 A/G - T C AG - Ku_c12383_1105 chr3A 532604262 T/G + G T AC - Tdurum_contig51995_474 chr3A 532645782 A/G + A G AG + BS00076631_51 chr3A 532663187 T/C - A G CT - RAC875_c842_1516 chr3A 532934735 T/C - A G CT - RAC875_c842_1476 chr3A 532934775 A/C - G T AC - RAC875_c10669_714 chr3A 533073198 T/C - G A CT - Ex_c66865_584 chr3A 533624074 T/C + C T CT + BobWhite_c8340_511 chr3A 533624557 A/C + C A AC + Ra_c72106_227 chr3A 533625934 T/C + T C CT + IAAV3900 chr3A 534176343 T/C - A G CT - Ra_c20211_1415 chr3A 534176343 A/G + A G CT - RAC875_rep_c108615_475 chr3A 534176810 T/C + T C AG - BobWhite_c18408_199 chr3A 535195574 T/C + T C AG - Tdurum_contig33100_127 chr3A 535219539 T/C - A G AG + BS00096642_51 chr3A 535224309 T/C - A G AG + BS00022882_51 chr3A 535224341 T/C - G A CT - BobWhite_c30232_154 chr3A 535323686 A/G + A G CT - BobWhite_rep_c49102_169 chr3A 535326733 T/C - G A AG + Kukri_c34195_357 chr3A 536627390 T/C + T C AG - BS00092735_51 chr3A 536634821 T/G - C A AC + BS00039357_51 chr3A 536638217 A/G - T C AG - Excalibur_c52446_519 chr3A 537508994 T/C + C T CT + BS00067997_51 chr3A 538004805 T/C + C T AG - RAC875_c5310_1729 chr3A 538008731 T/C + C T AG - Kukri_c80104_809 chr3A 539198714 T/C - G A CT - Kukri_c47643_920 chr3A 540666266 A/G - T C CT + BS00021871_51 chr3A 540669124 T/G - A C GT - Tdurum_contig50617_713 chr3A 541210394 A/G - C T AG - BS00032525_51 chr3A 541210584 A/G - T C AG - RAC875_c3427_734 chr3A 541258101 A/G NA NA NA AG NA flanks do not match reference at this position BS00022159_51 chr3A 541260879 A/G + A G CT - BS00009657_51 chr3A 543178660 A/G - C T CT + Tdurum_contig59531_892 chr3A 543178759 A/G + A G AG + Tdurum_contig59531_914 chr3A 543178781 A/G + A G CT - BS00067190_51 chr3A 543712443 T/C - A G CT - Excalibur_c31571_136 chr3A 543715142 A/G - T C CT + GENE-1820_661 chr3A 544396194 T/C NA NA NA CT NA flanks do not match reference at this position BS00047836_51 chr3A 547480866 A/C + C A AC + Excalibur_c46082_440 chr3A 556552568 T/C + C T CT + IAAV6317 chr3A 557018594 T/C + T C AG - Ex_c9685_1264 chr3A 557019686 A/G + A G AG + GENE-3343_183 chr3A 557259443 A/G - C T AG - IAAV242 chr3A 557409821 A/C - T G GT + BS00101401_51 chr3A 557414880 A/G - C T AG - BS00023026_51 chr3A 557415024 T/G - C A AC + CAP8_c1393_327 chr3A 557421760 T/C - G A AG + Ku_c68484_1276 chr3A 557956310 A/G - C T AG - Ra_c38505_544 chr3A 558890661 T/C + T C CT + Ex_c104581_457 chr3A 559528682 T/G NA NA NA AC NA flanks do not match reference at this position Ku_c13307_1116 chr3A 559531487 T/G - A C GT - RFL_Contig1034_2351 chr3A 559539719 A/G NA NA NA CT NA flanks do not match reference at this position IAAV1334 chr3A 560679082 T/G - A C GT - BS00070511_51 chr3A 560680682 T/C + T C CT + IAAV5030 chr3A 560680682 A/G - T C CT + Ku_c53625_627 chr3A 561118824 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c20889_526 chr3A 562194823 T/C - G A AG + Ku_c14313_1194 chr3A 562284079 A/C - T G GT + Kukri_c12301_227 chr3A 564344803 T/C - G A AG + RAC875_c19138_1390 chr3A 564941519 T/C - A G CT - RFL_Contig4921_2420 chr3A 564943946 T/C - G A CT - RAC875_c2786_1097 chr3A 564943973 T/C + T C AG - RAC875_c13183_369 chr3A 565357153 A/G + A G AG + Excalibur_c18089_1116 chr3A 565773671 A/G + G A CT - RAC875_c67309_634 chr3A 565794682 A/G + A G AG + Ku_c18564_1031 chr3A 566868685 T/C - A G AG + Tdurum_contig49981_703 chr3A 568382880 A/G - C T AG - Ku_c70534_1215 chr3A 569423894 T/C - A G AG + RAC875_c58159_521 chr3A 569425604 T/C - A G CT - Ra_c70087_485 chr3A 571407254 T/C - G A CT - IACX6277 chr3A 571407379 C/G - C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00107444_51 chr3A 571799101 T/C + T C AG - Excalibur_c33545_134 chr3A 572326622 T/C - A G AG + Kukri_rep_c87640_135 chr3A 573985537 T/G - C A AC + RAC875_c744_1935 chr3A 574341549 T/G NA NA NA AC NA flanks do not match reference at this position RAC875_c161_228 chr3A 574453230 T/C + T C AG - RAC875_c4024_112 chr3A 577576028 A/G + A G AG + IAAV583 chr3A 581407477 A/G + A G AG + RAC875_c33823_279 chr3A 585330850 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c7087_896 chr3A 594000776 A/G + A G AG + BS00067639_51 chr3A 594807591 A/G - C T AG - BS00065020_51 chr3A 594810552 A/G - T C AG - BobWhite_rep_c64211_305 chr3A 602272621 A/G - C T AG - Ex_c11297_687 chr3A 602686417 T/C + T C CT + CAP11_c1464_135 chr3A 611170155 T/C + T C CT + Tdurum_contig64606_1104 chr3A 611948314 A/G + G A AG + Tdurum_contig64606_1106 chr3A 611948316 T/C + T C AG - Tdurum_contig64606_1309 chr3A 611948519 T/C + T C AG - BS00056089_51 chr3A 616492185 T/C + T C CT + BS00074617_51 chr3A 620212087 T/C - G A CT - BS00066319_51 chr3A 623038468 T/G - C A GT - Tdurum_contig76105_124 chr3A 624534007 A/G + A G AG + Tdurum_contig76105_201 chr3A 624534084 A/G + G A CT - Excalibur_c21051_515 chr3A 624831881 A/G - T C AG - Excalibur_c39248_485 chr3A 624946762 A/G + A G AG + BS00000445_51 chr3A 625533807 T/G + T G GT + BS00093871_51 chr3A 627253838 T/C + C T CT + BS00001478_51 chr3A 627254091 A/G + G A CT - BS00080879_51 chr3A 627825027 T/G - C A GT - IAAV4560 chr3A 631282041 A/G + G A AG + Excalibur_rep_c105978_544 chr3A 633849431 A/G - T C AG - RAC875_c67998_96 chr3A 635151811 A/C + A C AC + RAC875_c26514_127 chr3A 635484339 A/C + A C AC + BS00073525_51 chr3A 636538954 A/C + A C AC + BS00027470_51 chr3A 636687809 A/G - C T CT + BS00027469_51 chr3A 636687912 A/G - T C CT + Kukri_c97654_90 chr3A 637111779 A/G + G A AG + Kukri_c33640_640 chr3A 638983477 T/C + C T AG - Excalibur_c60581_62 chr3A 639024949 T/C + T C AG - RFL_Contig5871_1650 chr3A 642039486 T/G + T G AC - BS00022989_51 chr3A 642160142 T/C + T C AG - GENE-1724_72 chr3A 642932657 A/G + A G AG + BS00038663_51 chr3A 642959221 T/C + T C AG - Tdurum_contig9912_228 chr3A 642959221 A/G - T C CT + Tdurum_contig13548_158 chr3A 643220097 A/G + G A CT - RAC875_c14370_1319 chr3A 644807339 T/C - A G CT - RAC875_c56612_1076 chr3A 645149281 A/G + G A AG + Excalibur_c18747_1292 chr3A 645546386 T/C - A G CT - RAC875_c947_383 chr3A 645547265 A/G - T C CT + IAAV969 chr3A 645560382 T/C + C T CT + Tdurum_contig61190_271 chr3A 645560382 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c62012_382 chr3A 645605592 T/C + T C AG - Tdurum_contig57552_327 chr3A 645605592 A/G - T C AG - Tdurum_contig42150_3417 chr3A 645995656 T/C - A G CT - Tdurum_contig42150_3348 chr3A 645995725 A/C - T G AC - Tdurum_contig42150_3198 chr3A 645995875 T/C - A G AG + Tdurum_contig42150_3190 chr3A 645995883 T/C - A G CT - CAP7_rep_c12940_130 chr3A 646272640 A/G - T C CT + Excalibur_c24402_471 chr3A 648023631 A/G + G A AG + Excalibur_c46600_919 chr3A 648027721 T/G - A C GT - Excalibur_c46600_160 chr3A 648038861 T/C - G A CT - Excalibur_c1001_586 chr3A 648260065 A/G + A G CT - IACX6054 chr3A 648859148 T/C + C T AG - Kukri_c10210_1700 chr3A 648867847 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c55381_67 chr3A 648868184 A/G - T C CT + Kukri_c10210_1387 chr3A 648868240 T/C - G A AG + Kukri_c11709_874 chr3A 649032401 A/G - C T CT + BS00022752_51 chr3A 649544558 A/G - C T CT + RAC875_c1619_120 chr3A 649631940 A/C + A C GT - Ra_c1619_250 chr3A 649632070 A/G + A G AG + Ra_c1619_432 chr3A 649632252 A/C + A C AC + BS00109700_51 chr3A 649811180 T/C + C T AG - BS00049636_51 chr3A 650008458 T/C + C T CT + BobWhite_c31500_144 chr3A 650041509 T/C - A G AG + RAC875_c31572_281 chr3A 650041783 A/G - C T AG - tplb0040h02_970 chr3A 650057664 T/C + T C AG - Ku_c69970_624 chr3A 650425772 A/G + A G CT - Ku_c69970_631 chr3A 650425779 T/G + G T AC - Kukri_rep_c69970_717 chr3A 650425865 A/G + G A CT - Ra_c3994_598 chr3A 650427560 T/C + C T CT + Excalibur_c56240_200 chr3A 651627266 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c56240_176 chr3A 651627366 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_c29826_602 chr3A 651627599 A/G + G A CT - CAP12_c5387_372 chr3A 652024913 T/G + NA NA GT NA reference base A not among SNP alleles Excalibur_rep_c67547_221 chr3A 653241800 T/G + G T GT + RAC875_rep_c77065_1532 chr3A 653243394 T/C + C T AG - Ra_c42858_91 chr3A 653244326 T/C + T C AG - Ra_c42858_503 chr3A 653244738 T/C + T C CT + RAC875_c47550_437 chr3A 653851706 T/C - G A AG + BS00063300_51 chr3A 654318780 A/G - T C CT + BS00060391_51 chr3A 655635732 A/G + G A AG + BS00072296_51 chr3A 655649702 A/G - C T CT + BS00023511_51 chr3A 656134941 A/G + G A AG + BS00083398_51 chr3A 657271121 T/C - A G CT - Excalibur_c39508_88 chr3A 657616589 A/G + A G CT - Kukri_rep_c114456_218 chr3A 658710000 A/G NA NA NA CT NA flanks do not match reference at this position BobWhite_c17879_519 chr3A 658905380 T/C + C T AG - CAP11_c3472_60 chr3A 659040313 T/C - G A AG + Kukri_c8400_2315 chr3A 659159514 T/C - G A CT - Ku_c19456_645 chr3A 659395398 T/C - A G CT - RAC875_rep_c81701_424 chr3A 659397224 A/G - C T CT + Kukri_rep_c103783_1380 chr3A 659400763 T/C - A G CT - IACX5899 chr3A 659529470 A/G + A G CT - BS00039420_51 chr3A 659978297 T/C - A G CT - RFL_Contig2787_634 chr3A 660235219 T/C + C T AG - Tdurum_contig8584_354 chr3A 662933621 T/G + T G AC - Tdurum_contig67196_285 chr3A 662940157 A/G - C T AG - Tdurum_contig44880_134 chr3A 662948415 A/C + C A AC + Tdurum_contig44880_314 chr3A 662948595 A/G + G A AG + Tdurum_contig44880_420 chr3A 662948701 T/C + T C AG - Kukri_c1526_616 chr3A 663178253 A/G + G A AG + Tdurum_contig4598_189 chr3A 663180594 A/G + G A AG + Tdurum_contig4598_249 chr3A 663180654 A/G + A G AG + Tdurum_contig4598_259 chr3A 663180664 A/G + G A CT - Kukri_c18420_705 chr3A 663180825 A/G - C T CT + Tdurum_contig4598_502 chr3A 663181023 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig4598_638 chr3A 663181839 A/G + G A CT - Tdurum_contig11473_516 chr3A 663293066 A/G + G A CT - BobWhite_c801_862 chr3A 663439287 A/G + A G AG + Kukri_c8601_817 chr3A 663580883 T/C + C T CT + RAC875_c79551_167 chr3A 666229525 T/C - A G CT - BS00091002_51 chr3A 666242544 T/C - A G AG + BS00068094_51 chr3A 667357789 A/G + A G CT - Kukri_c31546_66 chr3A 667794610 T/C - A G CT - BS00006822_51 chr3A 669524837 A/C + C A GT - RFL_Contig497_1114 chr3A 669526021 T/C + T C CT + Kukri_c63259_151 chr3A 669620805 T/C - G A AG + BS00084158_51 chr3A 671144035 A/G + A G CT - BS00084159_51 chr3A 671144077 A/G + A G CT - RAC875_c52805_182 chr3A 680356270 A/G - T C CT + Kukri_c49798_300 chr3A 681652806 A/G - T C AG - BS00022908_51 chr3A 682976438 T/G - A C GT - IAAV8218 chr3A 682976472 T/G - C A AC + RAC875_c10194_673 chr3A 683071091 T/C + C T CT + BS00022039_51 chr3A 683071217 T/C - A G AG + BobWhite_c21397_148 chr3A 683072555 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c29600_173 chr3A 683195193 T/C - G A CT - Kukri_c17966_561 chr3A 683440930 T/C + T C AG - RAC875_c15003_377 chr3A 683441459 T/C + C T CT + Excalibur_c39808_453 chr3A 683530233 A/G + A G AG + Kukri_c8465_54 chr3A 684044770 A/G + G A AG + IAAV5370 chr3A 685122614 A/G + G A AG + Ex_c66357_866 chr3A 685357916 T/C - G A AG + Kukri_c12079_204 chr3A 685359271 A/G + G A AG + BS00081610_51 chr3A 685781388 T/C + T C AG - Tdurum_contig62557_263 chr3A 686775946 A/G + G A CT - Tdurum_contig68305_597 chr3A 686783982 A/G + A G CT - Tdurum_contig68305_703 chr3A 686784088 A/G + G A AG + BS00088755_51 chr3A 686784181 T/C - A G AG + Tdurum_contig68305_796 chr3A 686784181 A/G + A G CT - RAC875_rep_c75557_177 chr3A 686785423 T/C - A G AG + BobWhite_c5337_225 chr3A 686787311 T/C - A G CT - Excalibur_c49743_97 chr3A 688580194 T/G + T G GT + BS00036168_51 chr3A 688617193 T/C + C T CT + Excalibur_rep_c110501_525 chr3A 688617382 A/G + G A AG + RAC875_c15109_106 chr3A 688675388 T/C NA NA NA CT NA flanks do not match reference at this position RFL_Contig4282_1420 chr3A 688679925 T/C - A G CT - BS00049977_51 chr3A 688688720 T/C - G A CT - Kukri_c10751_1031 chr3A 688883787 T/G - C A GT - IAAV7454 chr3A 688883958 T/C + C T CT + Kukri_c10751_860 chr3A 688883958 A/G - C T CT + BS00020459_51 chr3A 688884040 A/C - G T GT + Kukri_c10751_264 chr3A 688886994 A/G - T C CT + Kukri_c10751_158 chr3A 688887100 A/G - T C CT + RAC875_rep_c90531_283 chr3A 689498082 A/G - C T CT + Tdurum_contig12682_421 chr3A 691041990 T/C + C T AG - BS00022256_51 chr3A 691106924 A/C + C A AC + BS00110564_51 chr3A 691106993 T/C + C T CT + BS00035576_51 chr3A 691111148 A/G - C T AG - Tdurum_contig11443_1022 chr3A 692719099 T/C - G A AG + Kukri_c34806_112 chr3A 693158790 T/G + T G GT + Ex_c4465_1641 chr3A 693460938 T/G - C A GT - Ku_c1255_627 chr3A 693461948 T/C - A G CT - Excalibur_c32546_314 chr3A 693487088 T/C + T C CT + Kukri_c106254_386 chr3A 694968070 T/C + C T CT + BS00091887_51 chr3A 695729696 T/G - C A GT - BS00003935_51 chr3A 695729821 A/G - C T AG - IACX6065 chr3A 695729821 T/C + C T AG - BS00022459_51 chr3A 697454118 T/C + T C AG - BS00110550_51 chr3A 697456576 A/G - T C CT + BS00026396_51 chr3A 699765819 A/G - T C AG - BS00067228_51 chr3A 700422344 A/C - G T AC - BS00067163_51 chr3A 704584881 A/G - T C AG - Excalibur_c24354_465 chr3A 705309554 T/G - A C GT - Excalibur_c3969_713 chr3A 710831518 T/G + T G AC - Excalibur_c3969_1208 chr3A 710832013 T/C + C T AG - BS00065734_51 chr3A 711095135 A/G - T C CT + CAP11_c1022_66 chr3A 714156164 A/C + C A GT - Tdurum_contig42495_389 chr3A 714298995 A/G + A G AG + Kukri_c18258_440 chr3A 714425055 T/C - G A CT - BS00023222_51 chr3A 714587824 A/G - C T CT + tplb0036i05_182 chr3A 714951061 A/C - G T GT + RAC875_c10710_87 chr3A 716069442 T/C NA NA NA CT NA flanks do not match reference at this position BS00076751_51 chr3A 717653817 A/G - T C CT + BS00041742_51 chr3A 717903314 T/C - A G AG + BobWhite_c12428_371 chr3A 717903487 A/G + A G CT - Kukri_c30244_619 chr3A 721449692 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c24829_189 chr3A 721452492 T/C + C T CT + BS00065673_51 chr3A 721665960 A/C - T G AC - BobWhite_c15763_205 chr3A 724057588 A/G - T C AG - CAP8_c3568_256 chr3A 724200935 T/C - G A CT - CAP7_c3178_52 chr3A 724201149 T/G - A C GT - RAC875_c24982_202 chr3A 724319545 T/C - G A CT - BS00087533_51 chr3A 724493491 A/G - C T AG - BS00048633_51 chr3A 726137811 A/G + A G CT - Kukri_c22748_211 chr3A 726139704 T/C - A G AG + BS00075598_51 chr3A 726997325 T/C + C T CT + RAC875_rep_c109228_400 chr3A 727070435 T/C + T C AG - BobWhite_c29014_241 chr3A 727072881 T/C - G A CT - RAC875_rep_c72670_558 chr3A 727991325 T/C + C T AG - Kukri_c12212_182 chr3A 729576032 T/C + T C CT + CAP7_rep_c12537_81 chr3A 730278962 A/G - T C AG - BS00099980_51 chr3A 730279049 T/C - A G CT - BS00022419_51 chr3A 730849250 T/C + T C CT + BobWhite_c46361_331 chr3A 731222184 A/G + A G AG + BS00097939_51 chr3A 732042533 A/G - T C CT + RAC875_c3084_415 chr3A 732472525 T/C - A G CT - BS00029569_51 chr3A 732472553 A/G - C T AG - Excalibur_c64013_68 chr3A 732472694 A/G - C T AG - IAAV9044 chr3A 732668328 A/G + G A CT - Tdurum_contig31097_254 chr3A 732668624 A/G - T C CT + Excalibur_c51312_218 chr3A 733044350 A/G + A G CT - RAC875_c28721_290 chr3A 733571264 T/C + T C AG - CAP12_c869_150 chr3A 733965130 T/C + C T AG - RAC875_c61934_186 chr3A 733995625 A/G - T C AG - JD_c7714_954 chr3A 734130494 A/G - T C CT + JD_c7528_325 chr3A 734131189 T/C - G A AG + Kukri_c47887_111 chr3A 734788113 T/C + T C AG - CAP7_c915_121 chr3A 736388700 A/G - C T AG - Tdurum_contig18326_142 chr3A 737440799 T/C - G A CT - Ku_c12191_1123 chr3A 737800206 A/G + A G CT - BS00086050_51 chr3A 739147183 T/C + C T CT + BS00086051_51 chr3A 739147923 A/G + G A AG + Tdurum_contig93570_848 chr3A 739160711 A/G + A G AG + Tdurum_contig13011_381 chr3A 739166671 A/G + G A AG + Tdurum_contig50577_620 chr3A 739276806 T/G - C A AC + BS00074926_51 chr3A 739392416 T/C + T C CT + BS00093252_51 chr3A 739519042 T/C - G A CT - Kukri_c51666_401 chr3A 739520539 T/C - G A CT - Kukri_s117946_404 chr3A 739734944 T/C + C T AG - BobWhite_c21540_63 chr3A 740887234 T/G - A C GT - Tdurum_contig5009_349 chr3A 741240025 T/C + C T CT + Tdurum_contig67686_792 chr3A 741241502 T/C + T C CT + Tdurum_contig67686_851 chr3A 741241561 A/G + A G AG + Tdurum_contig67686_874 chr3A 741241584 T/C + C T AG - Tdurum_contig67686_1204 chr3A 741241914 T/G + G T GT + BobWhite_c2661_155 chr3A 742613007 T/C - A G AG + Excalibur_c3821_1355 chr3A 743190930 A/G + A G CT - Excalibur_c4302_2208 chr3A 744440943 A/G + A G CT - RAC875_c75663_115 chr3A 744664912 T/C NA NA NA CT NA flanks do not match reference at this position BobWhite_c5246_474 chr3A 746633485 T/G - A C GT - RAC875_c38975_411 chr3A 749110717 A/G - C T CT + GENE-1910_358 chr3A 749205737 T/C + T C AG - RFL_Contig2394_439 chr3A 749278597 A/G + A G AG + Tdurum_contig51914_500 chr3A 749278654 T/C - A G CT - Tdurum_contig55443_1361 chr3A 749404693 A/G - C T AG - Kukri_c1771_715 chr3B 219556 T/C + C T CT + Tdurum_contig50596_825 chr3B 219676 A/C + C A AC + GENE-1743_853 chr3B 985547 A/C - T G AC - CAP12_rep_c3868_270 chr3B 986669 A/C + A C GT - RAC875_c13385_1268 chr3B 2486766 A/G + G A AG + Kukri_c17082_519 chr3B 2487760 T/C + C T CT + RAC875_c5633_1748 chr3B 2512256 T/G - A C AC + RFL_Contig2549_565 chr3B 2519073 T/G + T G GT + tplb0028p23_691 chr3B 2519537 A/G + A G AG + Tdurum_contig77551_589 chr3B 2885581 A/G - C T CT + IACX4260 chr3B 3228129 T/C + T C CT + JD_c15022_218 chr3B 3237950 A/G + A G CT - TA004185-0427 chr3B 3238225 T/C + T C CT + Tdurum_contig50954_1264 chr3B 3240214 T/C - G A CT - IACX8570 chr3B 3241481 A/C - G T AC - RAC875_c29099_847 chr3B 3241739 T/G NA NA NA AC NA flanks do not match reference at this position GENE-3869_1166 chr3B 3408554 A/G + A G AG + BS00064776_51 chr3B 4468984 T/C - A G AG + RFL_Contig5360_1282 chr3B 5582815 T/C + T C CT + Tdurum_contig12008_842 chr3B 5584493 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c20277_483 chr3B 5585720 A/G - C T CT + Excalibur_c20277_436 chr3B 5585767 A/G - T C AG - IAAV6644 chr3B 5586001 T/G + G T GT + RAC875_c43163_189 chr3B 5952936 A/G - C T AG - RAC875_c48906_281 chr3B 6178220 A/G - C T AG - Excalibur_c94546_61 chr3B 6178322 A/G + G A CT - BobWhite_c27287_232 chr3B 6241138 A/G - C T AG - Tdurum_contig9514_807 chr3B 6250541 A/G - C T CT + BS00065248_51 chr3B 6379208 T/C - G A AG + Excalibur_c63477_90 chr3B 6666586 A/G + A G CT - Ra_c16527_465 chr3B 6670333 T/C - G A CT - RAC875_c14696_980 chr3B 6678787 T/C - G A AG + BobWhite_c7454_363 chr3B 6754488 T/G - A C GT - BS00047528_51 chr3B 6754648 A/G + G A AG + Excalibur_c8314_405 chr3B 7064041 T/C - G A CT - BS00088434_51 chr3B 7065041 A/G - T C CT + CAP7_c1997_79 chr3B 7186397 T/G - C A AC + CAP11_c2057_200 chr3B 7186428 T/C - A G AG + BS00011438_51 chr3B 7373468 T/C - A G AG + Excalibur_c11505_806 chr3B 7373756 T/C + C T CT + BobWhite_c3902_145 chr3B 7604656 A/G + A G CT - BobWhite_c3902_175 chr3B 7604686 A/G + G A CT - BS00022154_51 chr3B 8528918 T/C + T C CT + BS00111294_51 chr3B 8811576 T/G - A C GT - Ku_c519_281 chr3B 9166877 T/C + T C CT + BobWhite_c9711_71 chr3B 9780220 A/G - T C CT + RFL_Contig5709_3005 chr3B 9780261 A/G + G A AG + RFL_Contig5709_3312 chr3B 9780568 T/C + C T CT + RFL_Contig2585_547 chr3B 9916069 T/C + T C CT + RAC875_c53353_78 chr3B 9934273 T/C + T C CT + CAP7_c1576_371 chr3B 10708086 A/G + G A AG + Tdurum_contig80344_144 chr3B 10708086 T/C - G A AG + RAC875_c76367_523 chr3B 10709798 A/G + A G AG + tplb0043c20_1046 chr3B 10956465 A/G + A G AG + Tdurum_contig79629_538 chr3B 10956668 A/C - G T GT + RAC875_c4389_1412 chr3B 11087167 A/G - C T AG - RAC875_c8459_1291 chr3B 12288958 A/G - T C CT + BS00019919_51 chr3B 13764870 T/G - C A GT - BS00063445_51 chr3B 13964327 T/C + C T CT + Tdurum_contig93507_1345 chr3B 13966106 T/C - A G CT - Excalibur_c41820_354 chr3B 14163579 A/G + G A AG + BS00064956_51 chr3B 15521946 A/G - T C AG - BS00064177_51 chr3B 15522273 T/C + C T CT + Excalibur_c50808_326 chr3B 16055800 A/G + A G AG + tplb0041e10_1230 chr3B 16442309 A/C - T G AC - GENE-1856_1005 chr3B 16442663 A/G + A G AG + Excalibur_c9206_836 chr3B 16443214 T/C + T C AG - BS00088683_51 chr3B 16444257 T/C + T C AG - Excalibur_rep_c104498_168 chr3B 16444577 T/C - G A AG + Kukri_rep_c107316_393 chr3B 16453263 T/C - G A CT - Excalibur_rep_c67448_528 chr3B 16453620 T/G + T G GT + RAC875_c8885_74 chr3B 16455263 T/C + T C CT + BS00018764_51 chr3B 16455416 A/G - C T CT + Excalibur_c46345_100 chr3B 16459657 T/C - G A AG + RAC875_c36432_172 chr3B 16461823 A/G + A G AG + BS00022387_51 chr3B 17081456 A/G + G A AG + Excalibur_c25566_1000 chr3B 17562178 T/C + C T AG - BS00039218_51 chr3B 18026041 T/G - A C GT - IACX22 chr3B 18503568 T/C + T C CT + BS00090324_51 chr3B 18503985 T/C - A G CT - IACX6214 chr3B 18559070 A/G + A G AG + Tdurum_contig57914_745 chr3B 18821830 T/C + T C CT + BS00026471_51 chr3B 18873524 T/G + G T GT + Kukri_c40882_312 chr3B 19251097 A/G + G A AG + BS00046375_51 chr3B 19869710 A/G - T C CT + Tdurum_contig13898_648 chr3B 19869756 A/G - C T AG - IAAV3924 chr3B 20450624 T/C - G A AG + BS00062690_51 chr3B 20543664 T/C + T C AG - Tdurum_contig11297_571 chr3B 20829709 T/C - G A CT - Tdurum_contig49753_191 chr3B 21002904 T/C + T C CT + BobWhite_c12908_381 chr3B 21002980 T/C - A G CT - BS00097558_51 chr3B 21770352 A/G - C T AG - BS00030203_51 chr3B 23184582 A/G - C T AG - Tdurum_contig11684_144 chr3B 23184582 T/C + C T AG - Kukri_c13830_924 chr3B 23599364 T/C - G A CT - RFL_Contig5043_785 chr3B 23600044 A/C + C A GT - Tdurum_contig43252_1762 chr3B 23782130 T/G - A C GT - Tdurum_contig43252_1407 chr3B 23782485 T/C - G A CT - BS00070455_51 chr3B 24940119 T/G - C A GT - Tdurum_contig22897_107 chr3B 24942848 A/G - C T AG - GENE-4824_212 chr3B 25275838 A/G + A G CT - BobWhite_c28090_175 chr3B 25276429 A/C - G T AC - Kukri_c96747_274 chr3B 25417774 T/G - C A AC + RFL_Contig3455_629 chr3B 28105078 T/C + T C AG - RFL_Contig3455_700 chr3B 28105149 A/G + A G AG + Tdurum_contig46389_1838 chr3B 29355817 A/G - C T AG - Tdurum_contig46389_1540 chr3B 29356115 T/C - G A AG + Tdurum_contig46389_1459 chr3B 29356196 A/C - T G GT + Tdurum_contig46389_760 chr3B 29356895 T/C - G A AG + BS00025792_51 chr3B 29776852 T/C + T C CT + BS00010332_51 chr3B 32286178 A/G - C T CT + BobWhite_c23887_53 chr3B 32286994 A/C NA NA NA AC NA flanks do not match reference at this position GENE-1771_541 chr3B 32458897 T/C + T C AG - IAAV5662 chr3B 39905086 T/C + T C AG - RFL_Contig1456_842 chr3B 39907064 A/G - T C AG - RAC875_c56182_263 chr3B 40141083 T/C + C T AG - BS00056257_51 chr3B 40234216 A/C NA NA NA GT NA flanks do not match reference at this position BS00056258_51 chr3B 40234319 T/G + G T GT + BS00087825_51 chr3B 40245575 T/C - A G AG + RFL_Contig29_1062 chr3B 40908558 T/C - G A AG + BS00022242_51 chr3B 42340548 A/C + A C GT - Excalibur_c35645_587 chr3B 43275285 T/G + T G AC - Jagger_c4901_95 chr3B 43556351 T/C - G A AG + Tdurum_contig97412_402 chr3B 43736530 A/G + G A CT - Kukri_c17063_548 chr3B 43736620 A/G - C T CT + RAC875_c37084_143 chr3B 44283532 T/C - G A AG + JD_c14460_122 chr3B 48888853 A/G NA NA NA CT NA flanks do not match reference at this position BS00092492_51 chr3B 49861398 A/G + A G CT - BobWhite_rep_c55395_200 chr3B 50231211 T/C + T C AG - RAC875_c2529_1483 chr3B 53355184 T/C - A G CT - BS00076248_51 chr3B 53567376 A/G - T C CT + Kukri_c5252_107 chr3B 53804010 A/G + A G AG + Tdurum_contig67690_183 chr3B 53804337 A/G - T C CT + BobWhite_c4502_252 chr3B 54752162 T/C + C T AG - RAC875_rep_c111648_86 chr3B 54754066 T/C + C T CT + Excalibur_c8284_580 chr3B 54755720 A/G - C T CT + CAP8_c1799_237 chr3B 55456851 A/G + G A AG + Kukri_rep_c70103_146 chr3B 55736390 A/G + A G AG + BS00003822_51 chr3B 59064210 T/G - A C GT - BS00011728_51 chr3B 59064340 T/C - A G AG + BobWhite_c23019_513 chr3B 59961902 T/C + C T CT + Kukri_c23228_137 chr3B 59962915 A/C + C A AC + BS00079014_51 chr3B 60142171 A/G + G A AG + Excalibur_c11594_246 chr3B 60254138 T/C + T C AG - BobWhite_c828_329 chr3B 60254983 A/G + G A AG + Excalibur_c2820_1626 chr3B 60255016 A/G - T C AG - GENE-4064_715 chr3B 60255852 T/C + C T CT + RAC875_rep_c69316_1516 chr3B 60256760 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c2820_224 chr3B 60259928 A/G - T C AG - GENE-1900_115 chr3B 60867392 T/C + C T AG - RAC875_c20041_976 chr3B 60868255 T/C + T C AG - RAC875_c20041_1062 chr3B 60868341 T/C + T C CT + JD_c4128_277 chr3B 62392552 A/G + G A AG + RAC875_c2787_1260 chr3B 63110515 T/C + T C AG - Excalibur_c58066_180 chr3B 63393635 A/G - C T CT + Ku_c56846_964 chr3B 64696881 T/G - C A AC + BS00062940_51 chr3B 64699148 A/G - T C AG - IAAV4190 chr3B 65366861 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c57829_83 chr3B 66186184 T/C - G A CT - Kukri_c48750_1416 chr3B 66186940 T/C + C T AG - BobWhite_rep_c63085_120 chr3B 66581492 T/C - A G CT - Kukri_c32046_493 chr3B 66864822 T/C NA NA NA CT NA flanks do not match reference at this position BS00077528_51 chr3B 66864981 T/C - G A CT - BS00075108_51 chr3B 66870072 T/C - G A CT - Tdurum_contig51993_52 chr3B 66953509 A/G + G A AG + Excalibur_c21372_142 chr3B 66954023 A/C - G T GT + BS00063036_51 chr3B 67415931 A/C + A C GT - RAC875_c35310_987 chr3B 67929868 A/G - T C AG - RAC875_c35310_770 chr3B 67931549 T/C - A G AG + Kukri_c66923_217 chr3B 67933331 A/G + G A CT - Excalibur_c11246_659 chr3B 67933363 T/C + C T CT + BS00102622_51 chr3B 68464206 T/G - C A GT - BS00011570_51 chr3B 68590601 A/C + C A GT - Excalibur_c43468_438 chr3B 68879938 A/G + G A CT - JD_c20321_354 chr3B 68881319 A/G - C T CT + Excalibur_rep_c103016_430 chr3B 68903675 T/C - G A CT - BS00022072_51 chr3B 69359638 T/C + C T AG - RAC875_c5913_172 chr3B 69604725 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_c4661_915 chr3B 69605741 A/C + A C GT - Ra_c965_2575 chr3B 69818434 T/G + T G GT + Ra_c965_2579 chr3B 69818438 T/C + C T CT + Ra_c965_2702 chr3B 69818561 T/C + T C AG - Ra_c965_2703 chr3B 69818562 T/C + T C AG - IAAV6423 chr3B 70301913 A/G + G A CT - Ku_c3416_572 chr3B 70301913 T/C - G A CT - BS00065429_51 chr3B 71144419 A/G + G A CT - IAAV5819 chr3B 72716470 T/C - G A AG + BS00011064_51 chr3B 79289530 A/G + G A AG + Excalibur_c15944_70 chr3B 79947217 A/G + G A CT - GENE-1534_132 chr3B 79953872 A/G - T C CT + Tdurum_contig10014_561 chr3B 81167075 T/G - C A GT - IAAV7128 chr3B 81818253 T/C - A G AG + Ra_c3336_2247 chr3B 82447733 A/G - T C CT + Kukri_rep_c102953_304 chr3B 92333252 A/G - C T CT + BS00066108_51 chr3B 95155597 A/G - C T CT + RAC875_c1069_115 chr3B 100965785 T/C + C T AG - BobWhite_c10402_170 chr3B 100968204 T/C - A G CT - BobWhite_c10402_140 chr3B 100968234 T/C - A G CT - Kukri_c21467_571 chr3B 100968357 T/C - A G CT - BS00032830_51 chr3B 101313051 T/C + T C AG - IAAV8901 chr3B 102757515 A/G - C T AG - Jagger_c10720_161 chr3B 102757515 T/C + C T CT + Kukri_rep_c74178_178 chr3B 103244640 T/C + T C CT + Kukri_c23958_187 chr3B 106282784 A/G + G A CT - RFL_Contig2267_1589 chr3B 107967022 T/C - A G CT - Excalibur_rep_c68583_1067 chr3B 108813566 A/G - T C CT + Kukri_rep_c102888_154 chr3B 110454215 A/G - T C AG - Kukri_c20199_83 chr3B 116147521 T/C - A G CT - Kukri_rep_c102621_446 chr3B 116148539 A/G - T C CT + Kukri_rep_c101837_143 chr3B 116148860 A/G - T C AG - Excalibur_c32170_145 chr3B 116681603 T/G - C A GT - BS00022415_51 chr3B 117550086 T/G + T G GT + Kukri_c6460_1823 chr3B 117575457 A/C - T G AC - JD_c49675_408 chr3B 117931105 A/C - G T GT + Kukri_c8740_75 chr3B 119123052 A/G + A G AG + Tdurum_contig100403_128 chr3B 119393049 T/C + T C AG - RFL_Contig4169_289 chr3B 119420769 A/G - T C CT + Kukri_c8880_123 chr3B 120611473 A/G - C T AG - RFL_Contig3857_548 chr3B 126002180 A/G - C T CT + Kukri_s116671_78 chr3B 127292436 A/G + G A AG + RAC875_rep_c70009_157 chr3B 128669235 A/G - C T AG - RAC875_c5206_1396 chr3B 129716092 T/C - G A AG + Excalibur_c3103_878 chr3B 131517216 T/C - A G CT - Kukri_c39386_282 chr3B 131517706 T/C + T C CT + RAC875_c25375_236 chr3B 132904679 A/C + A C AC + BS00023120_51 chr3B 133774993 T/C + T C CT + TA002188-0143 chr3B 133819011 T/C + T C CT + BS00090227_51 chr3B 133819046 T/C + C T CT + BS00010795_51 chr3B 133819251 A/G + A G AG + IAAV993 chr3B 134274155 A/G + G A AG + BS00037469_51 chr3B 137325236 T/C + C T CT + CAP8_c8016_120 chr3B 139778064 A/G + A G AG + BS00086717_51 chr3B 140490793 T/C + T C AG - RFL_Contig738_557 chr3B 140688620 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig45431_607 chr3B 140688768 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig43263_243 chr3B 140987277 A/G + G A AG + Tdurum_contig43263_246 chr3B 140987280 A/G + G A CT - Tdurum_contig10455_262 chr3B 141125220 A/G + G A AG + BS00066149_51 chr3B 141132897 A/G + G A AG + Excalibur_c54025_104 chr3B 142870345 A/G + G A CT - CAP12_c4778_199 chr3B 144057147 A/G + A G CT - IACX971 chr3B 145313431 T/G + T G GT + Kukri_c3305_2048 chr3B 145904492 A/G + G A CT - Kukri_c3168_521 chr3B 147683211 T/C - G A CT - Excalibur_c34554_312 chr3B 148657466 T/C + T C CT + Kukri_c35146_2094 chr3B 151226394 A/G + G A CT - tplb0046p09_685 chr3B 152209979 T/C - G A CT - Kukri_c65979_387 chr3B 153607042 T/C + C T AG - Kukri_c65979_1410 chr3B 153608065 A/G + A G CT - Excalibur_c7742_2189 chr3B 158211666 A/G - C T AG - Excalibur_c10470_887 chr3B 158213348 T/C + T C AG - RAC875_c79844_323 chr3B 160841749 A/G + G A AG + BS00045195_51 chr3B 160842435 A/G - C T AG - Excalibur_c19108_321 chr3B 161642736 A/G + A G CT - Kukri_c4104_1347 chr3B 168690740 A/G - T C CT + tplb0062h15_59 chr3B 172321735 A/C - G T GT + RAC875_c37608_216 chr3B 175093516 A/C - G T AC - IAAV7548 chr3B 187819350 A/G - C T AG - RAC875_c29981_62 chr3B 190891456 T/G NA NA NA GT NA flanks do not match reference at this position BS00066904_51 chr3B 191213539 A/G + G A CT - tplb0056l14_1616 chr3B 194073119 T/C - A G CT - BobWhite_c1543_216 chr3B 194327314 T/G - A C GT - CAP7_c3916_256 chr3B 206193261 A/G + G A AG + RAC875_c34454_334 chr3B 206193261 T/C - G A AG + BS00029548_51 chr3B 207223999 A/G + G A AG + IAAV7265 chr3B 214547781 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c21955_719 chr3B 221985354 T/C - G A CT - BS00098496_51 chr3B 222192671 T/C - A G CT - BS00042337_51 chr3B 222197590 A/G - T C CT + CAP8_rep_c9413_186 chr3B 223034344 A/G + G A CT - BobWhite_c10823_405 chr3B 223036705 T/C + C T AG - GENE-1721_1383 chr3B 223036985 A/G - T C AG - Excalibur_c36818_752 chr3B 223346396 T/C + T C CT + Excalibur_c18641_1849 chr3B 230336603 A/G - T C AG - Kukri_c4747_330 chr3B 230336648 A/C + A C GT - RAC875_c2525_894 chr3B 230336798 A/G - C T CT + Excalibur_c19240_109 chr3B 230337457 A/C + A C AC + Excalibur_c30975_133 chr3B 230337457 T/G - A C GT - Excalibur_c14273_1928 chr3B 232603698 T/C - G A CT - Excalibur_c14273_1407 chr3B 232604406 T/C - G A AG + BS00106922_51 chr3B 232636240 A/G - C T CT + GENE-1840_122 chr3B 236359232 T/C - A G AG + Excalibur_c20599_411 chr3B 237291488 A/G + G A AG + CAP8_c490_120 chr3B 239895144 A/C - T G AC - Kukri_c14113_98 chr3B 239914702 T/C - A G CT - Tdurum_contig3182_132 chr3B 240269763 A/G + A G AG + RAC875_rep_c77173_208 chr3B 241273824 T/C - G A CT - Jagger_c1219_603 chr3B 241391873 A/G - T C AG - GENE-4829_238 chr3B 241396573 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig28033_420 chr3B 241396573 A/G - C T CT + Tdurum_contig1002_149 chr3B 241398529 A/C + C A AC + RAC875_c21086_130 chr3B 242166212 T/C + C T AG - BobWhite_c634_420 chr3B 242168670 A/C - T G AC - IAAV5505 chr3B 242746787 A/C + C A GT - Excalibur_rep_c108858_479 chr3B 244236992 A/C - T G AC - Excalibur_c24830_415 chr3B 244990683 A/G - C T AG - BS00049570_51 chr3B 245509557 T/C + T C CT + RAC875_c8755_314 chr3B 245948751 A/G NA NA NA CT NA flanks do not match reference at this position BS00091577_51 chr3B 245949056 A/G - T C AG - Excalibur_c3862_837 chr3B 245969143 T/C - G A AG + Excalibur_c574_809 chr3B 248249248 T/C - G A CT - tplb0057k16_1515 chr3B 250817975 A/G - T C CT + Kukri_c37029_761 chr3B 251183809 A/G + G A CT - Kukri_c23589_2147 chr3B 253894635 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c18900_146 chr3B 254951769 T/C - A G CT - BobWhite_c10997_421 chr3B 255991478 A/G - T C AG - CAP11_c1936_191 chr3B 256357337 A/C + C A AC + JD_c15900_315 chr3B 257318792 T/C + T C CT + Excalibur_c51923_181 chr3B 257841058 T/C + T C CT + RAC875_c9789_1341 chr3B 259455803 T/C - A G CT - IACX455 chr3B 259460457 T/G - C A GT - GENE-1480_74 chr3B 259461378 T/C - A G AG + BobWhite_c21003_148 chr3B 259858699 A/G - T C AG - BobWhite_rep_c49957_578 chr3B 263787910 T/G - C A AC + BobWhite_c27991_64 chr3B 264165442 T/C - G A AG + BobWhite_c19166_94 chr3B 269253017 A/G + A G AG + Excalibur_c26843_713 chr3B 271824235 A/G + G A CT - Excalibur_rep_c72744_1649 chr3B 275344576 A/G + A G AG + BS00069274_51 chr3B 278776367 A/G + G A AG + JD_c15105_367 chr3B 279495818 A/C - T G GT + BobWhite_rep_c63350_277 chr3B 281415425 A/C - T G AC - RAC875_rep_c117982_260 chr3B 283579527 A/G - C T AG - Ra_c1049_455 chr3B 289613629 A/G - C T CT + Kukri_c28989_244 chr3B 299144993 A/G - T C CT + GENE-1795_81 chr3B 304968918 T/G - C A GT - RAC875_c41758_106 chr3B 315420056 A/G + A G CT - Kukri_s118189_100 chr3B 333463552 T/C + T C AG - Kukri_c24007_83 chr3B 335131966 T/C + T C AG - JD_c48846_447 chr3B 336929406 T/G - A C AC + Excalibur_c52772_1592 chr3B 345705214 A/G - T C AG - IACX460 chr3B 349934855 A/C - T G GT + Excalibur_c35792_989 chr3B 352243059 A/G + G A AG + Excalibur_c4982_348 chr3B 353862873 T/C - A G CT - IACX301 chr3B 358678395 T/C + C T AG - tplb0032n11_558 chr3B 361753115 A/G - T C CT + JD_c119_119 chr3B 368090158 T/C + C T CT + Excalibur_c54388_193 chr3B 368904550 T/C - A G CT - IACX914 chr3B 370153923 T/C + C T AG - Excalibur_c14803_1088 chr3B 370966150 A/G + A G CT - RAC875_rep_c120973_187 chr3B 372245428 A/G + G A CT - RFL_Contig3799_987 chr3B 378688267 A/G + G A AG + IACX615 chr3B 380515476 T/C - G A CT - IAAV1808 chr3B 386585741 C/G - C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c76861_342 chr3B 387425735 A/G - T C AG - RAC875_c430_1072 chr3B 393319803 T/C + C T CT + Kukri_c29464_1343 chr3B 400651455 T/C + T C CT + BS00074287_51 chr3B 408354812 A/G + G A CT - Kukri_c2412_1421 chr3B 410367629 A/G - T C AG - RAC875_c19898_174 chr3B 414015556 A/C - T G AC - BobWhite_c16847_343 chr3B 414186071 A/G - C T AG - IAAV8368 chr3B 414186147 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BobWhite_c16847_99 chr3B 414186315 A/G - C T AG - Kukri_rep_c70097_286 chr3B 415930394 T/G - C A GT - Excalibur_c63730_660 chr3B 416279752 A/G + A G CT - Tdurum_contig28384_102 chr3B 416283216 A/G + G A AG + JD_c25982_176 chr3B 417265398 T/C + C T AG - Tdurum_contig5024_894 chr3B 417373922 T/C - A G AG + BS00072151_51 chr3B 419241149 T/G - C A GT - Kukri_c17718_145 chr3B 419556945 T/C + C T CT + BS00049639_51 chr3B 419566527 A/C + C A GT - RAC875_c2405_506 chr3B 421918109 A/G - T C CT + IAAV8536 chr3B 422523760 A/G - C T AG - Ku_c11466_1414 chr3B 422523760 T/C + C T AG - BS00003522_51 chr3B 432844990 A/G + A G AG + Kukri_c5793_1983 chr3B 434059148 T/C + C T AG - BobWhite_c11540_60 chr3B 452103444 T/C - A G AG + BS00084883_51 chr3B 452107771 T/C - A G AG + tplb0031e09_1230 chr3B 452553294 A/G + A G CT - tplb0031e09_1763 chr3B 452554552 T/C NA NA NA AG NA flanks do not match reference at this position BS00095061_51 chr3B 455065669 A/C - G T AC - Excalibur_rep_c94717_2115 chr3B 455676541 T/C - A G AG + Excalibur_rep_c94717_959 chr3B 455677696 A/G - T C AG - Excalibur_rep_c94717_415 chr3B 455678240 A/C - T G GT + RAC875_rep_c115365_100 chr3B 455678588 A/G - T C AG - RFL_Contig2538_533 chr3B 455679375 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig13377_89 chr3B 456110777 A/C - T G GT + Kukri_c7804_2504 chr3B 457025618 T/C + T C CT + Kukri_c18009_398 chr3B 462099522 A/C + C A GT - BS00062808_51 chr3B 463114882 A/C - T G AC - BS00109935_51 chr3B 463114882 T/G + T G AC - BS00082644_51 chr3B 463256858 A/G + G A AG + BS00090945_51 chr3B 465502688 T/C + T C CT + RAC875_rep_c104403_524 chr3B 466262952 T/C - A G CT - BS00030534_51 chr3B 466615585 A/G - T C AG - RAC875_rep_c112642_422 chr3B 466615617 A/C + A C GT - Ku_c8631_308 chr3B 467046943 T/C + T C CT + IAAV738 chr3B 467048012 T/C + C T CT + Kukri_c41191_703 chr3B 469767999 A/G + A G CT - BS00045330_51 chr3B 474028941 T/G - C A GT - BS00073407_51 chr3B 474317351 T/C + C T AG - IAAV1291 chr3B 475830091 A/G + A G AG + Kukri_rep_c110312_376 chr3B 475995928 T/C + T C CT + BS00090405_51 chr3B 476289723 T/C - A G AG + Kukri_c4599_482 chr3B 476290282 A/G - T C CT + Kukri_c4599_253 chr3B 476290511 T/C - A G CT - Excalibur_c26760_321 chr3B 477649634 A/C - G T AC - RAC875_c2523_1754 chr3B 477650015 A/G - C T AG - GENE-1657_48 chr3B 477652264 T/C - G A AG + Kukri_c10254_95 chr3B 477885359 A/G + A G AG + BS00053566_51 chr3B 478554776 T/C + C T CT + Excalibur_c29625_243 chr3B 479675211 A/C - G T AC - Excalibur_c29625_222 chr3B 479675232 A/G - C T AG - BS00023645_51 chr3B 479876161 T/G - C A GT - Excalibur_rep_c111297_98 chr3B 479904176 T/C - G A CT - IACX11401 chr3B 480424237 A/G - T C AG - BobWhite_c14606_452 chr3B 480426075 T/C + C T AG - RFL_Contig1945_110 chr3B 480427252 A/G - C T AG - Tdurum_contig54463_316 chr3B 480568032 A/G + G A CT - Excalibur_c16842_743 chr3B 480569151 T/G + G T GT + Excalibur_c77101_90 chr3B 480569927 T/C + T C CT + Kukri_rep_c70198_1436 chr3B 481605172 A/G + G A AG + RAC875_s115213_106 chr3B 481621029 A/C + C A GT - RAC875_c17884_616 chr3B 482994503 A/G + A G CT - Kukri_c15639_351 chr3B 482995819 A/G + A G CT - RAC875_c40919_1075 chr3B 482997575 A/G + A G AG + BS00105995_51 chr3B 484872339 A/G - T C CT + Kukri_c11259_55 chr3B 484872710 A/G - C T AG - IACX5407 chr3B 485388768 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00039734_51 chr3B 485693272 T/C + C T CT + TA002920-0166-w chr3B 485693879 T/C - G A AG + Tdurum_contig20950_359 chr3B 486812872 T/C - A G AG + Excalibur_c10219_352 chr3B 487495287 T/C - A G CT - BobWhite_c35249_110 chr3B 487882549 A/G + G A CT - TA002241-1114 chr3B 488187681 A/C + A C AC + BS00037898_51 chr3B 488543168 T/C + T C CT + Tdurum_contig75784_771 chr3B 488878690 A/G - C T CT + BobWhite_c24774_186 chr3B 488878863 A/G + A G CT - BS00074997_51 chr3B 490885651 A/C + C A AC + RAC875_rep_c82061_78 chr3B 492569270 T/G - A C AC + BS00036352_51 chr3B 493122649 T/C + T C AG - BS00026295_51 chr3B 493649137 A/G + A G CT - BS00057451_51 chr3B 493655368 T/C - G A AG + Ku_c27771_508 chr3B 495471609 T/C - G A CT - BobWhite_c42781_98 chr3B 496902276 T/C - A G CT - IAAV4105 chr3B 497089888 A/C - G T AC - RAC875_c46237_294 chr3B 498057856 A/G + G A AG + Excalibur_c14999_712 chr3B 499454449 T/C + T C CT + RAC875_c32792_231 chr3B 501108076 A/G - C T CT + BobWhite_c45623_215 chr3B 501115384 A/G + A G CT - RFL_Contig622_1601 chr3B 501128517 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_c46052_695 chr3B 502635564 A/C - T G AC - Tdurum_contig9132_102 chr3B 502644067 A/G - C T AG - BS00030430_51 chr3B 503989918 A/G - C T CT + BobWhite_c24718_225 chr3B 505016068 A/G + G A CT - Tdurum_contig10107_580 chr3B 506624017 A/G - T C CT + BobWhite_rep_c50457_813 chr3B 507301016 T/C + C T CT + BS00034257_51 chr3B 507501221 T/C - G A AG + BS00034260_51 chr3B 507501692 A/G - T C AG - RFL_Contig5682_86 chr3B 510000802 A/G + A G CT - BS00052423_51 chr3B 510000893 A/G + G A AG + BS00099331_51 chr3B 511072296 T/C - G A CT - BS00110292_51 chr3B 513665765 T/C - G A CT - BS00022219_51 chr3B 513987393 A/G + G A AG + BS00108055_51 chr3B 513987670 T/G + G T AC - Excalibur_c62737_131 chr3B 519057612 A/G - T C CT + BS00093886_51 chr3B 520330387 A/G + A G CT - JD_c6678_319 chr3B 520371956 A/C - T G AC - JD_c6678_311 chr3B 520371964 A/G - C T CT + BobWhite_c59494_113 chr3B 520610679 T/C - A G AG + BS00073304_51 chr3B 522246590 T/G + G T GT + RAC875_c76448_253 chr3B 522247357 T/C - G A CT - Kukri_rep_c99834_188 chr3B 522393388 A/G - T C CT + Kukri_c14072_188 chr3B 523152959 T/C - G A AG + BS00030580_51 chr3B 523558995 A/G - C T AG - Excalibur_rep_c67517_925 chr3B 523560530 A/G + A G CT - RAC875_c62872_293 chr3B 523570133 A/G - C T CT + Excalibur_c61285_135 chr3B 523570464 A/G - T C CT + BS00084911_51 chr3B 524449748 A/G - T C AG - BS00022140_51 chr3B 524449750 A/G - T C AG - RAC875_rep_c71561_619 chr3B 524451197 A/G - C T CT + JD_c11099_294 chr3B 527654432 A/G + A G AG + BS00067588_51 chr3B 527678644 T/C - G A AG + BS00049008_51 chr3B 542551792 A/G + G A CT - IACX11287 chr3B 542735314 T/C + C T CT + RAC875_c96638_103 chr3B 542918623 A/G - C T AG - BobWhite_c5095_634 chr3B 543690523 T/C - A G AG + BS00089954_51 chr3B 543718678 A/G - T C AG - RAC875_c11254_739 chr3B 543718849 A/G - C T CT + Excalibur_c26754_433 chr3B 543842390 A/G + A G AG + IACX3190 chr3B 543842633 T/C + T C CT + Excalibur_c44713_137 chr3B 543877389 T/C NA NA NA AG NA flanks do not match reference at this position BS00043664_51 chr3B 543885050 T/C + C T AG - RAC875_c87788_155 chr3B 544819031 T/C + C T CT + BS00062734_51 chr3B 545069001 A/G NA NA NA CT NA flanks do not match reference at this position BS00022122_51 chr3B 547450419 T/C - A G CT - RAC875_c53667_348 chr3B 548550603 T/C - A G CT - BS00094710_51 chr3B 551894132 T/C + C T CT + Kukri_rep_c102334_1871 chr3B 552228750 A/G + A G AG + Kukri_c13269_1094 chr3B 552230681 T/C + C T AG - BS00060073_51 chr3B 553065166 T/G - C A AC + Excalibur_rep_c101410_789 chr3B 553571527 A/G - C T AG - BS00066466_51 chr3B 553733057 T/C - G A CT - BS00066467_51 chr3B 553733088 A/G - C T CT + Kukri_rep_c101649_404 chr3B 554034008 T/C - A G AG + Excalibur_rep_c71107_517 chr3B 554036511 T/C - G A CT - BS00078127_51 chr3B 554117098 T/C + C T CT + Excalibur_c11242_301 chr3B 555091297 T/G + G T GT + TA001464-0572 chr3B 555738211 A/G - T C CT + Kukri_c21818_519 chr3B 556059780 A/G + G A CT - Kukri_rep_c108929_91 chr3B 556873386 A/G - C T AG - Ex_c5074_1390 chr3B 556874672 T/G NA NA NA AC NA flanks do not match reference at this position BS00042456_51 chr3B 557091406 T/C - A G CT - BS00066060_51 chr3B 558080892 T/C NA NA NA AG NA flanks do not match reference at this position BS00024783_51 chr3B 558510168 A/G - T C CT + Excalibur_c5182_93 chr3B 560116732 A/G + G A CT - BS00091867_51 chr3B 560428023 T/C + T C CT + Excalibur_c23486_1091 chr3B 561094323 A/G - T C AG - IACX3871 chr3B 561232503 A/G - T C CT + BS00089166_51 chr3B 561540543 T/G + G T GT + GENE-4795_75 chr3B 561544344 T/C - A G AG + Excalibur_c80041_400 chr3B 561544349 T/G NA NA NA AC NA flanks do not match reference at this position Ku_c101932_436 chr3B 562444907 T/G - C A AC + Ku_c47769_302 chr3B 562730602 A/G + A G CT - BobWhite_rep_c49225_231 chr3B 562731114 A/G - T C AG - Ku_c71049_1180 chr3B 564248861 T/C NA NA NA CT NA flanks do not match reference at this position BS00033372_51 chr3B 564760322 T/C - A G AG + Kukri_c11910_445 chr3B 565273322 A/G - C T AG - BobWhite_c19725_1329 chr3B 566278179 A/G - C T AG - Excalibur_c5298_171 chr3B 566281963 A/G - C T CT + RFL_Contig5418_347 chr3B 567245879 A/G + G A CT - RAC875_c3770_903 chr3B 569598283 A/G + A G CT - BS00064039_51 chr3B 571302990 T/C + T C AG - Kukri_c9571_73 chr3B 571603356 A/C + C A AC + IAAV4613 chr3B 572267276 T/C + C T AG - IACX438 chr3B 572746851 A/G + G A AG + Excalibur_c82403_135 chr3B 573470322 A/G + G A AG + BobWhite_c21036_213 chr3B 574265198 T/C - A G AG + RAC875_c62713_656 chr3B 574698781 A/C - T G AC - IAAV3174 chr3B 574698836 A/G + A G CT - Excalibur_c5977_383 chr3B 574699250 T/C + T C AG - Excalibur_c5977_440 chr3B 574699307 T/G + T G GT + BS00032694_51 chr3B 574703012 T/C - A G AG + Excalibur_c5977_1409 chr3B 574705235 T/C + T C AG - BS00032692_51 chr3B 574705940 A/C - T G AC - Kukri_rep_c117846_427 chr3B 574706092 T/G + G T GT + Excalibur_c62826_254 chr3B 578282448 T/C + T C CT + RAC875_c6176_1139 chr3B 578389267 A/G - T C AG - RAC875_c6176_978 chr3B 578389428 A/G - C T CT + BS00073011_51 chr3B 578616604 T/C - A G AG + Excalibur_c15332_1305 chr3B 578812738 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c15332_1194 chr3B 578812849 T/C - A G AG + Excalibur_c15332_453 chr3B 578813862 A/G - C T AG - RAC875_c53296_61 chr3B 579886945 A/C + A C GT - RAC875_c53296_378 chr3B 579887261 T/C + T C CT + RAC875_c53296_529 chr3B 579887412 A/G + G A AG + Ex_c5547_2037 chr3B 579890533 T/C + T C CT + Ku_c31046_525 chr3B 580033611 T/C + C T AG - tplb0024c09_1335 chr3B 580206826 A/G + G A CT - Excalibur_c6445_223 chr3B 581026522 T/C + C T CT + RAC875_c20275_1619 chr3B 581267807 T/C + C T CT + BS00087278_51 chr3B 581645604 T/C + T C CT + BS00087279_51 chr3B 581645709 T/C + C T AG - RFL_Contig4421_1490 chr3B 581658952 T/C + T C AG - RFL_Contig4421_1724 chr3B 581659186 A/G + A G CT - Kukri_rep_c107421_115 chr3B 581703898 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_rep_c116515_181 chr3B 581703898 A/G + G A AG + RAC875_c775_1135 chr3B 581964439 T/C - G A AG + Ku_c25346_508 chr3B 581964754 A/G - T C AG - TA002266-1244 chr3B 581964878 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig48224_272 chr3B 581968234 T/C + T C CT + BS00005265_51 chr3B 581979283 A/G + A G AG + Excalibur_c6325_949 chr3B 582407972 A/G NA NA NA AG NA flanks do not match reference at this position Jagger_c5649_59 chr3B 582408634 T/C + C T CT + Tdurum_contig49477_187 chr3B 582408643 T/C - A G CT - Kukri_c25794_863 chr3B 582408705 A/C + C A AC + Tdurum_contig63110_433 chr3B 582463409 T/C + C T CT + BS00068494_51 chr3B 582466573 T/C + C T AG - Excalibur_c30527_559 chr3B 584695129 T/G - A C GT - Excalibur_c30527_515 chr3B 584695173 A/G - C T AG - Tdurum_contig67693_344 chr3B 585606294 A/G - T C CT + Tdurum_contig4913_705 chr3B 585607536 A/G - T C AG - Ra_c4329_599 chr3B 585686362 A/G - T C AG - Tdurum_contig67750_272 chr3B 586142507 T/C - G A AG + Excalibur_c57658_54 chr3B 586142941 A/G - T C CT + IACX11310 chr3B 586512142 T/C - G A CT - Kukri_rep_c113146_128 chr3B 586513470 A/G + A G CT - Excalibur_c3096_1699 chr3B 586513966 A/G + G A AG + IACX5912 chr3B 586862735 T/C - G A AG + Excalibur_c26662_218 chr3B 587004213 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_c5347_811 chr3B 591366968 T/C - A G AG + Excalibur_c25678_337 chr3B 591455290 T/C NA NA NA AG NA flanks do not match reference at this position BobWhite_c1093_494 chr3B 591458363 T/C - G A AG + Tdurum_contig56661_291 chr3B 593869310 T/C + T C AG - Ku_c9822_828 chr3B 595288760 A/G + G A CT - RAC875_c106500_413 chr3B 595689830 A/G - T C AG - IAAV1801 chr3B 595694158 T/G - A C GT - Ra_c9061_2115 chr3B 595694158 A/C + A C GT - CAP7_c10624_88 chr3B 601120587 T/C + C T AG - BS00093816_51 chr3B 602356018 T/C - A G CT - Tdurum_contig44013_74 chr3B 602356018 A/G + A G CT - Tdurum_contig44013_164 chr3B 602356108 A/G + G A AG + BobWhite_rep_c64944_264 chr3B 602359304 T/C - G A CT - BS00091643_51 chr3B 603449518 T/C NA NA NA CT NA flanks do not match reference at this position BobWhite_c32864_250 chr3B 604774016 A/G - C T CT + RAC875_s108395_60 chr3B 605267456 A/G + G A AG + RAC875_c10595_473 chr3B 605449617 A/G - C T CT + BS00066718_51 chr3B 606571026 T/C + C T CT + BS00068816_51 chr3B 607812579 A/G + A G AG + BS00068817_51 chr3B 607812618 T/C + T C AG - BobWhite_c6974_329 chr3B 610177482 A/C + C A GT - RAC875_c48556_278 chr3B 610177784 T/C - G A AG + BS00071373_51 chr3B 610495161 A/G + A G AG + RAC875_rep_c77684_470 chr3B 611176652 A/G - T C AG - Excalibur_c48047_90 chr3B 617682871 A/G + G A CT - Excalibur_rep_c113405_180 chr3B 618151165 A/C - T G AC - IAAV5835 chr3B 618155198 T/C - G A AG + RFL_Contig1291_309 chr3B 625454207 T/G + T G GT + Tdurum_contig49052_223 chr3B 626090095 T/C + C T AG - BS00047274_51 chr3B 627749028 A/G + A G AG + Kukri_c62419_269 chr3B 627906952 A/C - G T AC - Tdurum_contig70056_255 chr3B 627907059 A/G - T C CT + Ra_c106076_67 chr3B 630003884 A/G + G A AG + Ku_c47648_1403 chr3B 630306189 T/C - G A CT - RAC875_c4745_733 chr3B 630307433 T/C + T C AG - Tdurum_contig49991_103 chr3B 630367275 A/C - T G AC - BS00065978_51 chr3B 636247641 A/G + A G CT - RAC875_c44290_511 chr3B 636451630 A/G + A G CT - BobWhite_c14365_59 chr3B 640059418 T/G + T G GT + tplb0040c19_302 chr3B 647547461 T/C - G A CT - Excalibur_c43822_370 chr3B 648752466 T/C + C T CT + Kukri_c40034_123 chr3B 650601930 T/C - G A AG + Ra_c69660_1589 chr3B 651720699 T/G - C A GT - BS00023641_51 chr3B 651738262 A/C + C A AC + Excalibur_c21751_421 chr3B 655310004 A/G + A G CT - BS00032926_51 chr3B 655637112 A/G + G A CT - Ex_c4757_695 chr3B 656582455 A/G + A G CT - BS00022611_51 chr3B 659787974 T/G + G T GT + BS00087427_51 chr3B 659788127 T/G + G T AC - RAC875_c39926_313 chr3B 660790348 A/G + A G CT - RAC875_c16281_167 chr3B 661827660 A/G + A G CT - Excalibur_c34069_487 chr3B 661836547 A/G + A G CT - Ra_c12192_382 chr3B 662978386 T/C + T C CT + BobWhite_c40087_93 chr3B 663133085 A/G - T C AG - Ra_c1117_1399 chr3B 664888718 A/G - C T AG - RFL_Contig5871_809 chr3B 664893790 T/C NA NA NA AG NA flanks do not match reference at this position RFL_Contig5871_1771 chr3B 664896524 T/C + T C CT + BS00090869_51 chr3B 665341112 T/C - G A CT - RAC875_c16628_500 chr3B 665467436 A/G + A G CT - Excalibur_c25567_225 chr3B 667382923 T/C + C T CT + Ex_c18926_626 chr3B 668071314 T/C NA NA NA CT NA flanks do not match reference at this position Ex_c18926_618 chr3B 668071322 T/C - G A CT - Excalibur_c18926_174 chr3B 668072728 A/G - T C AG - Tdurum_contig15150_2456 chr3B 668332106 A/G + A G AG + RAC875_c1057_224 chr3B 669282369 T/C + T C CT + RAC875_c24267_775 chr3B 669426961 T/C - G A CT - RAC875_c530_354 chr3B 669428017 T/C + T C CT + BS00009701_51 chr3B 669443034 A/G - T C CT + BS00110072_51 chr3B 669443292 A/C + A C AC + RAC875_c25203_969 chr3B 672104910 T/C - A G AG + TA002179-0963 chr3B 672865745 A/G + A G AG + BS00031402_51 chr3B 674424894 T/C + C T CT + IAAV3519 chr3B 674424894 A/G - C T CT + Kukri_c17561_1186 chr3B 675042401 T/C - G A CT - BS00026264_51 chr3B 675586020 T/G - A C AC + BS00093891_51 chr3B 676614758 T/C + C T AG - BS00083391_51 chr3B 687760612 A/C + C A AC + BobWhite_c40861_320 chr3B 687760635 T/C + C T CT + BS00022512_51 chr3B 687760635 T/C + C T AG - CAP12_c2400_438 chr3B 687760886 A/G + G A AG + CAP8_c674_126 chr3B 687761064 A/G - T C CT + IACX3426 chr3B 688385350 T/C - G A CT - BS00058272_51 chr3B 689167546 T/C + T C CT + Excalibur_c47250_726 chr3B 689512556 T/C + C T AG - TA003701-0787 chr3B 689684047 A/C NA NA NA AC NA flanks do not match reference at this position tplb0062a17_679 chr3B 690112743 T/C - G A CT - TA005260-0974 chr3B 690856457 A/G + A G AG + Excalibur_c24617_131 chr3B 690858049 A/C - T G AC - RAC875_rep_c74125_1150 chr3B 691267182 A/G - T C AG - Ku_c46571_2627 chr3B 691267619 A/G - T C AG - Ku_c46571_2583 chr3B 691267663 A/G - C T AG - GENE-2119_131 chr3B 691268297 T/G - C A AC + GENE-1739_321 chr3B 691747468 T/C - A G AG + IAAV3736 chr3B 691749981 A/C + C A GT - BobWhite_c10476_790 chr3B 691750249 A/G + A G AG + IAAV8080 chr3B 692221221 T/C - G A AG + Ra_c1891_435 chr3B 692221221 A/G + G A AG + IAAV3903 chr3B 692835837 T/G - A C AC + Kukri_c96922_98 chr3B 693467770 A/G - T C CT + Excalibur_c46437_169 chr3B 693645517 T/C - G A CT - RAC875_c26639_367 chr3B 694034135 T/C + C T AG - BS00047796_51 chr3B 694324638 A/G - C T CT + RAC875_c12200_57 chr3B 696738744 A/G + A G AG + BS00109764_51 chr3B 696778655 A/G + G A AG + Kukri_c12361_180 chr3B 697901675 T/C + T C CT + Kukri_c12361_641 chr3B 697902134 T/C + T C AG - RAC875_c583_1796 chr3B 697902584 A/G + G A AG + Kukri_c5541_204 chr3B 698613337 T/C + C T CT + Kukri_c4335_775 chr3B 698620679 A/G - T C CT + IAAV1797 chr3B 699693952 A/G + A G CT - Excalibur_c61191_77 chr3B 699694301 T/C - G A CT - Excalibur_c18172_2498 chr3B 700368426 T/G - C A GT - Excalibur_c18172_2105 chr3B 700368819 A/C - G T AC - Excalibur_c32708_86 chr3B 700793486 T/C + C T AG - IAAV8554 chr3B 702361876 A/G - C T CT + Kukri_c14832_407 chr3B 702694484 T/C - A G CT - BobWhite_rep_c66990_212 chr3B 705003622 A/G - C T CT + Excalibur_c8998_469 chr3B 705003622 T/C + C T CT + BS00009549_51 chr3B 705817220 A/G - C T AG - BobWhite_c7281_328 chr3B 705817348 T/C + T C AG - Kukri_rep_c116233_130 chr3B 707415828 T/C + T C CT + Kukri_rep_c106420_312 chr3B 707416040 T/C - A G CT - Excalibur_c15516_1105 chr3B 707441472 T/C + C T CT + RAC875_c20973_109 chr3B 707441536 A/G + G A CT - RAC875_c17269_541 chr3B 708492818 T/C NA NA NA CT NA flanks do not match reference at this position GENE-3543_165 chr3B 708492938 T/C + C T AG - BobWhite_c40305_243 chr3B 708516788 A/G + G A CT - CAP11_c797_273 chr3B 710382230 T/G + T G GT + BobWhite_c22794_111 chr3B 710977079 T/C + T C CT + BobWhite_c22794_470 chr3B 710977438 T/C + T C AG - Excalibur_c38785_222 chr3B 715892041 T/C + T C CT + Ra_c29672_518 chr3B 718289896 A/G + A G AG + Excalibur_c60319_127 chr3B 718693279 A/G - C T AG - IAAV4125 chr3B 719088800 A/C + C A AC + RAC875_c19810_278 chr3B 719088800 T/G - C A GT - RAC875_rep_c77521_194 chr3B 719778436 T/G NA NA NA AC NA flanks do not match reference at this position BobWhite_rep_c53007_100 chr3B 720218020 A/G NA NA NA CT NA flanks do not match reference at this position IACX7527 chr3B 721041719 T/C - G A CT - RAC875_c2879_2784 chr3B 721061504 T/C - A G AG + Tdurum_contig21756_137 chr3B 721071723 A/G + A G CT - BobWhite_c40244_73 chr3B 723030848 A/G + G A CT - BS00090599_51 chr3B 723443994 T/C - G A CT - BS00022025_51 chr3B 723444204 T/C - A G AG + GENE-1737_27 chr3B 723445028 T/C - G A AG + IAAV1606 chr3B 723503973 A/G - T C CT + Excalibur_c19367_76 chr3B 723504291 A/G + A G AG + BS00097541_51 chr3B 723506621 T/C - A G AG + IACX3169 chr3B 723648363 T/G - A C GT - Excalibur_c3341_519 chr3B 723789582 T/C + T C AG - BobWhite_c2937_1426 chr3B 724738449 T/C - A G CT - GENE-1511_622 chr3B 724738842 A/G + G A CT - RAC875_c35720_456 chr3B 724750625 T/G - C A GT - RAC875_c35720_229 chr3B 724750853 T/C - G A AG + Tdurum_contig20632_210 chr3B 724926212 T/C - A G CT - RAC875_c5739_1262 chr3B 724933733 A/G - T C CT + BobWhite_rep_c49274_425 chr3B 725707468 A/G - T C CT + CAP7_c2116_545 chr3B 725708202 T/C - A G CT - Excalibur_c30705_574 chr3B 727319159 A/C - T G AC - Excalibur_c20392_1075 chr3B 727323278 A/G + A G AG + Excalibur_c54205_320 chr3B 728904734 A/C - G T GT + IAAV4835 chr3B 728919137 A/G + A G AG + Kukri_rep_c112440_422 chr3B 728919759 A/G - T C CT + BS00047204_51 chr3B 729003257 T/C - A G CT - RAC875_rep_c69917_755 chr3B 729209475 A/G + G A AG + RAC875_c30507_292 chr3B 730235358 A/G + A G AG + Ku_c13676_1074 chr3B 730285411 T/G + G T GT + RAC875_c403_2247 chr3B 730309957 A/C - T G GT + Excalibur_c27120_789 chr3B 730344943 A/G + A G AG + Excalibur_c2850_126 chr3B 731263288 T/C + T C AG - Tdurum_contig28748_264 chr3B 732433180 T/C - G A AG + Excalibur_c82500_491 chr3B 732826885 T/C + C T AG - BS00099633_51 chr3B 734144009 T/G - C A GT - Excalibur_rep_c66942_58 chr3B 734430792 A/G - C T CT + BobWhite_c6015_141 chr3B 735381383 T/C - A G AG + Tdurum_contig8365_433 chr3B 736672399 A/C - T G AC - BobWhite_c33344_143 chr3B 736673223 T/C - A G CT - BobWhite_c1895_1953 chr3B 736711821 A/G - T C CT + IAAV5302 chr3B 737764637 T/C - A G AG + Ra_c14132_2575 chr3B 737764637 A/G + A G AG + Ra_c14132_2930 chr3B 737764992 A/G + A G AG + BS00064218_51 chr3B 738377396 T/G - C A GT - BS00059887_51 chr3B 738380143 A/G - T C AG - Excalibur_c35203_334 chr3B 738591266 T/C + T C CT + Kukri_c13345_481 chr3B 738699260 A/G - T C AG - BS00060666_51 chr3B 738752368 T/C - G A AG + Excalibur_rep_c111619_82 chr3B 739166525 T/C + C T AG - BS00072993_51 chr3B 739167926 T/C + T C CT + BS00072994_51 chr3B 739167938 A/G + A G AG + Excalibur_rep_c111619_724 chr3B 739170266 T/C + C T CT + Tdurum_contig93431_485 chr3B 739170620 T/C - A G AG + Tdurum_contig48528_144 chr3B 740040730 T/C + C T CT + Tdurum_contig48528_320 chr3B 740042528 T/C + T C CT + Tdurum_contig43498_519 chr3B 741303889 A/G - C T CT + BS00040742_51 chr3B 741304119 A/G + G A CT - Tdurum_contig69073_365 chr3B 741467175 T/C + C T AG - Kukri_c41129_344 chr3B 744730504 A/C + A C AC + BS00059416_51 chr3B 745289790 T/C + C T AG - Kukri_rep_c94476_152 chr3B 745714161 T/C + C T CT + Kukri_c66862_96 chr3B 746375003 T/C - A G CT - Ra_c16246_379 chr3B 747712272 A/G + G A CT - Excalibur_c5309_286 chr3B 747801193 A/G - C T AG - Excalibur_c50230_107 chr3B 749140341 A/G + G A CT - BS00077967_51 chr3B 749555162 A/C + C A AC + Excalibur_c36070_300 chr3B 749762533 A/G - T C CT + tplb0044b20_1610 chr3B 750137876 T/C + T C CT + BS00038349_51 chr3B 750138234 T/C + C T CT + Tdurum_contig61601_159 chr3B 750355852 A/G + G A AG + BS00085434_51 chr3B 750357915 T/C + C T CT + BS00105878_51 chr3B 750361340 T/C - G A CT - CAP7_c3746_137 chr3B 750361366 T/C + C T CT + Tdurum_contig32277_121 chr3B 750863381 A/C - G T GT + Excalibur_c18410_136 chr3B 752091310 T/C - G A CT - Excalibur_rep_c102300_102 chr3B 752092527 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_c602_523 chr3B 754810527 A/C + C A GT - RAC875_c18814_720 chr3B 755171762 T/C + T C CT + Tdurum_contig82231_204 chr3B 755324110 A/G - C T CT + Excalibur_rep_c97324_623 chr3B 756614001 T/C + C T AG - BS00099738_51 chr3B 759168681 A/G + G A AG + BS00057988_51 chr3B 759170505 A/G + A G CT - RAC875_c24504_119 chr3B 760136266 T/C + C T CT + GENE-1785_118 chr3B 760136494 T/C + T C AG - GENE-1785_626 chr3B 760136661 T/C - A G CT - BS00063624_51 chr3B 760578628 T/C - A G AG + Kukri_c17467_2711 chr3B 761576688 T/C - G A CT - BS00030651_51 chr3B 764694026 T/C + C T AG - Kukri_rep_c104399_156 chr3B 764696186 A/G + G A CT - BobWhite_c3721_224 chr3B 765059806 T/C NA NA NA AG NA flanks do not match reference at this position Jagger_c528_56 chr3B 765393234 A/C + C A GT - Tdurum_contig60330_126 chr3B 765394338 A/G - C T CT + Excalibur_c50953_96 chr3B 765923557 A/G - T C AG - GENE-0361_416 chr3B 769469154 A/G + G A AG + BS00068473_51 chr3B 769485323 A/G - T C AG - Tdurum_contig45817_193 chr3B 771132441 A/G + A G CT - BS00022861_51 chr3B 772399643 A/G + G A AG + RFL_Contig4186_852 chr3B 772399790 A/G + A G CT - Tdurum_contig59953_282 chr3B 772399790 T/C - A G CT - Tdurum_contig47776_377 chr3B 772664088 T/C + C T AG - BS00024496_51 chr3B 776031904 T/C + C T CT + BS00070210_51 chr3B 778277426 T/G - A C GT - BS00066806_51 chr3B 778679651 A/G + G A AG + BS00024883_51 chr3B 779135909 T/C + C T CT + BS00023017_51 chr3B 779366910 T/G + T G AC - RFL_Contig4792_379 chr3B 779541319 A/G + G A CT - CAP11_c59_418 chr3B 779542307 T/C + T C CT + CAP8_c42_161 chr3B 779542612 A/C - G T AC - RAC875_c24972_708 chr3B 779544967 A/G + A G CT - BS00056737_51 chr3B 779577805 A/G - C T AG - TA006103-0916 chr3B 781553302 T/C NA NA NA CT NA flanks do not match reference at this position TA006289-1238 chr3B 782112873 T/C + T C CT + Kukri_rep_c68685_795 chr3B 784554456 T/G - A C AC + BS00035190_51 chr3B 785551448 T/C + T C AG - BobWhite_c4103_79 chr3B 785551545 T/C - G A CT - BobWhite_c23937_453 chr3B 794865479 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c16703_430 chr3B 795333440 A/G - C T AG - RAC875_c24401_277 chr3B 795570699 T/C + C T AG - BS00071598_51 chr3B 796001785 A/C - G T AC - BS00071597_51 chr3B 796001790 T/G - C A GT - BS00074629_51 chr3B 796007536 T/C - A G AG + RAC875_rep_c111219_73 chr3B 796017042 T/G - C A AC + Tdurum_contig28053_218 chr3B 796018762 T/C + T C AG - RAC875_c2340_616 chr3B 796313530 A/G + G A AG + Excalibur_c15095_831 chr3B 796315702 T/C + C T CT + Excalibur_c15095_852 chr3B 796315723 A/G + A G CT - GENE-2712_367 chr3B 796464468 T/G + T G AC - GENE-2712_428 chr3B 796464521 T/C + C T AG - Tdurum_contig99764_139 chr3B 796651733 T/G + G T AC - Tdurum_contig99764_256 chr3B 796652156 T/C + C T AG - CAP12_c1468_114 chr3B 798164542 T/G - C A AC + Tdurum_contig9738_170 chr3B 798348318 T/C - A G AG + RAC875_c17373_848 chr3B 798503427 T/C - G A CT - RAC875_c68392_200 chr3B 798549466 T/G - A C AC + Jagger_c3839_60 chr3B 798549518 A/G + A G AG + RAC875_c68392_137 chr3B 798549529 A/C - G T AC - Kukri_c23955_144 chr3B 798549646 A/G + A G CT - IAAV5266 chr3B 798549677 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c23148_680 chr3B 798550424 T/G - A C GT - RAC875_c35672_73 chr3B 798550712 T/C + C T AG - RAC875_c35672_136 chr3B 798550775 A/G + A G AG + RAC875_c35672_205 chr3B 798550844 A/G + G A CT - RAC875_c35672_336 chr3B 798550975 T/C + C T CT + BS00065873_51 chr3B 801296650 T/C + C T CT + TA003797-0888 chr3B 803200706 A/G - T C CT + Kukri_c58054_59 chr3B 804671574 A/G - T C AG - RAC875_c10909_1180 chr3B 805643345 A/G + G A AG + RAC875_c5606_501 chr3B 807382780 A/G + A G AG + RFL_Contig5153_958 chr3B 808877689 A/G - T C AG - Excalibur_c63009_102 chr3B 809832553 A/G - C T AG - IAAV5507 chr3B 810327810 A/G + G A AG + BobWhite_c2486_239 chr3B 810329118 T/C - G A AG + Tdurum_contig47292_302 chr3B 810561057 T/G + G T GT + Kukri_c7860_911 chr3B 815046481 A/G - T C AG - RAC875_c66953_100 chr3B 815048857 T/C + C T CT + RAC875_c35074_452 chr3B 816607530 A/G + G A CT - BobWhite_c45118_495 chr3B 818275897 A/G - T C AG - BS00079029_51 chr3B 819503172 T/C + T C CT + Kukri_c29615_377 chr3B 819789521 A/G - T C AG - RAC875_c2106_882 chr3B 819860429 A/G - T C AG - BS00104177_51 chr3B 819860810 T/C - G A AG + BobWhite_c11000_1049 chr3B 819897386 T/G - C A GT - Kukri_rep_c114164_106 chr3B 820288799 T/C + C T AG - Kukri_c49220_167 chr3B 820288967 A/G + A G CT - RAC875_c37741_218 chr3B 820500837 T/C + T C CT + RAC875_c33083_451 chr3B 820503368 A/G + A G AG + RAC875_c5222_59 chr3B 820794040 T/G + G T AC - GENE-1618_780 chr3B 820894421 T/C - A G AG + CAP7_c3438_196 chr3B 821089312 A/C - G T GT + BS00091257_51 chr3B 822189314 A/C - T G AC - Tdurum_contig51605_542 chr3B 822681495 A/G - C T CT + Tdurum_contig51605_137 chr3B 822682132 A/G - T C CT + Tdurum_contig27982_568 chr3B 822884720 A/G + G A AG + Tdurum_contig59566_4435 chr3B 822969635 A/C - T G AC - Tdurum_contig59566_2309 chr3B 822971761 T/G - A C AC + Kukri_c55981_194 chr3B 822972117 A/C + C A GT - Tdurum_contig59566_1534 chr3B 822972536 T/C - A G CT - BS00063160_51 chr3B 825315063 A/G - T C AG - IAAV8659 chr3B 826082235 A/C + C A GT - IAAV1595 chr3B 826084813 T/C + C T CT + Kukri_c11814_425 chr3B 826096324 T/C + T C CT + BobWhite_rep_c50492_500 chr3B 826726043 T/C + T C CT + BS00073411_51 chr3B 829197946 T/G - A C AC + BS00074345_51 chr3B 829203687 T/C + C T AG - Kukri_c48601_98 chr3B 829541512 T/C - G A AG + BS00108577_51 chr3D 773159 A/G + A G CT - Excalibur_c20559_98 chr3D 774409 A/C + C A GT - tplb0050o09_895 chr3D 1110781 A/G + A G CT - Kukri_c88294_60 chr3D 1754484 A/G + A G AG + Kukri_c32803_217 chr3D 2242934 T/G + T G GT + Excalibur_c48057_110 chr3D 2449010 T/C - A G CT - Excalibur_c57482_242 chr3D 2595456 T/C + T C CT + Kukri_c23591_522 chr3D 2622459 T/G + T G AC - BS00080151_51 chr3D 2625688 A/C + A C GT - Kukri_rep_c117022_97 chr3D 2625900 T/C - A G CT - Tdurum_contig50954_880 chr3D 2626062 T/C - A G CT - RAC875_c29099_1366 chr3D 2626268 A/G - T C AG - RAC875_c62483_112 chr3D 2626337 A/G - T C CT + Excalibur_rep_c69004_1008 chr3D 2626510 A/G - T C AG - BS00011516_51 chr3D 2627219 A/G + G A CT - Kukri_rep_c94244_223 chr3D 3234491 A/G - T C CT + BobWhite_c18256_158 chr3D 3298609 A/G + A G CT - BobWhite_c18256_809 chr3D 3300046 T/C + T C CT + Kukri_c41361_186 chr3D 3338149 A/G + A G CT - Kukri_c12401_90 chr3D 4394659 T/G + G T AC - Kukri_c12401_301 chr3D 4394870 T/C + C T AG - Kukri_c1183_250 chr3D 4408743 T/C - A G CT - Excalibur_c11824_103 chr3D 4486783 A/G - T C AG - Excalibur_rep_c67048_452 chr3D 4487799 T/C - A G CT - RAC875_c13585_778 chr3D 5614652 T/C + C T AG - Excalibur_c62042_175 chr3D 6335188 T/G + G T GT + Excalibur_c27288_413 chr3D 7028442 T/C + C T AG - BS00004149_51 chr3D 8336561 T/C - NA NA AG NA reference base C not among SNP alleles Kukri_c15388_1205 chr3D 8697408 A/G - C T CT + GENE-1851_76 chr3D 8973187 A/G - C T AG - RAC875_c76611_364 chr3D 9632416 A/G - T C CT + RAC875_c18570_893 chr3D 9740114 A/G NA NA NA AG NA flanks do not match reference at this position BS00063245_51 chr3D 10518065 A/G + A G AG + GENE-1856_756 chr3D 11750482 A/C - T G GT + GENE-1579_18 chr3D 11761381 T/C NA NA NA AG NA flanks do not match reference at this position IACX8266 chr3D 11762489 A/T + A T AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Kukri_c2263_380 chr3D 13663963 T/G - C A AC + BS00064077_51 chr3D 15029534 A/G - C T CT + Kukri_c13830_487 chr3D 16055245 A/G + A G CT - RFL_Contig2471_119 chr3D 17413894 T/C - A G CT - BS00039852_51 chr3D 18881154 T/C + T C CT + RAC875_c5799_224 chr3D 19885883 T/C - A G CT - BS00093856_51 chr3D 22047445 T/C - A G AG + BS00093857_51 chr3D 22047707 A/G - C T AG - BS00038834_51 chr3D 22280299 A/G - C T CT + Excalibur_c79902_439 chr3D 22283478 A/G + A G AG + BS00095640_51 chr3D 22680123 A/C - G T GT + BS00095638_51 chr3D 22680295 A/G - C T AG - BobWhite_c2957_369 chr3D 26683458 A/G - T C CT + D_contig79290_372 chr3D 29706731 T/C + C T CT + Kukri_c2118_264 chr3D 39533156 A/C + A C AC + Kukri_rep_c85024_274 chr3D 40527301 T/C + T C CT + GENE-1674_631 chr3D 42094333 T/C - A G CT - RAC875_rep_c109320_139 chr3D 44194189 T/C + T C CT + IAAV6689 chr3D 44195652 A/G + A G AG + GENE-1587_448 chr3D 47190520 T/C + C T CT + Excalibur_c14608_261 chr3D 48444134 T/C - G A CT - GENE-4774_69 chr3D 64200505 T/C + C T CT + RFL_Contig5276_1756 chr3D 73898148 T/C + C T CT + RAC875_c15722_1081 chr3D 76920660 A/G + A G AG + BS00068485_51 chr3D 94239561 A/G + G A CT - Excalibur_c10470_1066 chr3D 107436468 A/G + A G CT - RAC875_c63814_251 chr3D 118536819 T/C - G A AG + RAC875_rep_c111455_130 chr3D 121696353 T/C + T C AG - Excalibur_rep_c114833_645 chr3D 132161971 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_rep_c116073_259 chr3D 138194078 A/G + G A CT - Kukri_c24392_115 chr3D 138889389 T/C + T C CT + Kukri_c128_877 chr3D 152487388 A/G - C T AG - D_GCE8AKX02H1T6A_80 chr3D 157550131 A/G + G A AG + GENE-1538_107 chr3D 161711440 A/G - T C CT + Kukri_c32802_706 chr3D 162512249 A/G - T C AG - BS00068556_51 chr3D 164218615 T/G - C A GT - Tdurum_contig26727_267 chr3D 165737653 A/G + A G AG + Ku_c22692_1021 chr3D 167770732 T/C + T C CT + Kukri_c43208_335 chr3D 175404753 A/G - T C AG - D_F5XZDLF01DJCC4_342 chr3D 199123704 T/C - A G AG + Ra_c10284_405 chr3D 209687062 T/C + T C CT + Kukri_rep_c109210_417 chr3D 234602543 T/G - C A AC + GENE-1668_295 chr3D 248536013 A/G - T C CT + GENE-2117_311 chr3D 261737431 T/C + C T AG - BobWhite_c10896_923 chr3D 264143223 A/G + G A AG + RAC875_c1197_286 chr3D 269284318 T/C + T C AG - BobWhite_rep_c66950_351 chr3D 269286107 T/C + T C CT + RAC875_rep_c75748_172 chr3D 275998125 A/G + G A AG + Kukri_c31733_290 chr3D 323719187 A/G - T C AG - D_contig57690_497 chr3D 335214335 T/C - A G CT - Ra_c4231_465 chr3D 340684070 T/C - G A CT - RFL_Contig304_729 chr3D 349636012 T/C + T C AG - GENE-1781_719 chr3D 349636369 T/C - A G AG + Kukri_rep_c71523_81 chr3D 351129692 A/C - G T AC - BS00062645_51 chr3D 355428521 A/G + G A AG + BobWhite_c17212_805 chr3D 360399155 T/C + T C AG - IAAV5687 chr3D 360869077 T/C + C T CT + Excalibur_c13242_1178 chr3D 362199514 A/G + A G AG + BobWhite_c5968_868 chr3D 363858849 T/C - G A AG + GENE-1966_110 chr3D 369799905 T/C - A G CT - IAAV1270 chr3D 374356675 T/C - G A AG + RAC875_c10203_2620 chr3D 386432232 A/G + A G CT - IAAV3488 chr3D 390411034 A/C + A C GT - Excalibur_c55621_291 chr3D 392056583 A/G - C T AG - Ra_c5515_1723 chr3D 394754616 T/C + T C CT + GENE-1624_198 chr3D 394913454 A/C - G T GT + GENE-1624_193 chr3D 394913455 A/G - T C AG - D_contig22919_290 chr3D 394914092 A/G + G A AG + Excalibur_c29205_537 chr3D 395079265 A/G - T C CT + GENE-3939_653 chr3D 410520869 A/G - C T AG - GENE-3939_576 chr3D 410520942 T/C - G A AG + GENE-2087_300 chr3D 415159108 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c4310_489 chr3D 418215546 A/G + G A AG + GENE-1469_196 chr3D 421318922 T/C - G A AG + GENE-1805_135 chr3D 422479578 T/G - A C GT - GENE-1805_65 chr3D 422479644 T/C - G A CT - IAAV8924 chr3D 422479926 T/C + C T CT + BS00011869_51 chr3D 426452313 A/G - C T AG - Kukri_c82117_279 chr3D 426925219 A/G - C T CT + GENE-1455_114 chr3D 427225131 A/G + A G AG + RAC875_rep_c117959_132 chr3D 427809978 A/C NA NA NA AC NA flanks do not match reference at this position BobWhite_c13099_755 chr3D 433743468 A/G + G A CT - D_GCE8AKX01C0776_247 chr3D 435648140 A/G - C T AG - BobWhite_c5605_195 chr3D 441147674 T/G + G T GT + RAC875_c50661_279 chr3D 443708107 T/G - A C AC + Kukri_rep_c73421_540 chr3D 445298013 T/G - A C GT - IAAV3838 chr3D 446849095 T/C - A G CT - GENE-1687_367 chr3D 450293455 T/C - A G AG + IACX7741 chr3D 455871281 T/C - A G AG + GENE-1617_188 chr3D 456632715 A/G - T C AG - GENE-1617_131 chr3D 456632768 A/G - T C CT + Excalibur_c85790_65 chr3D 456911889 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c28912_306 chr3D 460499860 A/G - T C AG - TA013009-0365 chr3D 463689441 A/G NA NA NA CT NA flanks do not match reference at this position BS00021909_51 chr3D 490839620 A/G - NA NA AG NA reference base A not among SNP alleles GENE-1634_405 chr3D 498882478 A/G + A G CT - BS00065107_51 chr3D 499582732 A/C + C A AC + GENE-1929_91 chr3D 502962329 A/C - G T AC - Excalibur_c31960_1492 chr3D 506174701 A/G - T C AG - IACX8336 chr3D 507029080 A/C + C A GT - RAC875_c24267_258 chr3D 507029514 A/G - C T CT + Kukri_c15102_505 chr3D 507043481 T/C - A G CT - Kukri_c8913_655 chr3D 512675121 T/C + T C CT + Ku_c172_840 chr3D 514920631 A/G + A G CT - BS00065701_51 chr3D 515699903 A/G - C T AG - BS00049637_51 chr3D 515749282 T/C + T C CT + BS00017988_51 chr3D 518152035 T/C - G A AG + BobWhite_c37216_572 chr3D 522778831 T/C + T C AG - RAC875_c16625_182 chr3D 523159202 A/G - C T CT + RAC875_c17735_569 chr3D 523812054 A/G NA NA NA AG NA flanks do not match reference at this position IAAV5136 chr3D 524870464 T/C + T C AG - BobWhite_c21589_200 chr3D 526047082 A/C + C A GT - GENE-1549_110 chr3D 526049437 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_rep_c72702_220 chr3D 527668588 A/G + A G CT - IACX20464 chr3D 545914600 A/G - NA NA CT NA reference base G not among SNP alleles RAC875_c101793_136 chr3D 547625537 A/G + G A CT - IAAV5984 chr3D 549515601 A/G NA NA NA AG NA flanks do not match reference at this position Jagger_c522_55 chr3D 550649003 T/G + T G AC - IACX1049 chr3D 551981733 T/C - G A CT - D_GDRF1KQ02GV96X_70 chr3D 552950372 A/G + G A AG + IACX7129 chr3D 552953384 T/C + C T CT + GENE-4927_846 chr3D 560107957 A/G - T C CT + RAC875_rep_c79167_809 chr3D 561455598 T/C + T C CT + IAAV8127 chr3D 562700343 T/G - C A AC + RAC875_c6062_75 chr3D 562700343 A/C + C A AC + Tdurum_contig61601_447 chr3D 562709360 T/C + T C CT + D_GA8KES402JVT1Y_74 chr3D 571550471 A/G + A G AG + Kukri_s110037_62 chr3D 575526404 T/C + T C AG - GENE-1833_70 chr3D 576568332 A/G - C T AG - CAP12_c2615_128 chr3D 578414376 A/G - T C AG - Kukri_c8099_1522 chr3D 583934703 A/G NA NA NA AG NA flanks do not match reference at this position BS00064227_51 chr3D 586200801 A/C + A C GT - Tdurum_contig55841_351 chr3D 587441718 T/C + C T AG - GENE-2405_141 chr3D 593222411 A/C - G T AC - Excalibur_c26349_503 chr3D 593440631 A/G - C T AG - GENE-1776_104 chr3D 593762055 A/G - T C CT + GENE-1776_40 chr3D 593762115 A/G - C T CT + GENE-1799_345 chr3D 593999785 T/C - A G AG + BS00063214_51 chr3D 594808176 T/C + C T CT + BobWhite_c42020_456 chr3D 595023944 T/C + T C AG - BS00023079_51 chr3D 595062861 T/C - A G AG + Kukri_c9001_345 chr3D 595070730 A/G - T C AG - Excalibur_rep_c101455_842 chr3D 595109882 A/G - T C AG - BS00088958_51 chr3D 595110546 T/C - A G AG + D_contig62053_349 chr3D 595681369 T/C + C T AG - D_GBF1XID01ETBRB_172 chr3D 596088741 A/G + A G AG + Kukri_c2289_635 chr3D 596718200 A/G - C T AG - Excalibur_c13336_670 chr3D 596915153 A/G + A G CT - BS00021919_51 chr3D 596916300 T/C - A G CT - Kukri_rep_c110158_202 chr3D 598011578 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_rep_c72275_185 chr3D 598012320 T/C + T C CT + BS00061125_51 chr3D 600261870 A/G - C T AG - Kukri_c4636_1032 chr3D 600413120 A/G + G A CT - CAP7_c4219_186 chr3D 601918251 A/G + A G AG + Kukri_c14943_753 chr3D 602797531 T/C + C T CT + RAC875_c5433_682 chr3D 603264120 A/G - C T CT + D_F1BEJMU01DVMII_118 chr3D 603380401 A/G - T C AG - RAC875_c31922_138 chr3D 603414487 T/C - A G AG + Kukri_c43464_89 chr3D 603414586 T/C - G A AG + D_contig15178_246 chr3D 603974674 T/C - A G AG + CAP12_rep_c3953_177 chr3D 604304060 A/G + A G CT - RAC875_c61950_1644 chr3D 604355667 A/G - T C AG - JD_c7714_966 chr3D 604400077 A/G - T C CT + RAC875_c63331_327 chr3D 604666729 A/G - T C CT + Kukri_c46716_211 chr3D 604864380 T/C - A G AG + Excalibur_c3556_520 chr3D 606299213 A/G + G A CT - Jagger_c367_427 chr3D 607091870 A/G + A G AG + GENE-1934_501 chr3D 607096479 A/G - T C AG - GENE-1925_118 chr3D 609364238 T/C + C T AG - BS00073760_51 chr3D 609923586 T/C - A G AG + BobWhite_rep_c52911_146 chr3D 610139401 T/C - A G CT - IAAV7013 chr3D 610346328 T/C + C T CT + BS00065603_51 chr3D 611497265 T/C + C T CT + RFL_Contig3966_1511 chr3D 613387721 A/G + A G AG + CAP11_c1051_121 chr3D 613390200 A/C - G T GT + Ku_c9895_1750 chr3D 613481128 A/G + A G AG + GENE-1910_113 chr3D 613601934 A/G + G A AG + Excalibur_c46790_502 chr3D 613618903 T/C - A G AG + BS00087693_51 chr3D 613621949 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_rep_c87658_1542 chr3D 613695974 A/G - C T AG - Excalibur_c54670_110 chr3D 613700075 A/G + G A CT - RAC875_c51595_177 chr3D 613700533 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c19514_1602 chr3D 613734623 A/G - C T CT + Excalibur_c15009_1082 chr3D 613735363 T/G + T G AC - Excalibur_c15009_1129 chr3D 613735410 T/G + T G GT + RAC875_c43838_146 chr3D 613782554 A/C + A C AC + Excalibur_c56069_128 chr3D 613783016 T/C + C T AG - RFL_Contig2432_953 chr3D 614202474 T/G - C A AC + BS00042131_51 chr3D 614366352 T/C - A G AG + BS00078532_51 chr3D 614366870 A/G + A G AG + BS00078092_51 chr3D 614367043 A/G + G A AG + BS00078098_51 chr3D 614367160 T/G + T G GT + D_GBF1XID02HLMWB_65 chr3D 614637287 A/G + G A AG + JD_c21248_511 chr4A 2791017 T/C - G A CT - BS00074614_51 chr4A 2989817 A/G + A G AG + BS00035307_51 chr4A 3381284 T/C - A G CT - BS00021716_51 chr4A 3442842 T/C - G A CT - BS00106545_51 chr4A 3445106 A/G - T C AG - Ku_c2478_227 chr4A 3868729 A/C - T G GT + IAAV2216 chr4A 4595409 A/C - G T AC - BS00069271_51 chr4A 4620085 A/G + G A AG + Excalibur_c320_431 chr4A 5464136 T/G + T G AC - Kukri_c1784_129 chr4A 5464358 T/C + T C AG - BobWhite_c47359_73 chr4A 5835599 T/C - G A AG + BS00043286_51 chr4A 7404947 A/G + A G AG + Tdurum_contig41185_259 chr4A 11319050 T/C + C T CT + BS00065863_51 chr4A 12208796 T/G - C A GT - BS00018120_51 chr4A 12402497 T/C + T C CT + IACX1035 chr4A 13655295 T/C + C T AG - Tdurum_contig10595_633 chr4A 13656290 T/C - A G AG + Excalibur_c17420_213 chr4A 14022182 T/C NA NA NA CT NA flanks do not match reference at this position Ku_c7594_1179 chr4A 16967067 T/C - A G AG + Ex_c7626_444 chr4A 16967638 A/G + A G AG + Ra_c74035_586 chr4A 16968002 A/G + A G AG + Ex_c883_2618 chr4A 17259209 T/C - G A AG + Ku_c22706_1527 chr4A 17261244 A/G + A G AG + RAC875_c1377_428 chr4A 17261481 A/G - T C AG - Kukri_rep_c101034_516 chr4A 21064253 A/G + A G CT - Ku_c16392_2687 chr4A 21211527 T/G - A C AC + Kukri_c53787_620 chr4A 21212673 A/C - T G GT + IACX3391 chr4A 21635914 A/G - C T CT + BS00021752_51 chr4A 24757355 A/C - G T AC - Tdurum_contig8061_56 chr4A 24764252 T/C - A G CT - Tdurum_contig30942_179 chr4A 24943135 T/C - G A CT - RAC875_c32657_295 chr4A 25201277 T/C - G A AG + Ku_c3891_395 chr4A 27673149 T/C - G A CT - Ku_c766_2292 chr4A 27673654 A/C - T G AC - Ku_c766_1798 chr4A 27674148 A/G - T C AG - RAC875_c28178_889 chr4A 28563674 T/C + C T CT + Excalibur_c40618_182 chr4A 29069840 A/G + A G CT - Tdurum_contig11919_360 chr4A 29069840 T/C - A G CT - BS00022015_51 chr4A 29077859 T/C - G A AG + Tdurum_contig33628_85 chr4A 29077859 A/G + G A AG + BS00089283_51 chr4A 29077903 A/G - T C AG - Tdurum_contig33628_129 chr4A 29077903 T/C + T C AG - BS00065607_51 chr4A 29793110 A/G + A G CT - Kukri_c16916_1073 chr4A 30290552 T/C - G A CT - GENE-2361_194 chr4A 30397789 T/G + G T AC - RAC875_c54178_90 chr4A 37047678 T/C - A G CT - BS00011060_51 chr4A 37049023 A/G + A G CT - Kukri_c22231_87 chr4A 37061723 A/G - T C AG - RAC875_c754_120 chr4A 38006546 T/C + C T CT + BobWhite_c5633_59 chr4A 38369380 A/G - T C AG - IAAV3697 chr4A 38369380 T/C + T C AG - BobWhite_rep_c66057_98 chr4A 38369643 A/C - T G GT + IAAV4754 chr4A 40442420 A/G - T C AG - Excalibur_c13276_1322 chr4A 40443646 A/G + A G AG + BS00011173_51 chr4A 40879371 A/G - T C AG - BS00110459_51 chr4A 41946152 A/G - C T AG - Ex_c103504_760 chr4A 41972436 T/C - G A CT - BS00040668_51 chr4A 43231880 A/G - C T CT + BS00022125_51 chr4A 43698829 T/C - G A CT - Tdurum_contig9906_89 chr4A 45109731 A/G - T C CT + BS00009970_51 chr4A 45338276 T/C + C T CT + BS00004170_51 chr4A 46050026 T/C + C T CT + Ku_c3686_52 chr4A 46123520 A/G + A G CT - Ra_c492_1845 chr4A 46123520 T/C - A G CT - BS00068244_51 chr4A 46125561 A/G - T C CT + Tdurum_contig13140_69 chr4A 59321657 A/C - G T GT + Ra_c7973_1185 chr4A 60043162 T/C + C T CT + Kukri_c6199_1183 chr4A 60352541 A/G - T C AG - Excalibur_c10673_118 chr4A 66145543 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c13260_348 chr4A 66146752 T/G - C A GT - Ra_c64313_1337 chr4A 67173347 A/C - T G GT + RFL_Contig1053_65 chr4A 68470282 T/C - G A CT - RAC875_c14911_1282 chr4A 68561974 T/C - A G CT - Excalibur_c10390_104 chr4A 68565670 T/G - C A AC + BobWhite_c32217_147 chr4A 71253494 T/C + C T CT + Kukri_c46421_168 chr4A 75919497 T/C + T C AG - Kukri_c4559_278 chr4A 80168426 T/G - A C GT - GENE-2875_113 chr4A 81819110 A/G + G A CT - BobWhite_c31621_148 chr4A 82739599 A/G + G A AG + tplb0060i01_819 chr4A 83321447 T/C - A G AG + RFL_Contig5626_821 chr4A 83356558 A/G - T C AG - Ex_c41192_1307 chr4A 83757181 T/G NA NA NA GT NA flanks do not match reference at this position Kukri_c27827_296 chr4A 85577366 T/C + T C AG - CAP11_c8388_194 chr4A 87412153 T/C + C T CT + IAAV8640 chr4A 88423889 A/G + G A CT - Kukri_rep_c69658_148 chr4A 88425678 A/G - T C CT + GENE-2264_72 chr4A 88429949 A/G - T C CT + Kukri_c6954_320 chr4A 97260638 A/G - T C CT + IAAV3115 chr4A 100671966 A/G - T C AG - RAC875_rep_c70191_89 chr4A 100672554 A/G - T C AG - RAC875_rep_c69241_454 chr4A 102387645 A/G - C T AG - RAC875_c59416_158 chr4A 102387852 T/G NA NA NA GT NA flanks do not match reference at this position Kukri_c22186_502 chr4A 102633226 T/G + T G GT + Excalibur_c6644_1461 chr4A 102633330 A/G + A G AG + RAC875_c38663_2179 chr4A 103079139 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c38886_129 chr4A 104267734 T/C - A G CT - CAP8_c541_362 chr4A 104704646 A/G + A G CT - Kukri_c20631_614 chr4A 106907294 A/C + C A AC + Kukri_c12878_659 chr4A 106910425 T/C - G A CT - IACX1896 chr4A 109431746 T/G - A C AC + BobWhite_c27944_234 chr4A 109443802 A/C NA NA NA AC NA flanks do not match reference at this position RAC875_rep_c71185_473 chr4A 111168369 A/C - G T GT + RAC875_c22562_429 chr4A 111292238 A/G + A G AG + Ku_c104619_404 chr4A 111910905 A/G + G A AG + BobWhite_c3325_613 chr4A 112767699 T/C + T C AG - BobWhite_c39599_82 chr4A 113853276 A/G + A G AG + IAAV3906 chr4A 113854919 T/C + T C CT + RAC875_c18564_222 chr4A 114587604 A/C - T G GT + RAC875_rep_c108287_212 chr4A 117093151 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c8131_385 chr4A 119088047 T/C - A G CT - RFL_Contig1320_726 chr4A 119931773 T/C + C T CT + Kukri_c48155_158 chr4A 120605031 T/G - C A GT - JD_c32759_313 chr4A 123914650 A/G + A G AG + Ex_c17894_1159 chr4A 123915517 T/C + T C AG - Tdurum_contig34920_104 chr4A 125404137 A/G - T C AG - GENE-2127_317 chr4A 126140620 T/C - G A AG + RAC875_c27776_86 chr4A 129089781 A/G + A G AG + Excalibur_c19065_589 chr4A 132993982 A/G - T C CT + IAAV8784 chr4A 135358615 A/G + A G AG + tplb0035b22_184 chr4A 135614180 A/C + C A AC + RAC875_c26184_273 chr4A 136235025 T/C + T C AG - RAC875_c34232_184 chr4A 136235380 A/G - T C CT + IAAV562 chr4A 136894930 A/G - C T AG - GENE-2354_155 chr4A 138832397 T/C NA NA NA AG NA flanks do not match reference at this position TA003708-0300 chr4A 142798028 A/G - T C CT + RAC875_rep_c74695_101 chr4A 164632278 A/G NA NA NA AG NA flanks do not match reference at this position GENE-2957_288 chr4A 167749021 T/C + C T AG - RAC875_rep_c70416_332 chr4A 191120890 T/C + T C AG - TA004304-0467 chr4A 196609867 T/G - A C AC + BobWhite_c1907_124 chr4A 216145861 A/C + A C GT - Kukri_c16665_595 chr4A 252683859 T/C + C T CT + Tdurum_contig42087_1941 chr4A 277890095 A/G - C T CT + Excalibur_rep_c113950_132 chr4A 299601174 A/G - T C CT + Excalibur_c27798_1068 chr4A 312718516 A/G - C T CT + BS00067486_51 chr4A 319667235 T/C + C T CT + Kukri_c30917_250 chr4A 340792721 T/C + T C CT + BobWhite_c6035_195 chr4A 342457974 A/G - C T AG - IAAV3854 chr4A 353870708 A/G + G A CT - BobWhite_rep_c50115_136 chr4A 449270007 T/C - G A AG + RAC875_c65295_290 chr4A 454117059 A/G + G A CT - Excalibur_c10157_180 chr4A 465407696 A/G - C T CT + Ex_c5979_1449 chr4A 467297840 A/G - C T AG - tplb0051b16_1324 chr4A 473688828 A/G NA NA NA AG NA flanks do not match reference at this position Ex_c70424_465 chr4A 476980555 A/G + A G AG + Excalibur_c37564_1228 chr4A 477311183 A/G - C T AG - Excalibur_c7658_1304 chr4A 481415147 A/G + A G CT - Kukri_c61419_550 chr4A 488252138 T/C - G A CT - Ra_c45147_1600 chr4A 492891477 A/G + G A AG + RAC875_c42756_168 chr4A 495799955 T/C + T C CT + RAC875_c37611_302 chr4A 500352785 T/C + C T CT + RFL_Contig2717_860 chr4A 514430898 A/G - C T AG - CAP11_c279_66 chr4A 520126362 A/G + G A CT - IAAV1461 chr4A 525119842 T/C + C T CT + tplb0024j12_840 chr4A 537592555 T/C - A G AG + IAAV7376 chr4A 538486678 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c39882_203 chr4A 538487006 A/G - T C AG - BS00103813_51 chr4A 541340628 T/C + C T CT + IAAV125 chr4A 541340685 A/G - T C AG - Kukri_c48385_121 chr4A 541340792 A/G - T C CT + Kukri_c2634_487 chr4A 541361689 T/C - A G CT - Tdurum_contig28171_254 chr4A 541670072 T/C + C T CT + BS00044898_51 chr4A 544390969 T/C - A G AG + RAC875_c21571_172 chr4A 544608241 A/C - T G GT + BS00075739_51 chr4A 544611126 A/G - C T AG - BS00075740_51 chr4A 544611163 T/C - A G CT - BS00109736_51 chr4A 544616548 A/G - T C AG - Kukri_c23469_1194 chr4A 544617292 T/C - A G CT - TA001512-0387 chr4A 545601805 A/G + A G AG + Ra_c37920_342 chr4A 545602028 T/C + T C AG - BobWhite_rep_c65013_174 chr4A 545603602 T/C - G A CT - BobWhite_c20183_318 chr4A 558217008 A/G + G A AG + BS00067456_51 chr4A 560898941 T/C + T C AG - BS00034174_51 chr4A 562408810 T/C - G A AG + BS00011261_51 chr4A 567704094 T/C + C T CT + GENE-2947_175 chr4A 570264518 T/C + T C AG - GENE-2947_357 chr4A 570264696 A/G + G A AG + BS00022174_51 chr4A 570267551 T/G + T G GT + BS00022160_51 chr4A 570269081 T/G - A C GT - RAC875_c27704_420 chr4A 570469586 T/C + C T AG - BobWhite_rep_c63429_271 chr4A 570478648 A/G + A G CT - BS00023522_51 chr4A 576568972 T/G + G T GT + GENE-3043_289 chr4A 576702847 T/C - A G AG + CAP11_c5598_321 chr4A 584523497 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c32735_603 chr4A 584799783 T/C + T C CT + Excalibur_c96303_224 chr4A 584812121 T/C + T C CT + RAC875_c37840_704 chr4A 585444538 T/C + T C CT + Kukri_rep_c69389_1215 chr4A 589591246 A/G + G A AG + Jagger_rep_c10288_53 chr4A 590112266 A/G + G A CT - BS00022534_51 chr4A 590208533 A/C + A C AC + RFL_Contig2226_1048 chr4A 593337515 A/G + G A CT - BobWhite_rep_c50869_1676 chr4A 594218393 T/C + C T CT + BS00041735_51 chr4A 594283597 T/C - A G CT - BS00040648_51 chr4A 594663815 T/C - G A CT - BS00040647_51 chr4A 594663833 T/C - A G AG + BS00009573_51 chr4A 594686061 T/C + C T CT + RAC875_c1022_3059 chr4A 595984457 T/C - G A AG + Excalibur_c18318_701 chr4A 596506856 A/G + A G AG + GENE-2384_84 chr4A 596506931 T/C + T C AG - IAAV8200 chr4A 596766051 T/C - A G AG + Ra_c3111_1623 chr4A 596821582 T/C + T C CT + BS00049911_51 chr4A 596827483 T/G + T G GT + Excalibur_c539_1253 chr4A 597692833 A/G - T C AG - BS00077716_51 chr4A 597693215 T/C - G A CT - Excalibur_c539_567 chr4A 597693518 T/C - A G AG + Kukri_c2706_1424 chr4A 597693615 A/G + A G AG + RAC875_c48107_65 chr4A 597916607 A/G + G A CT - RAC875_c50438_637 chr4A 598433143 A/G - C T AG - BS00003866_51 chr4A 598433552 T/G + G T AC - BS00023031_51 chr4A 598433633 A/G + G A AG + BS00092859_51 chr4A 599326547 A/C + C A AC + Excalibur_c58393_329 chr4A 599345721 A/G + A G CT - BS00107097_51 chr4A 599844663 T/C + T C AG - BS00107766_51 chr4A 599846393 T/C + C T CT + BS00107069_51 chr4A 600900582 A/G - C T CT + RAC875_c94519_419 chr4A 600904641 A/C NA NA NA GT NA flanks do not match reference at this position RAC875_c94519_448 chr4A 600904670 A/C + C A AC + BobWhite_c19919_516 chr4A 601279668 T/C + C T CT + BobWhite_c19919_572 chr4A 601279724 T/C + T C CT + BS00066413_51 chr4A 602245938 A/G + A G AG + BS00021715_51 chr4A 602911180 A/C - T G GT + IAAV3080 chr4A 603380455 A/G + G A AG + Kukri_c19562_127 chr4A 603451744 T/C NA NA NA CT NA flanks do not match reference at this position IAAV5818 chr4A 603452972 T/G - A C AC + RAC875_c19718_551 chr4A 603453604 T/C - G A AG + Ex_c66324_1151 chr4A 604210784 T/C + C T CT + IAAV615 chr4A 604846815 A/G - C T AG - BS00072025_51 chr4A 605664329 A/G - C T CT + Kukri_c12563_52 chr4A 605732894 T/C + C T AG - RAC875_c21369_425 chr4A 606365906 A/G + A G CT - BS00023151_51 chr4A 606586747 T/C + C T CT + RAC875_rep_c106988_401 chr4A 607311091 A/G - T C AG - RFL_Contig4609_315 chr4A 608603850 T/C + T C CT + IAAV3132 chr4A 608608141 T/C + T C CT + IAAV3480 chr4A 608832862 T/C + T C CT + Tdurum_contig14947_611 chr4A 608834862 A/G - T C CT + BS00030838_51 chr4A 608835056 T/C - A G AG + BobWhite_c10076_601 chr4A 610262985 A/G + A G AG + BS00037357_51 chr4A 610493930 T/C - A G CT - BobWhite_c12128_187 chr4A 610500094 A/G + A G AG + Kukri_c17355_1178 chr4A 610620154 A/G - T C CT + RAC875_c17918_321 chr4A 610640857 A/G - T C CT + Ku_c6779_1381 chr4A 610817240 T/C - G A AG + Ra_c23848_305 chr4A 610817260 T/C + C T CT + Ku_c46953_153 chr4A 611201122 T/C - G A AG + RAC875_c19919_724 chr4A 611264454 A/C - G T GT + Ex_c101416_378 chr4A 611581399 A/G - C T AG - RAC875_rep_c107578_166 chr4A 611581538 T/C + T C AG - RAC875_c25124_182 chr4A 612059662 T/C + C T AG - Ra_c49035_206 chr4A 612395996 T/C - G A AG + IAAV7132 chr4A 613582710 T/C + C T CT + Tdurum_contig42526_1914 chr4A 613611808 A/C + A C AC + Excalibur_c24511_1196 chr4A 613812680 A/G + A G AG + Tdurum_contig6030_377 chr4A 614111206 A/C + C A GT - BobWhite_c35402_66 chr4A 614241032 A/C + C A GT - Tdurum_contig10100_659 chr4A 614411236 A/G NA NA NA CT NA flanks do not match reference at this position Tdurum_contig98808_554 chr4A 614411367 T/C - A G CT - RFL_Contig3679_315 chr4A 615109647 T/C + C T CT + Ra_c2750_804 chr4A 615216257 T/C + C T CT + Excalibur_c30378_673 chr4A 615437578 T/C + T C AG - RAC875_c34231_812 chr4A 616310700 T/G - A C GT - RAC875_c34231_342 chr4A 616313093 T/C - G A AG + BS00064269_51 chr4A 616874275 T/C - G A CT - BS00109683_51 chr4A 616961398 A/G + A G AG + BS00099725_51 chr4A 617001884 A/G + G A CT - Excalibur_c21964_237 chr4A 617047335 A/G + G A CT - BS00022418_51 chr4A 617097345 T/G + T G GT + Excalibur_rep_c104791_231 chr4A 619283148 T/C + T C CT + D_F1BEJMU02I00U2_83 chr4A 619283330 T/C + T C AG - Kukri_c24695_273 chr4A 622202018 A/G - T C AG - Tdurum_contig10777_70 chr4A 622236135 A/G - C T AG - JD_c4438_839 chr4A 622236705 T/C + T C CT + Kukri_c1073_91 chr4A 622236936 T/C - A G CT - Excalibur_c687_961 chr4A 622237087 A/G - C T AG - Excalibur_c687_907 chr4A 622237141 T/C - G A AG + RAC875_c961_341 chr4A 622237760 A/G - C T AG - Kukri_c25832_794 chr4A 623318121 A/G - T C AG - Kukri_c25832_687 chr4A 623318228 A/C - T G AC - Excalibur_c25699_113 chr4A 623399949 T/C - A G CT - RAC875_c34515_86 chr4A 623951116 A/G - T C AG - Excalibur_rep_c74900_73 chr4A 625076711 T/C - A G AG + Kukri_c35049_357 chr4A 625396748 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c56535_256 chr4A 626021010 A/C - G T AC - BS00010144_51 chr4A 626063259 A/G - C T AG - Kukri_c17942_239 chr4A 626063724 T/G - A C GT - Excalibur_c5624_1026 chr4A 626309601 T/G - A C GT - Excalibur_c5624_845 chr4A 626309782 A/C - G T AC - RAC875_c8472_1174 chr4A 626311035 A/G - C T AG - IAAV3369 chr4A 627820076 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c88582_131 chr4A 627820174 A/G + A G CT - BS00064423_51 chr4A 627822186 A/G + A G CT - Kukri_c20012_1425 chr4A 628329113 T/C - A G AG + Kukri_c20012_1362 chr4A 628329176 A/G - T C CT + Tdurum_contig27973_306 chr4A 628492002 A/C + C A AC + Excalibur_c10696_3390 chr4A 629360157 A/G - T C AG - CAP11_c1989_183 chr4A 629475930 A/G - T C AG - RAC875_c49370_172 chr4A 629917536 A/G + G A CT - RAC875_c49370_327 chr4A 629917691 A/G + A G AG + Kukri_c33315_159 chr4A 630764552 T/C + T C AG - BobWhite_c33898_150 chr4A 630845865 T/C - A G AG + RAC875_c390_1494 chr4A 631574982 A/G - C T CT + RAC875_c15517_327 chr4A 631644034 T/G + T G AC - Excalibur_rep_c102020_253 chr4A 631922560 T/C + T C CT + Kukri_c25823_443 chr4A 631922630 T/C + T C CT + BobWhite_c3656_1155 chr4A 631923203 T/C - A G AG + RAC875_c47278_818 chr4A 632018361 A/G - C T CT + RAC875_c17197_504 chr4A 632018677 A/C + A C AC + RAC875_c10914_337 chr4A 632153888 T/C - A G CT - Excalibur_c9370_966 chr4A 632858940 A/G - T C CT + Excalibur_c9370_944 chr4A 632858962 T/C - G A AG + Kukri_rep_c109167_89 chr4A 634737636 A/G + A G CT - BS00090866_51 chr4A 640249469 T/C + T C AG - BS00039147_51 chr4A 641402910 A/G + G A CT - BS00039148_51 chr4A 641402987 A/G + G A AG + IAAV8683 chr4A 641591760 T/C + C T CT + Ku_c1125_814 chr4A 641591760 A/G - C T CT + Excalibur_rep_c68955_422 chr4A 646784486 T/C NA NA NA AG NA flanks do not match reference at this position IAAV1383 chr4A 646784623 T/G + G T AC - Tdurum_contig65718_209 chr4A 648893401 A/C - G T GT + RAC875_c35819_165 chr4A 649809026 A/G - C T AG - RAC875_c83401_115 chr4A 650375552 T/C - G A AG + GENE-0439_314 chr4A 652851749 A/G + A G AG + Excalibur_c1781_613 chr4A 653075112 A/G + G A AG + BS00056624_51 chr4A 659014450 T/C - G A AG + Tdurum_contig19920_463 chr4A 659014967 A/G + G A AG + BobWhite_c43728_100 chr4A 660790844 T/C - A G CT - GENE-4618_413 chr4A 660794446 T/G - A C AC + RAC875_c29282_566 chr4A 660985514 T/C - A G AG + RAC875_c29282_373 chr4A 660985707 T/C - A G AG + RAC875_c29282_216 chr4A 660985864 T/C - A G AG + RAC875_c29282_187 chr4A 660985893 T/C - A G CT - BS00101512_51 chr4A 660987308 A/G + G A CT - BS00101513_51 chr4A 660987322 T/C + T C AG - Excalibur_c7034_692 chr4A 660988406 T/C - A G CT - RAC875_c917_442 chr4A 660988603 T/C + T C CT + Excalibur_c53103_113 chr4A 661050246 A/G - T C CT + BS00066891_51 chr4A 661301800 T/C - G A AG + IAAV5722 chr4A 664478197 A/G - C T AG - RAC875_c37810_241 chr4A 665501156 A/C - G T AC - Excalibur_c4370_1221 chr4A 665504205 T/C + T C AG - Excalibur_c4370_1451 chr4A 665504435 A/G + A G AG + BS00064140_51 chr4A 666110922 T/C - G A CT - Excalibur_c3988_1660 chr4A 666149004 A/G - T C CT + BobWhite_c46381_91 chr4A 667353335 A/G NA NA NA CT NA flanks do not match reference at this position BS00010645_51 chr4A 669088351 A/G - C T CT + BobWhite_s66049_223 chr4A 670382625 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_c57078_255 chr4A 671933963 T/C + C T AG - Tdurum_contig75183_685 chr4A 673412993 A/G - T C AG - Excalibur_c53864_331 chr4A 673446735 A/C - T G GT + Tdurum_contig14075_630 chr4A 673960265 T/G + G T GT + GENE-3129_436 chr4A 674554513 T/C + T C AG - GENE-3129_890 chr4A 674554627 T/C - A G AG + Kukri_c106476_350 chr4A 674604369 T/C - A G AG + RAC875_c35979_263 chr4A 676421316 T/G - A C GT - Excalibur_c18660_1719 chr4A 681717541 A/G - T C AG - CAP11_c18_238 chr4A 684269297 A/G + G A CT - BobWhite_c7217_317 chr4A 684269586 T/C - A G AG + Excalibur_c4325_1440 chr4A 684616209 A/G - C T AG - Excalibur_c4325_1150 chr4A 684616499 A/G - T C CT + Excalibur_c4325_910 chr4A 684616739 A/G - T C AG - Excalibur_c4325_466 chr4A 684618055 A/G - C T AG - BobWhite_rep_c63422_83 chr4A 684661449 T/C - G A CT - Kukri_c96159_197 chr4A 684967029 A/G + A G AG + Kukri_c48943_1149 chr4A 684998641 T/C + T C CT + Kukri_c20236_209 chr4A 684998912 T/G + T G AC - RAC875_c95150_286 chr4A 685939413 A/G - T C CT + Kukri_c16103_88 chr4A 686173966 T/C - G A CT - BobWhite_c10610_149 chr4A 686383434 A/G - T C AG - Excalibur_c6749_694 chr4A 686383557 T/G + G T GT + Excalibur_c24600_733 chr4A 687547862 A/G - T C CT + Kukri_c17962_570 chr4A 687556568 T/C - A G AG + Kukri_c17417_407 chr4A 688095632 A/C - T G AC - Kukri_c17417_291 chr4A 688095748 A/G - T C AG - BobWhite_c17731_56 chr4A 689849795 A/G - T C CT + BS00064369_51 chr4A 692272800 A/C - T G AC - CAP8_rep_c3781_99 chr4A 692383279 A/C - T G GT + CAP12_c2972_140 chr4A 692962439 A/G + A G CT - RFL_Contig4095_1201 chr4A 693277415 A/G + A G AG + BS00021957_51 chr4A 693278307 A/G + G A AG + Excalibur_c22896_149 chr4A 696004794 T/G - A C GT - Excalibur_c19666_778 chr4A 697953133 T/C + T C CT + Excalibur_c19666_989 chr4A 697953552 T/C + T C AG - IAAV3960 chr4A 700422179 A/G - C T AG - Kukri_c46302_194 chr4A 701698934 A/C - T G AC - BS00039641_51 chr4A 702070444 T/C + T C AG - RAC875_c33109_72 chr4A 703261615 T/C - A G AG + BS00032622_51 chr4A 703340842 T/G + G T AC - Tdurum_contig93100_77 chr4A 705178300 T/C + C T CT + BS00091561_51 chr4A 705178372 A/C - G T AC - Tdurum_contig93100_149 chr4A 705178372 T/G + G T AC - BobWhite_c8680_918 chr4A 705179194 A/G + G A AG + BobWhite_c8680_993 chr4A 705179888 T/G + T G GT + BobWhite_s66966_118 chr4A 705180341 T/C - G A CT - Tdurum_contig43961_607 chr4A 705508194 T/C - G A AG + BS00084703_51 chr4A 705508465 A/G + A G AG + Kukri_c27648_350 chr4A 705517540 T/C + C T AG - Excalibur_c77192_78 chr4A 705517710 T/G + T G AC - GENE-4469_430 chr4A 705519728 T/G - C A AC + BS00064494_51 chr4A 705767505 A/G - C T CT + BS00099982_51 chr4A 707039362 A/C + C A GT - Ra_c1897_2401 chr4A 707040362 T/C - G A AG + Ex_c1246_1162 chr4A 708567783 A/C + C A AC + Ra_c60252_743 chr4A 708567974 A/G + G A CT - Ra_c60252_914 chr4A 708568145 A/G + G A AG + Ra_c60252_1208 chr4A 708568439 T/C + T C CT + Ra_c60252_1733 chr4A 708568964 A/G + A G AG + Tdurum_contig7992_173 chr4A 710412360 T/C + T C AG - Tdurum_contig7992_605 chr4A 710413163 T/C + T C CT + Excalibur_c15222_313 chr4A 710663272 T/C + C T CT + BS00111091_51 chr4A 710666536 A/G - C T AG - Kukri_c48194_641 chr4A 710744470 A/G + G A CT - IAAV4855 chr4A 710744548 A/G + G A AG + BS00000577_51 chr4A 710744556 T/C + C T CT + Tdurum_contig75819_338 chr4A 712863205 T/C + C T CT + RFL_Contig3841_3051 chr4A 712863720 A/G - T C AG - RFL_Contig3841_2433 chr4A 712865230 T/C - G A CT - Tdurum_contig75819_1471 chr4A 712865230 A/G + G A AG + RFL_Contig3841_2409 chr4A 712865254 A/G - C T CT + RFL_Contig3841_2313 chr4A 712865491 A/G NA NA NA CT NA flanks do not match reference at this position Tdurum_contig75819_1591 chr4A 712865491 T/C NA NA NA CT NA flanks do not match reference at this position RFL_Contig3841_1986 chr4A 712866970 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig45738_670 chr4A 713117841 A/C NA NA NA AC NA flanks do not match reference at this position BS00070687_51 chr4A 713518979 A/G - C T AG - BS00075049_51 chr4A 713519424 T/C - A G AG + JD_c581_466 chr4A 713519525 A/G + G A AG + Kukri_c20783_367 chr4A 713522136 A/G + G A AG + BobWhite_c11327_491 chr4A 713522176 A/G - C T AG - BobWhite_c20322_183 chr4A 713522736 A/G + A G CT - Tdurum_contig10482_110 chr4A 713522996 T/C + T C CT + BobWhite_c20322_559 chr4A 713523112 A/G + G A AG + Kukri_c20783_1016 chr4A 713523186 T/G + T G AC - BobWhite_c20306_88 chr4A 713523208 A/G + A G AG + BS00045554_51 chr4A 713523395 A/G + A G AG + BS00045555_51 chr4A 713523398 T/G + G T AC - RAC875_rep_c69632_65 chr4A 714179096 T/C - A G AG + BS00110021_51 chr4A 714295160 A/G + G A CT - Excalibur_c24664_1308 chr4A 714432378 T/G + G T GT + BS00110926_51 chr4A 715118313 T/C + T C CT + RAC875_c54248_724 chr4A 717740369 A/G - C T AG - Tdurum_contig81450_90 chr4A 717740369 T/C + C T AG - RAC875_c54248_499 chr4A 717740673 A/C - T G GT + Kukri_c20949_956 chr4A 717740751 A/C - T G AC - BS00023007_51 chr4A 717972040 A/G + G A AG + GENE-4440_490 chr4A 719164890 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig15126_286 chr4A 722839498 T/G - A C GT - Tdurum_contig15126_225 chr4A 722839559 A/C - T G GT + Kukri_c33449_309 chr4A 722841923 T/G - C A AC + Tdurum_contig46954_406 chr4A 722841933 T/C + T C CT + Excalibur_c33995_302 chr4A 722886222 T/C - A G AG + RAC875_c1899_1089 chr4A 722903425 T/C + T C CT + RAC875_rep_c117027_577 chr4A 722908769 T/G - C A GT - RAC875_rep_c117027_529 chr4A 722908817 A/G - T C AG - Excalibur_c13811_1086 chr4A 723810464 T/C + C T CT + Ra_c7318_685 chr4A 724797850 A/G + G A CT - BobWhite_c3259_96 chr4A 724855754 A/G - T C CT + RAC875_rep_c100803_217 chr4A 726120896 T/C + T C CT + IAAV3545 chr4A 726121749 T/C - A G AG + BobWhite_c47168_289 chr4A 726215250 A/G - C T AG - Excalibur_c6050_323 chr4A 726438739 T/C + C T CT + Excalibur_c2827_227 chr4A 726446463 A/G + G A AG + IAAV1943 chr4A 726447549 A/G - C T CT + BS00104640_51 chr4A 727128955 A/G + A G CT - Ra_c6672_1679 chr4A 729708169 A/G + G A AG + Ex_c101546_376 chr4A 729746391 T/C + T C AG - BS00049695_51 chr4A 731256155 T/C + T C AG - Excalibur_c21750_253 chr4A 732511757 T/C + C T AG - RAC875_c67909_226 chr4A 732512417 A/G + A G AG + Kukri_c19883_365 chr4A 732518661 A/C + A C GT - Tdurum_contig44771_984 chr4A 732518984 A/C + A C AC + Kukri_c19883_629 chr4A 732519006 A/C + A C AC + Kukri_c19883_816 chr4A 732519193 A/G + A G CT - Tdurum_contig27944_296 chr4A 732771251 T/C - A G AG + Tdurum_contig27944_266 chr4A 732771281 T/G - C A GT - CAP8_rep_c4703_101 chr4A 732771859 T/C + C T AG - BS00079092_51 chr4A 732772174 A/G + G A AG + CAP8_rep_c4703_313 chr4A 732772185 T/C + C T CT + Ku_c27642_444 chr4A 732772185 A/G - C T CT + BS00110281_51 chr4A 733639141 A/G - T C AG - BS00009680_51 chr4A 733696231 T/G - A C GT - BS00081698_51 chr4A 733696236 A/C - G T AC - Excalibur_c113341_139 chr4A 733707988 A/G + A G CT - Excalibur_rep_c101560_2243 chr4A 733999767 T/C - G A AG + Ku_c61_917 chr4A 734000492 A/G + G A CT - Excalibur_c17294_228 chr4A 735778689 A/G + A G AG + RAC875_rep_c77127_256 chr4A 737155901 T/C - G A AG + BobWhite_c20558_413 chr4A 737340062 A/G - T C CT + GENE-4644_70 chr4A 737385172 T/C + T C CT + RAC875_c58134_239 chr4A 737504882 T/C + T C CT + BS00084477_51 chr4A 738781159 A/G + A G CT - Tdurum_contig46583_2203 chr4A 738781296 A/G - C T CT + Tdurum_contig46583_1275 chr4A 738782305 A/C - G T GT + Tdurum_contig49559_2160 chr4A 738886492 A/G - C T CT + CAP8_c710_140 chr4A 738886582 A/C + C A AC + Tdurum_contig49559_2070 chr4A 738886582 T/G - C A AC + Excalibur_c22830_1500 chr4A 739035798 T/C + T C CT + Excalibur_c56798_364 chr4A 739037130 T/C - A G AG + Excalibur_c28898_668 chr4A 739038268 T/C - A G AG + TA004020-0357 chr4A 739038268 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c44248_242 chr4A 739038873 T/C + T C AG - BobWhite_c42170_144 chr4A 739038972 T/C - A G CT - BS00086733_51 chr4A 739066320 T/C + T C CT + Tdurum_contig47143_241 chr4A 739600427 A/G - T C AG - Kukri_c1488_1122 chr4A 739628807 T/C - A G CT - RFL_Contig3621_1157 chr4A 742335140 A/G - C T AG - RFL_Contig3621_947 chr4A 742335497 T/C - A G CT - GENE-4335_531 chr4A 742379189 T/C + C T CT + Kukri_rep_c102971_140 chr4A 742380900 A/G - C T AG - RAC875_c25194_55 chr4A 742382034 A/G + A G CT - Excalibur_rep_c107933_80 chr4A 742551759 T/C + T C AG - IAAV8135 chr4A 742552267 A/G + G A CT - Kukri_rep_c104153_109 chr4A 742553353 A/G + A G CT - Tdurum_contig54776_1396 chr4A 742558409 T/C + T C AG - Kukri_c9746_107 chr4A 742566394 T/C - G A CT - Ra_c3624_533 chr4A 743832591 A/G - C T AG - RAC875_c34981_294 chr4A 743868609 T/C + C T CT + Tdurum_contig31218_279 chr4A 743948884 A/G + A G CT - Kukri_rep_c70151_173 chr4A 743948909 A/G + G A CT - Kukri_c3866_196 chr4A 743953686 T/G - C A GT - Excalibur_c10699_404 chr4A 744309803 A/G + G A AG + RAC875_c55173_65 chr4A 744521720 A/C - G T AC - Tdurum_contig11733_825 chr4B 537188 T/C - A G CT - BS00056493_51 chr4B 622350 A/C + A C AC + BS00056495_51 chr4B 622455 A/G + A G CT - RAC875_c86104_111 chr4B 1047041 T/C - G A CT - Tdurum_contig47429_501 chr4B 1771356 A/G NA NA NA CT NA flanks do not match reference at this position Tdurum_contig47429_248 chr4B 1772368 T/G - A C GT - Tdurum_contig47429_149 chr4B 1772467 T/C - A G CT - Kukri_c109276_691 chr4B 1776338 T/C - A G AG + IAAV3405 chr4B 1783260 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c65707_171 chr4B 1783260 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_rep_c85960_209 chr4B 1989507 A/G + A G AG + Excalibur_rep_c85960_323 chr4B 1989621 T/C + C T AG - BS00022183_51 chr4B 2036703 A/C - T G AC - TA003111-1095 chr4B 2036852 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c78248_154 chr4B 3833434 A/G - T C CT + IAAV1120 chr4B 3860237 T/C - G A CT - BS00106142_51 chr4B 4537260 A/C - G T AC - tplb0025f09_1853 chr4B 4849968 T/C - A G AG + Tdurum_contig5427_314 chr4B 4852517 T/C - G A CT - CAP11_c6632_160 chr4B 6141444 A/G - T C CT + Kukri_c64744_698 chr4B 6149767 T/C NA NA NA AG NA flanks do not match reference at this position IAAV7323 chr4B 6149830 T/C + T C CT + Excalibur_c14401_743 chr4B 6149863 A/G + G A AG + BS00060041_51 chr4B 7027418 T/C - A G AG + BobWhite_c1656_186 chr4B 7037407 T/C + T C AG - BobWhite_c1656_845 chr4B 7038221 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c49061_138 chr4B 7038414 T/G + T G AC - Tdurum_contig49608_1185 chr4B 7043773 A/G - T C AG - IAAV1775 chr4B 8983101 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles CAP11_rep_c4893_84 chr4B 10437508 A/C - T G AC - RAC875_rep_c106667_302 chr4B 10590797 A/G - C T CT + GENE-2267_428 chr4B 10591540 T/G NA NA NA AC NA flanks do not match reference at this position Excalibur_c18318_665 chr4B 12528838 T/C + T C AG - CAP12_rep_c4571_181 chr4B 12613365 A/G + G A AG + Kukri_c66885_230 chr4B 12888652 A/G - C T CT + Tdurum_contig47622_234 chr4B 13411281 A/G - C T CT + Tdurum_contig67399_676 chr4B 13945600 A/G - T C AG - Tdurum_contig31139_143 chr4B 13976526 T/C - A G AG + Tdurum_contig31139_79 chr4B 13976590 A/G - C T AG - RAC875_c10850_316 chr4B 13977274 A/G + G A AG + Excalibur_c7581_1266 chr4B 14110534 T/C - G A AG + Tdurum_contig76559_124 chr4B 14110534 A/G + G A AG + Excalibur_c7581_791 chr4B 14112477 T/C - G A CT - Tdurum_contig50625_2342 chr4B 14118136 T/G - A C AC + Excalibur_rep_c79414_306 chr4B 14118214 A/G - T C AG - BS00010115_51 chr4B 14118285 T/C + T C CT + IACX8647 chr4B 14118285 A/G - T C AG - BS00009480_51 chr4B 14118304 A/G + G A AG + IACX7746 chr4B 14118304 T/C - G A AG + GENE-4933_1095 chr4B 14122763 T/C - G A AG + GENE-4933_1085 chr4B 14122769 A/G - T C AG - Tdurum_contig76213_958 chr4B 15412916 T/C + T C CT + Tdurum_contig76213_1156 chr4B 15413216 T/C NA NA NA AG NA flanks do not match reference at this position Tdurum_contig82942_681 chr4B 15416606 A/G - T C AG - tplb0024a16_411 chr4B 15416606 T/C + T C AG - BS00011510_51 chr4B 16056716 A/C + A C AC + tplb0060n12_565 chr4B 16089005 T/C + C T AG - Kukri_rep_c106598_51 chr4B 17043972 A/G - C T AG - Kukri_c49506_396 chr4B 17044051 A/G + G A CT - Kukri_c8594_203 chr4B 17255250 A/G + A G AG + IAAV2271 chr4B 17470095 T/C - A G CT - Kukri_c34633_69 chr4B 21377911 T/C + C T CT + Excalibur_rep_c68588_1196 chr4B 21377973 T/C + C T AG - Kukri_rep_c69273_148 chr4B 21555133 T/C - A G AG + Tdurum_contig64772_417 chr4B 26491532 T/C + T C CT + Ex_c101685_705 chr4B 28959979 A/G + A G CT - Ex_c101685_711 chr4B 28959985 A/G + A G CT - BS00023766_51 chr4B 31875304 T/C - A G CT - RAC875_c27536_611 chr4B 32250770 T/C - G A CT - BS00022785_51 chr4B 35258738 T/C - A G CT - BS00084070_51 chr4B 35514978 A/G + A G AG + Tdurum_contig82378_561 chr4B 35520604 T/C - G A AG + Tdurum_contig82378_264 chr4B 35520901 T/C - A G AG + Tdurum_contig33737_157 chr4B 37694529 A/G + A G AG + RAC875_c19303_228 chr4B 37851446 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_rep_c49034_167 chr4B 38028398 A/C - T G AC - RAC875_rep_c105718_304 chr4B 38282897 T/C - A G CT - Excalibur_c36630_2194 chr4B 38283932 A/G + A G CT - IAAV971 chr4B 40752468 T/C + C T CT + BS00022258_51 chr4B 45511484 A/G + G A CT - GENE-2621_193 chr4B 46608469 A/C + C A GT - JD_c30756_562 chr4B 46608609 T/C + T C CT + BobWhite_c44691_648 chr4B 46609214 T/G - C A AC + Tdurum_contig81797_369 chr4B 46609742 A/C - T G AC - CAP11_c3631_75 chr4B 46621251 T/C + C T AG - IAAV585 chr4B 49761591 T/G - C A GT - Tdurum_contig13979_143 chr4B 54544529 T/C - A G CT - BS00040305_51 chr4B 54742372 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c11201_111 chr4B 57318614 A/C + A C GT - Excalibur_c56787_95 chr4B 59207925 T/G + G T AC - RFL_Contig3827_173 chr4B 66103174 T/C + T C AG - Excalibur_c17607_542 chr4B 78025849 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig94240_501 chr4B 82163888 A/G - T C AG - Tdurum_contig83679_255 chr4B 83140712 A/G + G A AG + Tdurum_contig83679_281 chr4B 83140738 A/G + A G CT - Excalibur_rep_c106567_561 chr4B 85696644 T/C + T C CT + BobWhite_c6178_393 chr4B 85698891 T/C - A G CT - Excalibur_c100336_106 chr4B 85895786 A/G + G A CT - Tdurum_contig61465_781 chr4B 86064674 T/G - C A AC + Excalibur_rep_c67779_2380 chr4B 89518533 T/C - G A CT - IACX773 chr4B 90457876 T/C - A G CT - Tdurum_contig65570_163 chr4B 95072128 T/C - A G AG + Tdurum_contig93168_52 chr4B 96641992 A/G + A G AG + Tdurum_contig42211_2280 chr4B 97922320 T/G - C A GT - Tdurum_contig42211_1897 chr4B 97922703 A/G - T C CT + Tdurum_contig42211_1634 chr4B 97922966 A/C - G T AC - BS00025819_51 chr4B 97924593 T/C - A G AG + BS00075746_51 chr4B 99064194 T/C - G A AG + IAAV3868 chr4B 100847211 T/C + T C AG - Tdurum_contig62016_241 chr4B 103054645 T/C + C T AG - BS00022576_51 chr4B 103527655 T/C + T C AG - BS00007684_51 chr4B 103528062 T/C + T C CT + Tdurum_contig31250_273 chr4B 104338971 T/C - A G CT - BS00065422_51 chr4B 106837521 T/C + C T CT + Kukri_c20822_1029 chr4B 106973454 A/G - T C CT + BS00034255_51 chr4B 107658792 A/G - T C CT + Tdurum_contig62310_490 chr4B 108352300 A/G - C T CT + BS00022988_51 chr4B 109925556 A/G - C T CT + BS00100610_51 chr4B 109925637 T/C - G A CT - Excalibur_c46143_143 chr4B 129053639 T/C - A G CT - BS00030843_51 chr4B 132334116 T/G - A C GT - BS00075631_51 chr4B 136528522 A/G + A G AG + BS00067428_51 chr4B 139766572 A/G + G A CT - BS00064032_51 chr4B 144927462 A/G + A G AG + BobWhite_c39452_90 chr4B 149034289 T/C - G A AG + BobWhite_c21181_787 chr4B 155761076 T/G - C A AC + BS00062691_51 chr4B 156308909 T/G + G T GT + GENE-2129_76 chr4B 158277993 A/G + G A AG + Excalibur_c57766_92 chr4B 165019096 A/G + G A CT - RAC875_c35152_372 chr4B 165019408 A/G + A G CT - Tdurum_contig57516_269 chr4B 167168156 A/C NA NA NA GT NA flanks do not match reference at this position Excalibur_c52517_464 chr4B 167346674 T/G + G T GT + BS00071792_51 chr4B 167929254 A/G - C T AG - RAC875_c45747_87 chr4B 169749077 T/C + T C AG - RAC875_c63892_170 chr4B 169926271 A/G - T C CT + BS00074439_51 chr4B 169935736 A/G + A G CT - BS00074440_51 chr4B 169935769 T/C + C T CT + IAAV5923 chr4B 178354186 A/C + A C GT - RAC875_rep_c70391_128 chr4B 179738095 T/C - G A CT - BS00066271_51 chr4B 187359421 T/C - A G CT - Ex_c56313_332 chr4B 199720566 A/G + A G CT - RAC875_c101563_102 chr4B 208678334 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c46966_193 chr4B 241185383 A/G + A G CT - BobWhite_c29304_397 chr4B 251368067 T/C - G A AG + Excalibur_c29141_864 chr4B 281735002 T/C + T C CT + RAC875_c75075_313 chr4B 311352103 A/G - T C AG - BS00078055_51 chr4B 326085412 A/G + A G AG + RAC875_c14627_330 chr4B 357906331 T/C + C T CT + RAC875_c12495_1391 chr4B 363305958 T/C - G A AG + IACX1164 chr4B 373995417 T/C - A G CT - BobWhite_c9876_331 chr4B 376031558 A/G - T C CT + GENE-2637_396 chr4B 387503291 T/C + C T CT + RAC875_c5351_780 chr4B 387880294 A/G - C T CT + Tdurum_contig94032_1528 chr4B 389467685 A/G + G A CT - Tdurum_contig94032_1688 chr4B 389467845 A/G + G A AG + Tdurum_contig5562_730 chr4B 392042922 T/C - G A AG + Tdurum_contig5562_441 chr4B 392043211 A/G - C T CT + RAC875_rep_c91551_80 chr4B 398197975 T/G - A C GT - Excalibur_rep_c66744_2113 chr4B 398568269 A/G - C T CT + Excalibur_c42233_368 chr4B 399956799 T/C - G A CT - Excalibur_c19996_1417 chr4B 403443201 T/C + C T AG - Tdurum_contig52805_183 chr4B 404513834 T/C + T C CT + IACX5989 chr4B 405375163 C/G - C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00040159_51 chr4B 406458288 T/C - G A AG + BS00064142_51 chr4B 413192431 T/C + C T CT + GENE-0037_298 chr4B 413447595 A/G - C T CT + Tdurum_contig12812_83 chr4B 414707955 A/G + A G AG + BS00064884_51 chr4B 414799611 T/C - G A CT - Kukri_c44469_1240 chr4B 415507395 T/C - A G CT - RAC875_c25710_297 chr4B 420206437 A/C - T G GT + BobWhite_c38340_243 chr4B 424062278 T/C + C T CT + BobWhite_c4810_190 chr4B 427276620 A/G + G A AG + Tdurum_contig98255_84 chr4B 427276620 T/C - G A AG + IAAV2880 chr4B 427494423 T/C + T C CT + Kukri_c21270_1870 chr4B 427511902 A/G + G A AG + IAAV4437 chr4B 427809296 A/G + G A CT - RAC875_c15835_454 chr4B 427809296 T/C - G A CT - IAAV773 chr4B 428009260 T/C + T C AG - Kukri_rep_c104321_201 chr4B 428396487 A/G + A G AG + IAAV4595 chr4B 428704415 A/G + A G AG + GENE-2491_309 chr4B 434467240 T/C - G A CT - IAAV1630 chr4B 440328201 T/C - A G AG + GENE-2768_352 chr4B 448533197 A/G + G A AG + BobWhite_c20051_53 chr4B 449124867 A/G + G A CT - CAP7_c501_143 chr4B 451490105 A/C - G T GT + Tdurum_contig42366_818 chr4B 456363191 T/G - C A AC + GENE-2730_171 chr4B 462237180 T/C + T C CT + Kukri_c9931_1627 chr4B 467275611 A/G + A G CT - Kukri_c6150_575 chr4B 469247385 A/G - T C CT + BS00022194_51 chr4B 475806832 T/C + T C CT + Tdurum_contig51818_145 chr4B 475806832 A/G - T C AG - Excalibur_c42450_727 chr4B 479154283 T/C + T C CT + Tdurum_contig37811_134 chr4B 480922743 T/C + C T CT + Jagger_c1432_289 chr4B 480924000 A/G - T C AG - Excalibur_c33204_1120 chr4B 488672919 T/C - G A AG + RAC875_c22681_97 chr4B 491009959 T/G - A C AC + RFL_Contig5498_1000 chr4B 495602520 T/C - G A AG + IAAV5117 chr4B 497229321 A/C - G T AC - BS00096604_51 chr4B 497229357 T/C - A G CT - Ku_c33858_325 chr4B 499848937 T/C - G A CT - GENE-2331_126 chr4B 513725175 A/G - T C CT + RAC875_c9318_401 chr4B 515161620 A/G - T C AG - RFL_Contig3563_1130 chr4B 517623777 T/C + T C AG - BS00020575_51 chr4B 519257712 T/G - A C AC + Ra_c27465_564 chr4B 519257966 T/C + C T CT + Ra_c27465_569 chr4B 519257971 A/G + A G AG + RAC875_c6865_349 chr4B 519794605 T/C + C T AG - Kukri_c11415_1074 chr4B 520214509 A/G + G A AG + Kukri_c94033_432 chr4B 520221801 T/C + T C CT + Kukri_c322_1394 chr4B 520238759 T/C + T C AG - Tdurum_contig54559_211 chr4B 521706608 T/C - A G AG + Kukri_c2526_1375 chr4B 523447728 T/G + G T AC - GENE-2771_327 chr4B 526728116 A/C - G T GT + BS00022653_51 chr4B 526928534 A/C - T G AC - IAAV163 chr4B 527297720 A/G + A G CT - Kukri_c32064_629 chr4B 527957416 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c15807_669 chr4B 527983063 A/G - C T AG - Excalibur_c65023_62 chr4B 530522905 T/G - A C AC + Excalibur_c5769_798 chr4B 531053575 A/G - T C CT + Tdurum_contig86933_317 chr4B 531340714 T/C - A G CT - BS00087144_51 chr4B 532439915 T/C + T C AG - Tdurum_contig47552_957 chr4B 532627451 A/G - C T AG - Tdurum_contig27809_177 chr4B 533501041 T/C - G A AG + CAP7_c10839_300 chr4B 533724474 T/G + T G GT + Excalibur_c32467_676 chr4B 534735432 T/C - A G AG + GENE-2636_193 chr4B 535049948 A/G + G A CT - Kukri_c5502_2513 chr4B 535070511 T/G - A C AC + BS00046613_51 chr4B 535085059 T/C - G A CT - Kukri_rep_c79943_189 chr4B 536490901 A/G - T C AG - Kukri_c89906_197 chr4B 536704856 T/G + G T AC - Tdurum_contig27038_135 chr4B 536889322 T/C - G A CT - RAC875_c5087_310 chr4B 536919230 A/G - T C AG - Tdurum_contig55374_309 chr4B 536919272 A/G - T C AG - IAAV4665 chr4B 537154239 A/G + G A CT - BS00010659_51 chr4B 537479699 T/C + C T CT + BS00077411_51 chr4B 538266878 A/G + A G CT - Tdurum_contig45550_918 chr4B 538271021 A/G + A G AG + IAAV3421 chr4B 538997269 T/C - G A AG + IAAV3896 chr4B 538999611 A/G - C T CT + BobWhite_c665_296 chr4B 539967096 A/G - T C CT + BS00107247_51 chr4B 541929187 A/G - T C AG - Excalibur_c56741_119 chr4B 544022791 A/G - C T AG - Ex_c7514_3072 chr4B 544025602 T/C + T C AG - Ex_c7514_3078 chr4B 544025608 A/G + A G CT - BS00022136_51 chr4B 544028282 A/G - C T AG - BS00089282_51 chr4B 544598348 A/G - T C CT + IAAV1931 chr4B 544598355 A/G - T C AG - Kukri_c13639_1326 chr4B 545026243 T/C NA NA NA AG NA flanks do not match reference at this position BS00072206_51 chr4B 545864914 T/C - G A CT - BS00091035_51 chr4B 547557054 A/G + A G AG + BS00022184_51 chr4B 548120966 A/G + A G AG + Excalibur_c82684_66 chr4B 548121101 T/G + T G GT + RAC875_c103110_275 chr4B 548862990 T/C + T C CT + BS00037442_51 chr4B 549131963 A/G + A G AG + Excalibur_c23403_1118 chr4B 549134653 T/C + T C AG - CAP8_c3273_136 chr4B 552018214 A/G + A G AG + CAP12_rep_c4000_432 chr4B 552018601 A/G + A G CT - IAAV2228 chr4B 552029880 T/C - G A AG + BS00022181_51 chr4B 552827869 T/C - A G AG + BS00069989_51 chr4B 553258318 T/C - G A AG + RAC875_c18195_718 chr4B 553356419 T/C - A G AG + BS00058659_51 chr4B 555213918 T/G - C A GT - BobWhite_c5694_1201 chr4B 555933347 T/C + C T AG - BS00031652_51 chr4B 556060465 A/G - C T AG - BobWhite_c17457_89 chr4B 556060842 A/C + C A AC + Excalibur_rep_c70127_360 chr4B 556061692 A/G + G A CT - IACX9010 chr4B 556072414 T/C - G A CT - Ku_c24961_1176 chr4B 556072495 A/G - C T AG - Ex_c57212_719 chr4B 556073751 A/G + A G CT - BS00066024_51 chr4B 557453045 A/G - C T AG - Kukri_c16392_1468 chr4B 558051937 A/G + A G CT - Ra_c41921_951 chr4B 558053870 T/C + C T CT + Ra_c41921_1056 chr4B 558053975 T/G + T G GT + IAAV4191 chr4B 558055759 A/G + G A AG + IAAV8975 chr4B 558057733 A/G - T C CT + RAC875_rep_c95493_490 chr4B 558059460 A/G - T C CT + RAC875_rep_c69370_218 chr4B 558059765 T/C - G A AG + Ku_c3385_441 chr4B 558579270 T/G + G T AC - Ku_c3385_521 chr4B 558579350 T/C + T C CT + RAC875_c12762_791 chr4B 558580372 T/C - G A CT - RAC875_rep_c79201_153 chr4B 558583758 A/G + G A CT - RAC875_c2545_1186 chr4B 558596709 T/C + C T CT + RAC875_rep_c73988_307 chr4B 560010358 A/G + G A AG + RAC875_c39226_131 chr4B 560014632 A/G + A G CT - RAC875_c39226_372 chr4B 560014873 T/C + T C AG - Excalibur_c27948_1073 chr4B 561513476 T/C + C T CT + RAC875_c2456_849 chr4B 562356579 A/G + G A AG + Ra_c67368_1218 chr4B 562710559 A/C - T G GT + Ra_c15473_681 chr4B 563626169 A/G + G A AG + BobWhite_c12067_311 chr4B 563786382 A/G + A G AG + Tdurum_contig67477_136 chr4B 564871082 A/G - T C AG - Tdurum_contig61572_344 chr4B 565578403 A/G + G A CT - Tdurum_contig49781_213 chr4B 566597752 A/G + A G AG + Tdurum_contig29054_478 chr4B 567175053 T/C - G A CT - BobWhite_c1295_470 chr4B 567175953 T/C + C T CT + Tdurum_contig29054_113 chr4B 567176258 A/G - T C CT + Tdurum_contig28121_180 chr4B 567176984 A/G + G A CT - BobWhite_c4311_148 chr4B 570086002 T/C + C T CT + BS00068456_51 chr4B 570893191 A/G + A G AG + Tdurum_contig28920_296 chr4B 573276005 T/C - A G CT - Tdurum_contig31737_203 chr4B 574950598 A/G + A G AG + Tdurum_contig61302_347 chr4B 575608552 A/G - C T CT + BobWhite_c11005_236 chr4B 575609091 A/C - T G AC - Excalibur_c12925_510 chr4B 575618012 T/C - A G AG + Tdurum_contig42107_2295 chr4B 575620760 A/G + G A AG + RAC875_c77652_348 chr4B 575904287 T/C + C T CT + Kukri_c12814_763 chr4B 575909836 A/C + A C AC + Tdurum_contig93160_155 chr4B 576200087 T/C + T C CT + RAC875_c62816_54 chr4B 578031318 T/C - A G CT - Tdurum_contig48088_463 chr4B 578031318 A/G + A G CT - RAC875_c89195_138 chr4B 579101620 A/G NA NA NA CT NA flanks do not match reference at this position GENE-2422_208 chr4B 579391518 A/G - C T CT + Tdurum_contig4795_439 chr4B 579458999 T/C - G A AG + Tdurum_contig4795_404 chr4B 579459034 A/G - C T AG - IAAV2591 chr4B 583241058 A/G NA NA NA AG NA flanks do not match reference at this position GENE-2812_300 chr4B 583594203 T/C + T C CT + BS00012457_51 chr4B 586584289 A/G + A G CT - TA004905-0613 chr4B 588432587 T/C - A G AG + Ex_c25467_851 chr4B 588433698 T/C - G A CT - Ex_c25467_796 chr4B 588433753 A/C - G T AC - IAAV558 chr4B 588436507 T/C - G A CT - Ku_c700_2585 chr4B 588436507 A/G + G A CT - Ex_c9296_605 chr4B 589178247 T/C + T C CT + Ku_c462_1417 chr4B 589809824 A/G - T C AG - Ku_c48056_436 chr4B 590438342 T/C + C T CT + Ra_c10455_3226 chr4B 590442040 T/C + C T AG - RAC875_c1828_1130 chr4B 590854543 T/C NA NA NA AG NA flanks do not match reference at this position Ku_c14007_1088 chr4B 590858817 A/G + G A AG + Ra_c32919_1289 chr4B 590859317 A/G + A G AG + BS00021722_51 chr4B 590983388 A/G + G A AG + BS00037020_51 chr4B 595271138 T/G + G T AC - RAC875_c18200_929 chr4B 596344063 T/C - A G AG + BS00022364_51 chr4B 597032112 A/G - C T AG - BS00011492_51 chr4B 597033017 T/C NA NA NA AG NA flanks do not match reference at this position BS00003765_51 chr4B 597970217 T/C - A G CT - IACX5896 chr4B 597970217 A/G + A G CT - TA005854-0536 chr4B 597970509 T/G + T G GT + RFL_Contig583_419 chr4B 597979657 T/C + T C AG - Tdurum_contig60114_525 chr4B 597979917 A/G - T C CT + BS00062892_51 chr4B 598610705 A/G + G A CT - BS00067938_51 chr4B 599166886 T/C + T C AG - tplb0026o15_1634 chr4B 600655623 T/C - G A AG + Excalibur_c710_1554 chr4B 601052182 T/C - A G AG + IAAV5572 chr4B 601198368 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Kukri_c36207_91 chr4B 601376256 A/G - C T AG - BS00048794_51 chr4B 601931300 A/G + A G CT - BS00030571_51 chr4B 602404467 A/G + A G CT - BS00064041_51 chr4B 602781552 A/G - C T CT + BS00109813_51 chr4B 603144715 A/C - T G GT + RAC875_c56040_216 chr4B 603148911 A/G + A G CT - BS00039402_51 chr4B 603186311 T/C - A G CT - Excalibur_c47209_87 chr4B 604203886 T/G + G T AC - BS00106143_51 chr4B 604204052 A/C - T G GT + BS00063008_51 chr4B 605162864 T/C + C T AG - BS00104364_51 chr4B 605829021 T/C - G A AG + BS00057153_51 chr4B 609317748 A/G + G A AG + BS00076033_51 chr4B 609515921 A/G + A G AG + IACX938 chr4B 611426252 A/G - C T AG - BS00068540_51 chr4B 611505807 T/C - G A CT - Excalibur_c37565_709 chr4B 612026209 T/C - A G AG + Kukri_c20125_281 chr4B 612214564 T/C - A G CT - IACX2314 chr4B 612253913 A/G - T C AG - BobWhite_c2646_141 chr4B 612253957 T/C - A G CT - Tdurum_contig10137_89 chr4B 612327389 A/G - T C CT + Kukri_c64668_958 chr4B 612760967 A/G - C T AG - Ra_c106922_1879 chr4B 612844326 A/G - T C AG - Ku_c101046_1063 chr4B 612846857 T/C + T C AG - BS00042105_51 chr4B 616274526 T/C - G A CT - RAC875_c14455_1148 chr4B 617875666 T/C + T C AG - Excalibur_c19976_382 chr4B 619078908 T/G - A C GT - Excalibur_c25270_218 chr4B 619970175 T/C + T C AG - Excalibur_c19547_128 chr4B 621326999 T/C + C T AG - BS00022830_51 chr4B 621327033 T/C - A G CT - Tdurum_contig61242_161 chr4B 621327033 A/G + A G CT - Excalibur_c19547_1012 chr4B 621330560 A/G + A G CT - IACX6482 chr4B 621436932 A/T + A T AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c65292_58 chr4B 631547099 T/C + T C AG - RAC875_c32826_485 chr4B 634078490 T/C + T C AG - Tdurum_contig5470_570 chr4B 634321986 T/C - A G CT - Tdurum_contig45927_1211 chr4B 634340247 A/G - C T AG - Tdurum_contig97499_167 chr4B 634732156 T/C - G A CT - RFL_Contig5869_863 chr4B 635944776 T/C - A G AG + BS00022972_51 chr4B 636739593 T/C - A G CT - Kukri_c28022_54 chr4B 636779274 T/G + G T GT + Ra_c5508_706 chr4B 636789410 T/C - A G CT - Ku_c3924_451 chr4B 636790319 T/C - G A CT - Excalibur_c1706_1413 chr4B 636916811 T/C - G A CT - BS00023035_51 chr4B 636917387 T/G + G T GT + BS00102481_51 chr4B 636917907 A/G NA NA NA CT NA flanks do not match reference at this position Tdurum_contig48366_1324 chr4B 637387355 T/C - G A AG + Tdurum_contig50783_67 chr4B 637387809 T/C + C T CT + Kukri_c7241_322 chr4B 637387933 T/C + C T AG - Tdurum_contig50783_285 chr4B 637388027 T/C + T C CT + Kukri_c7241_689 chr4B 637388300 A/G + G A CT - Jagger_c10189_75 chr4B 637389833 T/C + C T CT + BS00035426_51 chr4B 637390229 T/C - G A CT - GENE-2566_317 chr4B 637736967 A/C - G T AC - Kukri_c4309_407 chr4B 638118846 A/G - T C CT + tplb0027f12_503 chr4B 638588950 A/C + A C AC + Excalibur_rep_c102761_90 chr4B 641611465 T/C - A G CT - RAC875_rep_c119568_203 chr4B 642192477 T/C + T C AG - tplb0056i06_856 chr4B 643283605 T/C + C T CT + Tdurum_contig59914_323 chr4B 643650789 T/C - G A CT - BS00022466_51 chr4B 643650978 T/C - A G AG + Tdurum_contig60051_169 chr4B 644679603 T/C + T C CT + Tdurum_contig60051_838 chr4B 644681231 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig50861_106 chr4B 644784478 T/C + C T AG - Tdurum_contig50861_532 chr4B 644785534 T/C + C T AG - IAAV2725 chr4B 645298597 T/C + T C AG - Tdurum_contig62286_271 chr4B 645298597 A/G - T C AG - BobWhite_c12593_361 chr4B 646140316 T/C + T C CT + Kukri_c2148_137 chr4B 646256845 T/C + C T CT + Ku_c2639_1715 chr4B 646264146 A/G - C T AG - Excalibur_c29568_163 chr4B 646267523 A/C + A C AC + Excalibur_c29568_191 chr4B 646267551 A/G + A G CT - Kukri_c2639_290 chr4B 646267645 A/G - T C CT + GENE-2538_158 chr4B 646316892 A/G + G A AG + Kukri_rep_c103450_1504 chr4B 646658306 A/G - T C AG - Ku_c103450_879 chr4B 646658931 T/C - G A CT - Tdurum_contig51356_290 chr4B 648314518 A/G + G A CT - RAC875_c107130_384 chr4B 649471268 T/C + C T CT + GENE-1584_692 chr4B 649473985 T/C - A G CT - Kukri_c44559_429 chr4B 649525657 T/C - G A CT - Kukri_c18722_425 chr4B 649602930 T/C - A G CT - Kukri_c18722_56 chr4B 649603299 A/G - C T AG - IAAV8848 chr4B 649605317 T/C - G A CT - RAC875_c87897_333 chr4B 650937771 A/G + G A AG + Ku_c12557_1183 chr4B 651988223 A/G - C T CT + BS00022808_51 chr4B 651991480 A/G - C T AG - IAAV8622 chr4B 651991480 T/C + C T AG - BS00094252_51 chr4B 651991699 A/G - C T CT + Kukri_c4260_1139 chr4B 651992206 A/G - C T CT + Excalibur_rep_c114140_567 chr4B 651992276 A/G - C T CT + Tdurum_contig9893_492 chr4B 652001257 T/C - G A CT - BS00022055_51 chr4B 652253149 T/C + C T AG - Kukri_c29008_195 chr4B 652283224 A/C + A C GT - RAC875_c51375_238 chr4B 652373316 A/C + C A AC + RAC875_c51375_394 chr4B 652373472 T/C + C T AG - RAC875_c51375_430 chr4B 652373508 A/C + A C AC + Kukri_c93922_206 chr4B 653011491 A/G - C T AG - Kukri_rep_c71670_163 chr4B 654267329 A/G - C T CT + BS00109456_51 chr4B 656163142 T/C + C T AG - BS00023204_51 chr4B 656163187 T/C + C T AG - BobWhite_c4256_213 chr4B 657172059 A/G + G A AG + BobWhite_c8266_582 chr4B 657173256 T/C - A G AG + Kukri_rep_c101259_81 chr4B 657274181 T/C - A G CT - BS00104279_51 chr4B 657295342 T/C - A G CT - Excalibur_c57603_523 chr4B 657467120 T/G - A C AC + Kukri_c26905_392 chr4B 657825649 A/G - T C AG - BS00023024_51 chr4B 657986642 T/C - G A CT - IAAV7394 chr4B 658196665 A/G + A G AG + IACX7540 chr4B 660465409 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles JD_c15782_595 chr4B 660481593 T/C - G A CT - BobWhite_c47144_153 chr4B 660589159 T/C + T C AG - BS00008627_51 chr4B 660589226 T/C + T C AG - Tdurum_contig52336_160 chr4B 660665042 T/G - A C AC + Tdurum_contig10302_240 chr4B 660666062 A/C - T G AC - Tdurum_contig10302_187 chr4B 660666115 A/G - T C CT + BS00027054_51 chr4B 662147986 A/G + A G AG + BS00034148_51 chr4B 663106686 T/C - A G AG + BS00034147_51 chr4B 663106715 T/C - G A CT - RAC875_c5802_144 chr4B 666049203 A/G + G A CT - Kukri_c7838_1343 chr4B 670440472 T/C + T C CT + Excalibur_c1692_1225 chr4B 670443744 A/G NA NA NA CT NA flanks do not match reference at this position GENE-0111_378 chr4B 672236471 A/G + A G AG + BS00010234_51 chr4B 672237547 A/G + G A AG + RAC875_c6026_963 chr4B 672305586 T/C + T C AG - Ku_c9134_255 chr4B 673100315 A/G - C T AG - GENE-3126_21 chr4D 1186724 A/G - T C CT + Excalibur_c26088_184 chr4D 1242225 T/G + G T GT + RAC875_c19718_192 chr4D 1372801 A/G - C T AG - Kukri_c64744_1087 chr4D 3395890 T/G - C A GT - BS00108770_51 chr4D 3429990 A/G - T C CT + BS00022283_51 chr4D 3436415 T/C - G A CT - BS00099053_51 chr4D 3612586 T/C - A G CT - tplb0025f09_973 chr4D 3726280 T/C + T C AG - tplb0025f09_1052 chr4D 3726359 A/G + A G AG + D_GA8KES402IGAPX_198 chr4D 4107388 T/C - G A AG + Kukri_c7791_99 chr4D 4131849 T/C - G A AG + Excalibur_rep_c113131_624 chr4D 4978333 A/G - C T AG - BS00009492_51 chr4D 6585367 T/C - G A AG + GENE-4933_489 chr4D 7829947 T/C - G A AG + BS00009426_51 chr4D 7832996 A/G + G A CT - Excalibur_c7377_445 chr4D 8083584 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_c10445_225 chr4D 8084249 A/G - C T CT + RAC875_c6749_954 chr4D 11567401 A/G + A G CT - Kukri_rep_c68594_530 chr4D 12773209 A/G - T C AG - RAC875_c1673_193 chr4D 16587729 A/C - T G GT + D_F5XZDLF01AI24N_101 chr4D 16650803 T/G - C A GT - RAC875_rep_c105718_585 chr4D 25989112 T/C - A G AG + D_F5XZDLF01CSICV_77 chr4D 26108141 T/G + G T GT + GENE-3043_279 chr4D 26669029 A/G + A G AG + RAC875_rep_c107210_217 chr4D 38446266 A/G - T C CT + Excalibur_rep_c70578_299 chr4D 38447262 A/G - T C CT + Excalibur_c3667_1238 chr4D 57075285 A/G + G A CT - tplb0022j01_1046 chr4D 58134654 A/C NA NA NA GT NA flanks do not match reference at this position Ex_c6665_1067 chr4D 65075329 T/C - A G CT - BS00068242_51 chr4D 75780079 A/G + G A AG + BS00067786_51 chr4D 96909199 T/G - C A GT - RAC875_rep_c118305_446 chr4D 105892222 T/C + C T AG - D_contig18193_134 chr4D 124263575 T/C - G A AG + RAC875_c48283_1574 chr4D 134127549 A/G - T C CT + RAC875_rep_c109674_414 chr4D 185796315 A/C + C A GT - Excalibur_c43752_142 chr4D 208557773 A/C - G T GT + BS00066188_51 chr4D 215185603 A/G + G A AG + BS00065981_51 chr4D 239345868 T/C + C T CT + RAC875_c60218_63 chr4D 263948709 A/G - C T AG - D_GCE8AKX01BOGN5_399 chr4D 291766713 T/C - A G AG + RAC875_rep_c77874_269 chr4D 310101041 T/C + T C CT + GENE-2637_94 chr4D 310102364 T/C + C T CT + RAC875_c9526_88 chr4D 310104099 T/C + T C AG - BS00094770_51 chr4D 335782110 A/C + C A GT - RAC875_c5827_554 chr4D 337152963 A/G + A G AG + Ex_c7593_754 chr4D 337263929 A/C - T G GT + GENE-3078_101 chr4D 346130219 T/C + T C CT + BS00067901_51 chr4D 348050228 A/G - C T AG - Kukri_c46057_646 chr4D 348800218 T/C + T C AG - RAC875_rep_c72131_1005 chr4D 384266948 A/C + C A AC + Ex_c32540_659 chr4D 402555800 A/G - T C CT + D_GB5Y7FA02HBLTO_213 chr4D 438159120 T/C + C T AG - Kukri_c27107_760 chr4D 441838594 A/G - C T AG - Ex_c42133_630 chr4D 455250917 T/C - G A AG + Kukri_c4210_240 chr4D 455252974 T/G - C A GT - D_GDS7LZN02F0W89_230 chr4D 455339222 T/C - A G CT - BS00081724_51 chr4D 455343928 A/G - C T AG - BS00022436_51 chr4D 455344169 T/C - A G CT - IACX378 chr4D 455488896 A/G + A G CT - BS00068013_51 chr4D 455489627 A/G - T C AG - IACX5985 chr4D 455491691 A/C + C A AC + IAAV5065 chr4D 455532069 A/G - C T AG - D_GDEEGVY01C7BQU_446 chr4D 455746524 T/C - G A CT - BS00047797_51 chr4D 456087458 T/C + T C CT + BS00009677_51 chr4D 459226922 A/G - T C AG - Kukri_rep_c103156_235 chr4D 462838116 T/C - G A CT - RAC875_c6992_396 chr4D 464989287 A/G - T C AG - Kukri_rep_c102863_772 chr4D 469303556 A/G + G A CT - Excalibur_c29496_799 chr4D 475027867 T/G - C A GT - Excalibur_c22632_576 chr4D 481042045 A/G + A G CT - RAC875_c14085_1709 chr4D 482773964 T/C - A G CT - GENE-2372_108 chr4D 483064776 T/C + C T CT + Excalibur_c31044_482 chr4D 485524985 T/C + C T CT + IACX11246 chr4D 485525182 A/T + A T AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BobWhite_c14304_687 chr4D 487671744 A/G - C T AG - RAC875_c47328_483 chr4D 494056291 T/C + T C CT + GENE-2608_504 chr4D 497034462 T/C - G A AG + BobWhite_rep_c50013_65 chr4D 499449815 T/C + C T AG - BobWhite_s66943_270 chr4D 499451814 T/C + T C CT + Excalibur_c1954_930 chr4D 499503090 A/G + A G CT - Kukri_c29521_123 chr4D 502066957 A/G - C T CT + BS00066434_51 chr4D 502402896 A/G - C T AG - Excalibur_c15141_684 chr4D 503271370 A/C - G T GT + Ku_c4260_441 chr4D 505332733 A/G - C T AG - BS00067206_51 chr4D 507477611 A/G - T C CT + Excalibur_c27357_146 chr4D 509369305 T/C - A G CT - GENE-2278_444 chr4D 509371859 T/C + C T AG - RAC875_c8642_231 chr4D 509666767 T/C + C T AG - Kukri_rep_c95804_119 chr5A 10488 A/G - T C AG - BobWhite_c7114_237 chr5A 644225 T/G - A C AC + BobWhite_c41542_354 chr5A 693246 T/C + T C AG - BS00067606_51 chr5A 1275096 T/C + T C AG - BS00067647_51 chr5A 1275183 T/C + T C CT + BS00001525_51 chr5A 2414818 A/G + G A AG + RAC875_c1503_642 chr5A 2646813 T/C - G A CT - Excalibur_c22465_625 chr5A 2648868 A/C + C A AC + GENE-3324_338 chr5A 3521275 A/G - T C AG - IAAV5087 chr5A 4850696 A/G + A G AG + BS00064188_51 chr5A 4997860 A/G - C T CT + RAC875_c68530_59 chr5A 5998441 T/C NA NA NA AG NA flanks do not match reference at this position BobWhite_c7246_643 chr5A 6213549 A/G - T C CT + Excalibur_c6714_246 chr5A 6422288 A/G + G A CT - TA003745-0632 chr5A 6622326 A/G + A G AG + BS00023008_51 chr5A 8059408 T/C + T C CT + BS00101071_51 chr5A 8059452 A/G + A G AG + Kukri_c25201_305 chr5A 8239020 A/G - T C AG - Ku_c9559_737 chr5A 8243302 T/C + T C AG - BS00031073_51 chr5A 8243622 A/G + A G CT - Kukri_c17126_1211 chr5A 8244602 T/C NA NA NA AG NA flanks do not match reference at this position Ra_c10762_1137 chr5A 8246363 T/C + T C AG - Ex_c95453_1499 chr5A 9614797 A/G + A G AG + BS00003696_51 chr5A 9652546 T/C + T C CT + IACX5832 chr5A 9652546 A/G - T C AG - BS00022353_51 chr5A 9835076 T/C + C T CT + BS00086096_51 chr5A 9840279 T/C + T C AG - RFL_Contig3352_463 chr5A 11068471 A/G NA NA NA AG NA flanks do not match reference at this position BS00100185_51 chr5A 14844490 T/C - G A CT - GENE-3092_257 chr5A 15846578 T/C + C T CT + BS00079189_51 chr5A 15851119 T/C + C T CT + Kukri_c23694_370 chr5A 17222922 A/G - T C CT + IAAV7519 chr5A 17840086 C/G NA NA NA CG NA flanks do not match reference at this position Kukri_c2514_490 chr5A 18637963 A/G - T C AG - Tdurum_contig25432_1020 chr5A 18638044 T/G + G T AC - Tdurum_contig25432_1218 chr5A 18638242 T/C + T C AG - RAC875_c2926_371 chr5A 19232048 A/G + A G CT - GENE-3622_277 chr5A 19272287 A/G - C T AG - BS00111119_51 chr5A 19272838 A/G + A G AG + RFL_Contig3674_847 chr5A 19667864 T/C + C T AG - Excalibur_rep_c115510_314 chr5A 19979291 T/C NA NA NA AG NA flanks do not match reference at this position Ra_c7322_2294 chr5A 20816395 A/G - T C AG - BS00099700_51 chr5A 20993327 A/C NA NA NA GT NA flanks do not match reference at this position Kukri_c8835_579 chr5A 20994259 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c8835_112 chr5A 20998504 T/C - G A CT - BobWhite_rep_c50145_387 chr5A 26461227 T/G - A C AC + BS00094095_51 chr5A 28104282 T/C - G A AG + GENE-3321_201 chr5A 28104875 A/C - G T GT + BS00040933_51 chr5A 28228667 A/G + A G AG + Kukri_c93951_126 chr5A 29882064 A/G + A G AG + Excalibur_c94962_57 chr5A 31454401 T/C + C T AG - Kukri_c24642_426 chr5A 32669204 T/C + T C AG - BS00056932_51 chr5A 32880888 T/C + T C CT + BS00056933_51 chr5A 32881026 T/G + G T AC - BS00047242_51 chr5A 32883123 A/G + A G AG + BS00057293_51 chr5A 32887648 A/G + G A AG + BS00062907_51 chr5A 33012106 A/G + A G AG + Tdurum_contig11173_79 chr5A 35258888 A/G - C T AG - Tdurum_contig45977_1319 chr5A 35656265 T/C - G A AG + BS00081120_51 chr5A 35822927 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c32833_466 chr5A 36021661 T/C + C T AG - RFL_Contig2251_1349 chr5A 37620263 T/C + T C AG - Ra_c69221_1167 chr5A 41427501 T/C + T C CT + BS00031177_51 chr5A 41427631 T/G - A C GT - IAAV4072 chr5A 42106313 A/C - T G AC - Ra_c108731_554 chr5A 45986521 T/G + G T GT + BS00045473_51 chr5A 45990143 T/G + G T GT + BS00029347_51 chr5A 46230667 A/G - C T AG - BS00077990_51 chr5A 46234121 A/G + G A AG + BobWhite_c5564_86 chr5A 46502733 A/G + G A AG + BS00042511_51 chr5A 46572675 A/G - C T AG - Kukri_rep_c107435_940 chr5A 46621901 T/C + C T AG - BS00094396_51 chr5A 47448717 A/G + A G CT - BS00021660_51 chr5A 47459963 A/G - T C AG - BS00097623_51 chr5A 47645097 A/G - C T CT + BS00078654_51 chr5A 48174400 T/G + T G GT + Tdurum_contig10128_593 chr5A 48464957 T/C + C T AG - RAC875_c15192_51 chr5A 48465040 A/G - T C AG - Excalibur_c9836_408 chr5A 48467353 A/C - T G GT + Tdurum_contig10128_1532 chr5A 48467353 T/G + T G AC - Kukri_rep_c71114_838 chr5A 48890999 A/G + A G CT - tplb0056h22_2113 chr5A 48894719 A/G + A G AG + Ra_c23129_348 chr5A 49513603 A/G - T C AG - BS00071087_51 chr5A 51736684 A/C - T G GT + BS00041077_51 chr5A 52443448 T/G + G T GT + BS00048536_51 chr5A 54464713 A/G + A G AG + BS00013703_51 chr5A 57375725 T/G NA NA NA GT NA flanks do not match reference at this position BS00078288_51 chr5A 59026869 A/G + G A AG + Tdurum_contig10191_996 chr5A 59710985 T/C + C T CT + RAC875_c5699_352 chr5A 60118091 T/C - A G AG + RAC875_c45650_178 chr5A 63376844 A/G + A G CT - BS00079532_51 chr5A 64365984 T/G - A C GT - Jagger_c4425_128 chr5A 65980655 A/G + G A CT - BS00040403_51 chr5A 66089829 T/C + T C AG - RAC875_c323_257 chr5A 66091474 T/C - G A CT - RFL_Contig4646_526 chr5A 66091661 T/C + T C CT + RFL_Contig4646_564 chr5A 66091699 A/G + G A CT - BS00070550_51 chr5A 66092888 T/C + C T AG - BS00081565_51 chr5A 68549689 A/G + A G AG + BS00054690_51 chr5A 69101292 T/C - G A CT - IAAV2194 chr5A 69846902 T/G + T G GT + Ex_c6212_715 chr5A 69847908 A/G + G A AG + RAC875_c60415_154 chr5A 69848055 A/G + G A AG + BS00064371_51 chr5A 70000518 T/C - G A CT - GENE-0860_96 chr5A 70490417 A/G + G A CT - Ku_c30943_843 chr5A 71501725 T/C - A G CT - BS00060841_51 chr5A 74106016 A/G - T C AG - Kukri_c21380_833 chr5A 74106814 A/G + G A AG + Ra_c1184_61 chr5A 74752246 T/G - A C AC + IAAV456 chr5A 76910470 A/C + A C AC + IAAV5419 chr5A 77087934 T/C - A G AG + Kukri_c9885_1273 chr5A 77087934 A/G + A G AG + RAC875_rep_c72343_341 chr5A 78144828 T/C + T C CT + BobWhite_c19985_446 chr5A 78159813 T/C + C T CT + Kukri_c12439_876 chr5A 80153859 T/C + T C AG - BobWhite_rep_c49176_485 chr5A 86181443 T/C - G A CT - Tdurum_contig81753_70 chr5A 86181443 A/G + G A AG + Tdurum_contig81753_159 chr5A 86181532 A/G + A G AG + Ex_c13534_401 chr5A 86873587 T/C - G A CT - Excalibur_c25331_1224 chr5A 86873804 A/G - T C AG - RFL_Contig4653_1217 chr5A 89705501 T/C + T C AG - IAAV5061 chr5A 91119601 T/C - A G CT - RAC875_c29957_355 chr5A 92185272 A/G + G A AG + Kukri_c40804_171 chr5A 92443695 A/G - C T AG - Excalibur_c22926_514 chr5A 93198656 A/G - T C AG - Ku_c69633_1873 chr5A 97227315 A/G - C T AG - RAC875_rep_c114924_726 chr5A 104240514 A/G + G A CT - Ex_c1344_1859 chr5A 104625421 A/G - T C AG - Kukri_c19815_106 chr5A 105705945 A/G - T C CT + RAC875_c20021_615 chr5A 106748482 A/G - C T AG - Ex_c5902_360 chr5A 107271348 A/C NA NA NA GT NA flanks do not match reference at this position RAC875_rep_c80358_120 chr5A 107893260 T/C - G A CT - IAAV4939 chr5A 108266521 T/C + C T AG - BS00045284_51 chr5A 109342918 T/G + T G GT + Tdurum_contig18901_188 chr5A 114397891 A/G NA NA NA AG NA flanks do not match reference at this position GENE-3500_336 chr5A 117495535 T/C + T C AG - IAAV1838 chr5A 130537613 A/G + G A CT - Excalibur_c51133_246 chr5A 149209213 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_rep_c69186_666 chr5A 151253418 T/C + T C AG - Kukri_rep_c69378_1842 chr5A 174574211 A/G - C T AG - IAAV6849 chr5A 229501643 A/G - T C CT + BS00021901_51 chr5A 230072818 A/G + G A AG + Jagger_c5743_187 chr5A 259061990 T/C - G A CT - Ku_c70246_944 chr5A 263507209 A/C + C A GT - Ku_c26178_636 chr5A 269278255 T/C + C T AG - Kukri_c52733_358 chr5A 277334289 A/G - T C CT + BS00062996_51 chr5A 304461034 A/G - C T AG - JD_c424_170 chr5A 326043452 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c12738_882 chr5A 331401559 A/C + C A AC + Excalibur_rep_c67123_986 chr5A 331402786 A/G + A G CT - RFL_Contig3290_726 chr5A 344535943 T/C + C T CT + RAC875_rep_c109210_88 chr5A 368553215 A/C + C A AC + IAAV7800 chr5A 377940816 A/G - C T CT + BobWhite_rep_c49979_373 chr5A 381301752 T/C - G A CT - Excalibur_c30148_589 chr5A 381761549 A/G - T C AG - BobWhite_rep_c49700_452 chr5A 382778448 T/C + C T AG - BS00001322_51 chr5A 389718131 A/G + A G AG + GENE-3218_77 chr5A 389764433 A/C - T G GT + Kukri_c9247_1252 chr5A 390231073 A/G + G A AG + Tdurum_contig11815_195 chr5A 391543029 A/G + G A AG + BS00064945_51 chr5A 391543140 T/C - A G CT - BS00040623_51 chr5A 391548937 A/G - T C AG - BS00064120_51 chr5A 391754007 T/C + C T CT + BS00036839_51 chr5A 393918785 T/G + G T AC - RAC875_c12507_531 chr5A 393918861 T/C + T C CT + tplb0043g09_926 chr5A 395057867 A/G + G A CT - BS00056248_51 chr5A 395058143 T/C + C T AG - Tdurum_contig61258_264 chr5A 395304064 A/C + C A AC + Kukri_c24771_821 chr5A 395870811 A/G + G A AG + BS00068257_51 chr5A 395875736 T/C - G A CT - BS00084580_51 chr5A 396223859 A/C - G T GT + RAC875_c25733_2477 chr5A 398191083 A/C - T G AC - tplb0041o08_974 chr5A 399298139 A/G - T C AG - tplb0041o08_752 chr5A 399298361 A/G - C T AG - BobWhite_c17170_99 chr5A 406837723 T/C - A G AG + BS00078076_51 chr5A 409323809 T/G - A C GT - BS00067776_51 chr5A 410201584 A/G - C T AG - BS00066127_51 chr5A 414048529 A/G - T C AG - BS00063823_51 chr5A 414048806 A/G - C T CT + BS00063822_51 chr5A 414048811 A/G - T C CT + RAC875_c13_2330 chr5A 414049700 A/G - C T CT + RAC875_c13_2075 chr5A 414050055 T/G - A C GT - RAC875_c13_2042 chr5A 414050088 T/C - A G AG + RAC875_c13_1965 chr5A 414050165 T/C - G A CT - RAC875_c13_1589 chr5A 414050686 T/C - G A CT - RAC875_c13_1458 chr5A 414050817 T/C - G A CT - TA003225-0566 chr5A 414411825 T/G NA NA NA GT NA flanks do not match reference at this position Tdurum_contig49844_958 chr5A 414755544 A/G NA NA NA CT NA flanks do not match reference at this position tplb0031i04_452 chr5A 414755544 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig45240_1309 chr5A 415356017 A/G + A G CT - Ra_c33743_472 chr5A 415628849 T/C - A G CT - Ku_c21587_754 chr5A 415630714 T/G + G T GT + Excalibur_c53930_53 chr5A 416169608 A/G + G A CT - BS00070903_51 chr5A 416170601 A/G + A G CT - Excalibur_c26984_128 chr5A 416225479 T/C + T C CT + BS00086963_51 chr5A 419363482 A/G + A G CT - Tdurum_contig10546_273 chr5A 419688578 A/G - T C AG - BS00063425_51 chr5A 419868569 T/C + C T CT + BS00034303_51 chr5A 422077634 A/C - G T AC - BS00034304_51 chr5A 422077781 T/C - A G AG + BobWhite_c26540_273 chr5A 423251409 A/G - C T CT + Kukri_c3338_271 chr5A 423252192 T/C - A G CT - BS00068069_51 chr5A 423682122 T/C + C T CT + IAAV2080 chr5A 430246218 T/C + C T AG - BS00046529_51 chr5A 434725472 T/C - A G AG + BS00039188_51 chr5A 434794293 A/G + G A CT - BS00073215_51 chr5A 436080191 A/G - C T AG - BS00022683_51 chr5A 436081427 T/C - A G CT - BobWhite_c17440_130 chr5A 437208847 T/C + T C CT + BobWhite_c4336_127 chr5A 437926016 A/G + A G AG + BS00036907_51 chr5A 438149947 T/C + C T CT + Excalibur_c38185_633 chr5A 438334934 T/G + G T GT + Excalibur_c7180_862 chr5A 438468124 T/C + T C CT + Kukri_c5501_1515 chr5A 438469558 T/C + C T AG - BS00022500_51 chr5A 438471823 A/G - T C CT + BS00021939_51 chr5A 439186551 A/G + A G CT - BS00110139_51 chr5A 439186565 A/G + A G AG + RAC875_c100918_453 chr5A 439228657 A/G + G A AG + BS00076256_51 chr5A 439419144 T/C + C T CT + Excalibur_c22052_303 chr5A 439434065 T/C - A G AG + tplb0039m09_92 chr5A 439557828 T/G - C A GT - BobWhite_c1796_701 chr5A 439557857 T/G + G T GT + IAAV9057 chr5A 442271807 T/G + T G GT + RAC875_c95309_460 chr5A 442271807 A/C - T G GT + Kukri_c45983_524 chr5A 442271857 A/G - C T AG - BS00065693_51 chr5A 442353026 A/G + A G AG + IAAV3512 chr5A 442700425 T/G - C A AC + Kukri_c7633_724 chr5A 442700425 A/C + C A AC + BS00034704_51 chr5A 444264113 A/C + A C AC + RAC875_c4033_192 chr5A 444264987 A/G + G A CT - BS00066569_51 chr5A 444529828 T/C + C T AG - BobWhite_c14705_487 chr5A 444595597 A/G - T C CT + BS00005311_51 chr5A 444596286 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig102312_245 chr5A 444891174 T/G + G T GT + Tdurum_contig48766_257 chr5A 445191816 T/C - G A AG + Tdurum_contig54737_537 chr5A 445195933 T/G + T G GT + BS00040916_51 chr5A 445277514 A/G - C T AG - Tdurum_contig67516_236 chr5A 445281396 T/C NA NA NA AG NA flanks do not match reference at this position BS00109052_51 chr5A 445287948 T/C + C T AG - RAC875_c15713_943 chr5A 447536794 A/G + A G CT - BS00073404_51 chr5A 448092793 A/G + A G CT - RAC875_c58966_471 chr5A 450164108 T/C - A G CT - BS00076221_51 chr5A 450463831 T/C - G A CT - BS00067453_51 chr5A 450465560 T/C - G A CT - Tdurum_contig88305_380 chr5A 450467320 T/C + C T AG - BS00034101_51 chr5A 450541195 T/G + G T GT + Tdurum_contig81510_198 chr5A 450541955 T/C - A G AG + BS00089968_51 chr5A 450555688 A/G + G A AG + Ex_c6161_335 chr5A 451483907 T/C - G A AG + Excalibur_c15014_1170 chr5A 451784233 A/G - T C AG - Kukri_c2781_719 chr5A 451886259 T/C - G A CT - Tdurum_contig28306_292 chr5A 455206735 T/C - G A CT - BS00076190_51 chr5A 456059051 A/G - C T AG - JD_c64219_207 chr5A 456608136 A/G - T C CT + RAC875_c86270_269 chr5A 456972955 A/G + A G AG + RFL_Contig5137_602 chr5A 457076409 A/G + G A AG + RFL_Contig5137_917 chr5A 457076823 T/C + T C CT + BS00075308_51 chr5A 457089720 T/C + C T CT + IAAV4830 chr5A 457437230 A/G - C T AG - RFL_Contig727_736 chr5A 458203514 T/C + C T AG - GENE-3101_137 chr5A 458969969 A/G - C T AG - GENE-3101_854 chr5A 458970026 T/C NA NA NA CT NA flanks do not match reference at this position BS00058591_51 chr5A 459003147 T/C - G A CT - Tdurum_contig43874_1129 chr5A 460518596 A/G + G A CT - CAP8_c4920_219 chr5A 461484553 A/G - T C AG - BS00083507_51 chr5A 461490272 A/G + G A CT - Kukri_c46666_171 chr5A 461493131 T/G NA NA NA AC NA flanks do not match reference at this position GENE-3493_612 chr5A 461519165 A/G - T C AG - RFL_Contig1929_805 chr5A 461850056 T/G NA NA NA GT NA flanks do not match reference at this position Excalibur_rep_c74009_217 chr5A 462154990 T/C - G A AG + BobWhite_c34650_78 chr5A 462155287 A/G - T C CT + BS00100167_51 chr5A 462164350 A/G + G A AG + BobWhite_rep_c67156_244 chr5A 462164377 T/C + T C CT + BS00100178_51 chr5A 462165434 A/G + G A AG + BS00088895_51 chr5A 462843850 T/C + T C CT + BS00004202_51 chr5A 462843853 A/G + A G CT - BS00091219_51 chr5A 462862458 T/C - A G CT - BS00024854_51 chr5A 463061920 T/C + T C CT + BS00013563_51 chr5A 463066939 A/C + C A AC + Excalibur_c56861_322 chr5A 463601125 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c22020_280 chr5A 463603917 T/C + C T CT + RFL_Contig4500_912 chr5A 463762999 A/C - T G GT + Tdurum_contig11054_307 chr5A 463763245 T/C - G A CT - Kukri_c5460_1063 chr5A 464477165 T/C - G A AG + BS00022358_51 chr5A 464477457 T/C + T C CT + Tdurum_contig4567_1290 chr5A 464477457 A/G - T C CT + BS00080090_51 chr5A 464477486 T/C + C T CT + BS00080093_51 chr5A 464478485 T/C + C T AG - IAAV2127 chr5A 464478517 T/C + T C CT + Kukri_rep_c68263_453 chr5A 464478587 A/G + A G CT - Kukri_rep_c68263_657 chr5A 464478791 A/C + A C GT - Tdurum_contig4567_172 chr5A 464478791 T/G - A C GT - Ra_c30977_330 chr5A 465541060 T/C - G A CT - BS00066916_51 chr5A 466014043 A/C - G T AC - Tdurum_contig94007_225 chr5A 466035966 T/C + C T AG - Kukri_c75644_104 chr5A 466036183 A/G - T C CT + BobWhite_c9931_915 chr5A 466613819 T/C - A G AG + RAC875_c42037_363 chr5A 466615937 A/G + A G CT - IACX3152 chr5A 466985355 T/G - A C GT - Tdurum_contig49751_2646 chr5A 466985363 T/G - C A GT - IACX3154 chr5A 466985415 T/C - A G AG + Tdurum_contig49751_2541 chr5A 466985468 A/C - G T AC - RAC875_rep_c110032_448 chr5A 466985885 A/G - T C CT + BS00069980_51 chr5A 466988912 T/C - G A AG + Excalibur_c32630_104 chr5A 467379070 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c24787_51 chr5A 467381820 A/G - T C CT + Kukri_c35744_213 chr5A 467780860 T/C + T C AG - Kukri_c30875_283 chr5A 468466792 A/G - C T AG - Kukri_c17430_972 chr5A 468467313 A/G + A G CT - BS00067797_51 chr5A 468468250 A/G + G A AG + Kukri_c43155_247 chr5A 469046611 T/G + T G GT + Excalibur_c92838_112 chr5A 469609412 A/G - T C AG - BS00022914_51 chr5A 469610589 T/C + C T CT + BS00097930_51 chr5A 469610676 T/C + C T AG - BS00078242_51 chr5A 469612690 T/C - A G CT - Excalibur_c19647_703 chr5A 470034298 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_c19647_294 chr5A 470036164 T/C - A G CT - Ku_c6319_201 chr5A 470036249 T/C - G A CT - RAC875_c21338_329 chr5A 470080587 T/C + T C AG - Kukri_c98958_532 chr5A 470157627 A/C + A C AC + Ku_c24324_850 chr5A 470174498 A/C - T G GT + Excalibur_c97639_173 chr5A 471475653 T/C + C T CT + BS00027465_51 chr5A 471695011 A/G + A G AG + BS00027466_51 chr5A 471695018 A/G + A G AG + BS00022509_51 chr5A 472278404 T/C - A G CT - BS00090309_51 chr5A 472342800 A/G + A G CT - RFL_Contig3882_550 chr5A 472703234 T/C - A G CT - Ex_c19057_965 chr5A 473625322 T/C - G A AG + Excalibur_c19057_701 chr5A 473625586 T/C - A G CT - CAP8_c2014_192 chr5A 473637733 A/G - C T AG - BS00065386_51 chr5A 474482949 A/G - T C AG - Ku_c3432_336 chr5A 474816049 T/C - A G CT - RAC875_c52086_340 chr5A 475268291 A/G + A G CT - BobWhite_rep_c64197_143 chr5A 475268320 A/G + G A CT - tplb0051d06_1385 chr5A 475296150 A/G + A G CT - Kukri_c36630_225 chr5A 475315347 A/G NA NA NA AG NA flanks do not match reference at this position BS00022815_51 chr5A 475321461 A/G + A G CT - BobWhite_c13900_53 chr5A 475466443 T/G + G T AC - Kukri_c53586_128 chr5A 475466518 T/C + T C AG - tplb0057m23_1318 chr5A 475466701 T/C - A G CT - tplb0057m23_716 chr5A 475467302 A/G - C T AG - CAP8_c5592_77 chr5A 476403261 A/C + C A GT - Kukri_c2326_1037 chr5A 476602412 T/G - C A AC + Kukri_c2326_995 chr5A 476602454 T/C - G A AG + IAAV6342 chr5A 477296101 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BobWhite_c13238_386 chr5A 478018620 A/G + A G CT - BobWhite_rep_c61813_322 chr5A 478820958 A/G + A G CT - BS00107192_51 chr5A 478821075 A/G + G A AG + IAAV3514 chr5A 478822209 T/C - A G AG + RAC875_c232_1895 chr5A 478896740 A/G - C T AG - RAC875_c54622_446 chr5A 479395582 T/C - G A AG + BS00062939_51 chr5A 479601620 T/G + G T GT + BobWhite_rep_c64579_593 chr5A 480041094 A/G + G A AG + GENE-3439_205 chr5A 480088854 T/C - A G CT - RFL_Contig389_913 chr5A 480176540 T/C + T C AG - BS00022495_51 chr5A 480176958 A/G - C T AG - RAC875_c11695_2194 chr5A 480284549 A/C - T G AC - Kukri_rep_c104877_2166 chr5A 480285224 A/C - G T GT + Ex_c3838_1246 chr5A 480285516 T/C + C T AG - Ex_c3838_1252 chr5A 480285522 T/C + C T CT + RAC875_c9531_1544 chr5A 480289328 A/C + A C AC + BS00068096_51 chr5A 481207857 T/C - G A AG + BS00100108_51 chr5A 481896757 T/C - G A AG + BS00100107_51 chr5A 481896860 T/C - G A AG + IAAV2363 chr5A 481901424 A/G + G A AG + GENE-3528_61 chr5A 481912674 T/C + C T CT + IACX5879 chr5A 482120725 A/C + C A GT - Tdurum_contig49187_601 chr5A 482375764 T/C + C T AG - IACX8002 chr5A 485201265 T/C - G A AG + BS00069175_51 chr5A 485598127 T/C - G A CT - IACX7820 chr5A 485841457 T/C + C T AG - BS00023407_51 chr5A 486063072 A/G + A G CT - Ra_c9938_1294 chr5A 486750034 T/C + C T CT + Ra_c9938_1299 chr5A 486750039 A/G NA NA NA AG NA flanks do not match reference at this position Ra_c9938_1734 chr5A 486750616 T/C + C T AG - Ku_c47168_563 chr5A 487844882 A/G - T C AG - CAP8_c1066_309 chr5A 488262170 T/C - A G AG + RAC875_c1437_1644 chr5A 488416614 T/C - A G CT - Tdurum_contig76136_404 chr5A 488629640 A/G - C T CT + Ex_c9327_1907 chr5A 488633534 T/C - A G CT - Ex_c9327_1198 chr5A 488634243 A/G - T C AG - Tdurum_contig59338_1902 chr5A 488635079 T/C + T C CT + IAAV6488 chr5A 488893324 A/C + C A GT - Tdurum_contig43844_1266 chr5A 490039168 T/C + C T CT + RAC875_c99519_227 chr5A 490310874 A/G - T C CT + Excalibur_c94356_529 chr5A 490311005 A/C + A C AC + BobWhite_c2905_590 chr5A 492902851 A/C + C A AC + RAC875_c3925_1043 chr5A 493464719 T/C - A G CT - GENE-3471_298 chr5A 493469121 T/C - G A CT - BS00094342_51 chr5A 494870893 T/G + G T GT + BS00094343_51 chr5A 494870904 A/G + G A AG + IACX2640 chr5A 495100618 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Kukri_rep_c114331_346 chr5A 495869078 T/G + T G GT + GENE-3211_99 chr5A 495883662 A/C + A C GT - BS00024602_51 chr5A 499660213 T/G - A C AC + Excalibur_c1208_72 chr5A 502219493 A/C + A C AC + JD_c20036_865 chr5A 503055092 T/G - C A AC + Ra_c700_1024 chr5A 503055822 A/G + A G AG + Ra_c700_2210 chr5A 503057017 A/G + G A CT - Ra_c700_3506 chr5A 503058946 T/C + T C CT + BobWhite_c9057_118 chr5A 503782973 A/G + A G CT - Kukri_rep_c103857_458 chr5A 503943412 A/G + G A CT - RAC875_c56635_1008 chr5A 503946033 T/C - A G AG + Excalibur_c54514_248 chr5A 503946111 A/G - C T CT + Excalibur_c6567_845 chr5A 504573907 A/C + C A AC + RAC875_c28819_281 chr5A 504873208 A/G + G A CT - BobWhite_c5457_1440 chr5A 504873507 T/C + C T CT + tplb0056b09_1000 chr5A 505509570 T/C + T C AG - GENE-3791_463 chr5A 507967048 T/C NA NA NA AG NA flanks do not match reference at this position TA004548-0753 chr5A 507967048 A/G + A G AG + Excalibur_c60388_189 chr5A 510160673 T/C + T C AG - Kukri_s112067_110 chr5A 510161035 T/C + C T CT + Excalibur_rep_c69868_123 chr5A 510891390 A/G - T C AG - Ex_c104539_35 chr5A 512234990 T/C - A G AG + Kukri_rep_c72046_78 chr5A 512234990 T/C - A G AG + Jagger_c550_91 chr5A 512237645 A/G - T C CT + RAC875_c30711_544 chr5A 512828173 A/C NA NA NA AC NA flanks do not match reference at this position BobWhite_c11512_157 chr5A 514092445 T/C + C T AG - RAC875_c31670_389 chr5A 514094600 T/C - G A CT - RAC875_c68120_285 chr5A 514153610 T/G - C A GT - BS00085826_51 chr5A 519885504 A/G + G A AG + Kukri_c29998_1417 chr5A 519896473 A/G + G A AG + Excalibur_c22783_765 chr5A 519898550 T/C - A G CT - BobWhite_c5540_416 chr5A 519905799 A/G + A G AG + Excalibur_c2598_2052 chr5A 519951564 A/G - C T AG - Ra_c6930_1753 chr5A 519951786 A/G - C T AG - BS00000244_51 chr5A 520755750 T/C + C T AG - Excalibur_c29626_353 chr5A 521296092 A/G - T C AG - RAC875_c8544_646 chr5A 524228905 T/C + C T CT + Excalibur_c12332_161 chr5A 524229949 A/G - C T AG - RAC875_c8544_1562 chr5A 524230251 T/C + C T AG - CAP11_c3591_72 chr5A 525115978 T/C + C T AG - JD_c5000_410 chr5A 526619471 A/G + A G AG + RAC875_c15929_925 chr5A 527918421 A/G + A G AG + IAAV2077 chr5A 528114070 T/G + G T GT + BS00022761_51 chr5A 528114084 A/G + A G AG + BobWhite_c31565_576 chr5A 528114443 A/G + A G AG + BobWhite_c1387_798 chr5A 528114567 A/C + C A GT - RAC875_c61597_406 chr5A 528603768 T/G - C A GT - RAC875_c61597_327 chr5A 528603847 A/G - C T CT + BS00061387_51 chr5A 529807605 A/G + G A CT - Excalibur_c9846_1720 chr5A 533022565 A/G + A G AG + BobWhite_c19155_246 chr5A 533071439 T/C - A G AG + BobWhite_c2715_411 chr5A 533291065 A/G - T C AG - GENE-3156_152 chr5A 533488184 T/C + T C AG - BS00049135_51 chr5A 534272341 A/G - C T AG - tplb0058c02_1053 chr5A 535012968 T/C NA NA NA CT NA flanks do not match reference at this position GENE-3575_1073 chr5A 535137831 A/G + G A AG + BS00021805_51 chr5A 535138069 T/C - A G CT - IACX1055 chr5A 535138071 A/G NA NA NA AG NA flanks do not match reference at this position BS00067882_51 chr5A 536352784 A/G - T C CT + BobWhite_c23972_892 chr5A 536772801 T/G + T G AC - Excalibur_c31404_184 chr5A 536797217 T/C - G A CT - BS00010698_51 chr5A 536814357 A/G + A G AG + IAAV5811 chr5A 537123967 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c103967_76 chr5A 537354508 A/G + A G AG + Kukri_c6148_74 chr5A 537354791 T/C + T C AG - JD_c6094_241 chr5A 537355199 T/C + C T CT + Kukri_c101160_163 chr5A 537355346 T/G + T G GT + BobWhite_c6094_740 chr5A 537355698 A/C + C A GT - RFL_Contig4162_1285 chr5A 537634487 A/C - T G AC - BS00000365_51 chr5A 538000523 A/G - C T CT + RFL_Contig3135_689 chr5A 538314550 T/C + C T CT + GENE-3155_652 chr5A 538320187 T/C + T C CT + Kukri_c8237_1883 chr5A 538320668 T/C - A G CT - GENE-4139_155 chr5A 538321523 A/G - T C AG - BS00096758_51 chr5A 538757159 T/G - C A AC + Excalibur_c12678_238 chr5A 538758282 T/G - A C GT - CAP7_c1404_72 chr5A 539092970 T/C - G A AG + Jagger_c6106_119 chr5A 539945381 A/G + A G CT - Kukri_s112978_54 chr5A 539947181 A/G + G A CT - Kukri_c14889_1086 chr5A 540052320 T/C - G A AG + Kukri_c14889_116 chr5A 540053290 T/C - A G CT - GENE-3189_377 chr5A 540060736 T/C - G A CT - RAC875_s114930_80 chr5A 540285782 A/G + A G CT - BS00072156_51 chr5A 540611588 A/G - T C AG - BS00072155_51 chr5A 540611744 A/G - T C CT + Kukri_c20258_143 chr5A 540613124 T/C - G A AG + Tdurum_contig30558_109 chr5A 544566505 A/G NA NA NA AG NA flanks do not match reference at this position IAAV5029 chr5A 545564461 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c19099_434 chr5A 545639356 T/C + T C AG - BS00010366_51 chr5A 546528118 A/G - T C CT + BS00083514_51 chr5A 546531060 T/C - G A CT - RAC875_c93097_105 chr5A 546552653 T/C - A G CT - BS00045759_51 chr5A 546791148 A/G - T C CT + BS00045758_51 chr5A 546791150 T/C - A G AG + Kukri_c22195_440 chr5A 546793443 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_c9210_168 chr5A 547171688 A/G - T C CT + Excalibur_rep_c68708_80 chr5A 547173269 A/G - T C CT + Kukri_c94493_273 chr5A 547410539 A/G - C T CT + BobWhite_rep_c63943_76 chr5A 547415476 T/G + T G GT + Excalibur_c52167_355 chr5A 549578750 T/C + T C AG - BS00021678_51 chr5A 549800726 T/C + C T AG - BS00110075_51 chr5A 549800748 A/G + A G AG + Kukri_c64573_443 chr5A 550646329 A/G - T C AG - Kukri_c27591_1180 chr5A 551044050 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c45894_552 chr5A 552070989 T/C - A G CT - Excalibur_c45853_1161 chr5A 552161370 T/C - G A AG + BS00022215_51 chr5A 552162031 A/G + G A AG + IAAV2328 chr5A 555540548 T/C - G A AG + BS00065292_51 chr5A 555542319 A/G - C T AG - BS00065551_51 chr5A 556531590 A/G - T C CT + IAAV1016 chr5A 557321443 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_rep_c91682_90 chr5A 558689000 T/C - A G CT - Tdurum_contig54785_216 chr5A 558692830 T/C - A G CT - RAC875_c32611_347 chr5A 559013526 T/C - A G CT - Kukri_c52_225 chr5A 559070986 T/G + G T GT + RFL_Contig2031_2040 chr5A 559071692 A/G + G A AG + Kukri_rep_c98079_222 chr5A 559073893 T/C - G A CT - BS00077858_51 chr5A 559505920 A/G + A G CT - BS00077855_51 chr5A 559506284 T/C + T C AG - BS00010179_51 chr5A 559507385 A/G - T C AG - RAC875_c23340_2243 chr5A 559738002 T/C + T C CT + IACX3911 chr5A 561173979 T/C + C T CT + Excalibur_c51589_200 chr5A 561660942 A/G - T C CT + BobWhite_rep_c56312_106 chr5A 561693130 A/G + G A AG + BobWhite_c46489_189 chr5A 561972896 A/G + A G CT - Tdurum_contig49576_75 chr5A 561973065 A/C - T G GT + Excalibur_c7556_381 chr5A 562484499 A/G - T C CT + RFL_Contig1284_640 chr5A 564595426 A/G - C T AG - BS00035256_51 chr5A 565540546 T/C + T C AG - RAC875_c60522_1278 chr5A 565547322 T/C - A G AG + Excalibur_c37642_1416 chr5A 565549090 A/G - T C AG - Excalibur_c37642_493 chr5A 565550130 A/C - G T GT + Tdurum_contig12066_247 chr5A 565753079 A/G + G A CT - Excalibur_c8030_2139 chr5A 567526679 T/G + T G AC - Tdurum_contig60421_74 chr5A 567526989 A/G - T C AG - RAC875_rep_c107228_92 chr5A 567691316 A/G + A G AG + Excalibur_rep_c71254_415 chr5A 567917336 T/C + T C AG - Excalibur_c33923_592 chr5A 568157020 T/C - A G CT - Ku_c915_507 chr5A 568269384 T/C + C T AG - Excalibur_c472_914 chr5A 568272270 T/G - A C AC + Kukri_c96249_58 chr5A 569285729 T/C - A G CT - GENE-3278_642 chr5A 569288197 T/C - A G CT - BS00022994_51 chr5A 569452562 A/G + G A CT - Kukri_c38748_174 chr5A 569452729 A/G - C T CT + BS00109395_51 chr5A 569456354 T/C + C T AG - BS00109396_51 chr5A 569456404 A/G + G A CT - Jagger_c8122_139 chr5A 569463780 A/G + A G AG + BS00022644_51 chr5A 569464087 T/C + T C AG - Excalibur_c64487_146 chr5A 569464215 A/G - T C AG - BS00002800_51 chr5A 569469628 A/G + G A AG + IACX4952 chr5A 569469628 T/C - G A AG + IACX4951 chr5A 569469674 T/C - G A AG + Excalibur_c14745_268 chr5A 569655017 T/C + C T CT + IAAV4695 chr5A 569701613 T/C + T C AG - GENE-3383_162 chr5A 569717669 T/G + G T GT + IAAV1311 chr5A 569806062 T/C + C T AG - Kukri_c31479_147 chr5A 569989461 A/G - C T CT + Kukri_c28080_887 chr5A 570187361 A/G - T C AG - BS00073670_51 chr5A 570716270 A/G - T C AG - Tdurum_contig71499_211 chr5A 570934010 A/G + A G CT - BobWhite_c40633_308 chr5A 570934273 A/G + G A AG + RAC875_c25339_200 chr5A 571683265 A/G - T C AG - Ra_c50261_717 chr5A 571787892 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_c14028_182 chr5A 571789646 T/G + T G AC - BS00029871_51 chr5A 572817662 A/G - T C CT + Tdurum_contig36142_150 chr5A 572840902 T/C - A G CT - BS00071869_51 chr5A 573040464 T/C - G A AG + Kukri_c2414_544 chr5A 573042453 A/G + A G CT - Ku_c13370_656 chr5A 573042833 A/G + G A CT - Tdurum_contig44343_1039 chr5A 573589851 A/G + A G AG + BobWhite_c48730_723 chr5A 573650455 A/G + G A CT - Ku_c19858_2078 chr5A 577942805 T/C + C T CT + Kukri_c31599_1456 chr5A 577951255 A/G - T C AG - BS00076246_51 chr5A 578058189 T/C - G A AG + BS00074299_51 chr5A 578061400 T/C - G A CT - Tdurum_contig86202_145 chr5A 578063900 T/C + C T CT + Tdurum_contig86202_175 chr5A 578063930 A/G + A G CT - BobWhite_c23736_153 chr5A 578448167 A/G + A G CT - Tdurum_contig52695_388 chr5A 578449291 T/C - A G AG + GENE-3601_145 chr5A 580465717 T/C NA NA NA CT NA flanks do not match reference at this position BS00044408_51 chr5A 580802763 T/C - A G CT - Excalibur_c37943_221 chr5A 580948088 T/C + C T AG - Kukri_c29560_455 chr5A 581302317 A/G - T C CT + BS00065481_51 chr5A 581479138 T/C - G A CT - BS00097986_51 chr5A 582961427 T/C - A G AG + Ex_c24587_139 chr5A 583558199 T/C NA NA NA CT NA flanks do not match reference at this position Ra_c14657_919 chr5A 584056533 A/G - T C CT + BS00096940_51 chr5A 584419616 A/G + A G CT - Excalibur_rep_c103747_193 chr5A 584614282 T/C + T C CT + IAAV1650 chr5A 584614282 A/G - T C CT + IAAV3043 chr5A 584672964 A/C + A C AC + Tdurum_contig55097_601 chr5A 584713871 A/G - C T CT + IACX9023 chr5A 584713910 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Excalibur_c7729_144 chr5A 585412855 A/G - T C CT + RAC875_c9984_1003 chr5A 585458451 T/G - A C GT - BS00098062_51 chr5A 585489452 A/G - T C CT + RAC875_rep_c109716_67 chr5A 586597476 A/G - C T AG - BobWhite_c471_2245 chr5A 586599649 T/C + C T CT + BS00022071_51 chr5A 586604611 T/C + T C CT + IAAV3365 chr5A 586605778 A/G - T C CT + Excalibur_c23354_187 chr5A 586724570 T/C - A G AG + Kukri_c9411_676 chr5A 586726350 T/C + C T CT + BobWhite_c10385_374 chr5A 587412185 T/C - G A AG + BS00031117_51 chr5A 588375806 T/C - A G CT - IACX448 chr5A 588377241 T/C - A G CT - BobWhite_c21949_117 chr5A 588552603 A/G + A G CT - BobWhite_c21949_150 chr5A 588552636 T/C + C T CT + BS00075959_51 chr5A 588741114 A/G + G A CT - Kukri_c6669_145 chr5A 588872163 T/C + T C AG - Kukri_c33022_198 chr5A 589223758 A/G + A G CT - Ex_c67086_584 chr5A 590599855 A/G NA NA NA AG NA flanks do not match reference at this position BS00088851_51 chr5A 591463499 T/C - A G CT - RAC875_rep_c76193_513 chr5A 591487483 T/C - G A CT - CAP11_c3209_76 chr5A 592036346 A/G - C T CT + Tdurum_contig50175_875 chr5A 594351599 A/G - T C CT + BobWhite_c658_377 chr5A 594352331 A/G - T C AG - BS00041063_51 chr5A 594960175 A/G + G A AG + Tdurum_contig10843_745 chr5A 594962106 T/C + C T AG - CAP8_c8785_136 chr5A 595038086 T/C - A G AG + RFL_Contig316_572 chr5A 595372494 A/G + A G AG + BS00059098_51 chr5A 595407698 A/C + A C AC + BS00108474_51 chr5A 595537702 T/C + C T AG - BS00100510_51 chr5A 596010510 T/G + T G AC - tplb0044j06_689 chr5A 596013562 A/G + G A CT - Ra_c3966_2205 chr5A 596465279 T/C + T C CT + Ku_c12469_983 chr5A 596520995 A/C - G T AC - Ku_c12469_837 chr5A 596521141 A/G - C T CT + Tdurum_contig14490_593 chr5A 601433412 A/G + A G CT - IAAV4145 chr5A 602356473 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles CAP11_c1685_149 chr5A 607835124 T/C - A G CT - RAC875_c3964_752 chr5A 608624574 T/C + C T AG - RAC875_c7132_134 chr5A 609195920 A/G - C T AG - BS00067150_51 chr5A 609243917 A/G + A G CT - BS00074855_51 chr5A 609870544 A/G - T C AG - Excalibur_c99584_170 chr5A 610211291 A/G - T C AG - BS00022754_51 chr5A 610212890 T/C + C T AG - BS00022753_51 chr5A 610217061 A/G + G A CT - Excalibur_c9258_1222 chr5A 610483160 A/G - T C AG - Tdurum_contig47101_301 chr5A 611130640 T/C + T C CT + Ex_c6479_750 chr5A 611649863 A/G - T C AG - RAC875_rep_c112818_307 chr5A 613477789 A/G + A G AG + BobWhite_rep_c64315_180 chr5A 613543528 T/G + G T AC - BobWhite_rep_c64315_248 chr5A 613543596 A/G + A G AG + CAP7_c5006_150 chr5A 613588303 T/C - G A CT - RAC875_c8231_1578 chr5A 613588303 A/G + G A AG + Excalibur_c57920_54 chr5A 613703510 A/G + A G CT - BS00032146_51 chr5A 615186761 T/C + T C CT + Kukri_c17691_158 chr5A 615299152 T/C + T C CT + Excalibur_c92705_94 chr5A 615305089 T/C + C T CT + BS00010882_51 chr5A 615318703 A/G - T C AG - BobWhite_c14486_122 chr5A 615864204 A/G + G A AG + RAC875_c40928_60 chr5A 617347931 T/C + T C AG - BS00065067_51 chr5A 618602625 T/C + C T AG - Ku_c21235_676 chr5A 618950521 T/C - G A CT - BobWhite_c16397_524 chr5A 619682348 T/G + T G GT + IACX2540 chr5A 619684883 A/G - C T AG - IACX2539 chr5A 619685355 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Kukri_c13776_512 chr5A 619692449 T/C + T C CT + IACX7615 chr5A 621759901 C/G + NA NA CG NA reference base A not among SNP alleles Kukri_c10508_755 chr5A 622052621 T/C + T C CT + BobWhite_c15476_88 chr5A 625732721 T/G + T G GT + Kukri_c55310_94 chr5A 633843999 A/G - C T CT + GENE-2848_248 chr5A 633863559 A/G - T C AG - BS00104432_51 chr5A 636413931 A/C + A C GT - Excalibur_c3339_139 chr5A 640172781 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_rep_c95692_396 chr5A 640941627 T/C + C T CT + Kukri_c267_77 chr5A 644137644 T/C - A G AG + CAP12_c2984_189 chr5A 645980313 A/G + A G CT - Tdurum_contig13810_485 chr5A 647364709 T/C - A G AG + BobWhite_c14360_420 chr5A 649246508 T/C NA NA NA AG NA flanks do not match reference at this position IAAV4395 chr5A 649782477 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c6890_150 chr5A 650270583 T/C + C T CT + Kukri_rep_c112425_506 chr5A 650273052 A/G NA NA NA CT NA flanks do not match reference at this position tplb0041f23_1202 chr5A 654151067 T/C + C T CT + Excalibur_c60554_394 chr5A 654622159 T/G + T G AC - BobWhite_c43389_1243 chr5A 656943065 A/C NA NA NA GT NA flanks do not match reference at this position RAC875_c55872_149 chr5A 657047639 A/G + A G CT - BS00085711_51 chr5A 657057643 A/G + G A AG + CAP8_rep_c4852_130 chr5A 657382435 T/G NA NA NA AC NA flanks do not match reference at this position Ra_c106922_334 chr5A 659712644 T/C + T C AG - Tdurum_contig29112_483 chr5A 659725866 A/G + A G CT - GENE-2380_71 chr5A 660436518 A/G + A G AG + RAC875_c9617_395 chr5A 662351129 T/C - G A CT - RAC875_c9617_373 chr5A 662351151 T/C - A G AG + Excalibur_c61241_109 chr5A 662361484 T/C + T C CT + CAP8_c317_307 chr5A 663306575 A/G + A G AG + Kukri_c86812_193 chr5A 663374213 A/C + A C GT - BS00022378_51 chr5A 663914423 A/G - T C CT + BS00003088_51 chr5A 663941710 A/G + G A CT - BS00090847_51 chr5A 664274385 T/C + C T CT + BS00043676_51 chr5A 664483630 T/C + T C CT + TA006296-0731 chr5A 664483630 A/G - T C CT + BobWhite_c37076_229 chr5A 664800745 T/C + C T CT + BobWhite_c42349_99 chr5A 665471409 A/G - C T AG - Excalibur_c60150_107 chr5A 665473759 T/C - G A AG + BS00009342_51 chr5A 665596956 A/G + NA NA CT NA reference base T not among SNP alleles GENE-2725_217 chr5A 665614169 A/G + G A AG + GENE-2725_244 chr5A 665614192 T/C + C T AG - Excalibur_c79009_75 chr5A 665775686 T/C + T C AG - RAC875_c57603_144 chr5A 666228776 A/G + A G AG + RFL_Contig5787_2311 chr5A 666230627 A/G - T C CT + Kukri_c44572_797 chr5A 666303416 A/G - T C CT + BS00024230_51 chr5A 666315529 T/C + C T CT + BobWhite_c17045_186 chr5A 666742928 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c8647_141 chr5A 666932202 A/G + G A AG + BS00089076_51 chr5A 667102912 T/C + C T AG - RFL_Contig840_961 chr5A 670623373 T/C + C T CT + RAC875_c24767_132 chr5A 670819759 A/G + A G AG + Excalibur_c104037_107 chr5A 670820085 A/G + A G AG + BS00063793_51 chr5A 671393458 A/G - C T AG - Kukri_rep_c91370_381 chr5A 671444797 T/C + T C CT + BS00055102_51 chr5A 671551588 T/C + C T CT + Kukri_c18023_553 chr5A 672407756 T/C - A G AG + BS00065915_51 chr5A 672574128 T/G + T G GT + BS00068435_51 chr5A 673549516 A/G - C T CT + Kukri_c49033_52 chr5A 676600603 T/C - A G CT - BS00022867_51 chr5A 677130302 T/C - A G CT - CAP11_c2623_196 chr5A 677160779 A/G - T C CT + BS00081951_51 chr5A 677631836 T/C - A G CT - BS00021968_51 chr5A 677631915 A/G - C T AG - BobWhite_rep_c63332_67 chr5A 677845610 A/G - T C CT + BS00022838_51 chr5A 678229521 A/G + G A AG + RAC875_c32639_395 chr5A 679489743 T/C - G A CT - Kukri_c75091_154 chr5A 679657910 T/C + T C CT + Kukri_c75091_220 chr5A 679657976 T/G + G T AC - Tdurum_contig42962_2138 chr5A 680116503 A/G + A G AG + BobWhite_c8906_83 chr5A 680209988 T/C + T C CT + BS00023070_51 chr5A 680743604 A/C - T G GT + Excalibur_c32414_861 chr5A 681487154 A/G - T C CT + Excalibur_c32414_705 chr5A 681487310 A/G - T C AG - Excalibur_c9901_251 chr5A 682898508 T/G NA NA NA AC NA flanks do not match reference at this position Excalibur_c9901_163 chr5A 682903506 A/G - T C CT + BobWhite_c6966_236 chr5A 683353694 T/C - A G AG + CAP12_c956_61 chr5A 684939752 A/G - C T AG - CAP7_c9530_138 chr5A 685012468 A/C + A C AC + Kukri_c31705_105 chr5A 685441494 A/G + A G AG + BS00036851_51 chr5A 685543216 T/C - A G AG + tplb0029a15_1300 chr5A 685543373 A/C - G T GT + Ku_c19516_384 chr5A 687278999 T/G + T G AC - GENE-2826_325 chr5A 688319509 A/C - T G AC - BS00020605_51 chr5A 689609466 T/G - C A GT - BS00107823_51 chr5A 690546923 T/G + T G AC - BS00065714_51 chr5A 691027878 T/C + T C CT + CAP12_c2569_346 chr5A 691030920 A/C + A C GT - BobWhite_c4818_173 chr5A 692163603 A/G - C T AG - Excalibur_c46261_342 chr5A 697998969 T/C - G A AG + tplb0049a09_2097 chr5A 698002707 T/C - A G AG + tplb0049a09_1302 chr5A 698003772 T/C - G A CT - BobWhite_c8266_227 chr5A 698508163 T/G + G T AC - BobWhite_c15206_166 chr5A 700208187 T/C NA NA NA AG NA flanks do not match reference at this position tplb0036c11_641 chr5A 700211516 T/C - A G AG + BS00022864_51 chr5A 700371802 T/C + C T AG - Excalibur_c79156_402 chr5A 700441168 A/G - C T AG - Excalibur_c79156_129 chr5A 700441440 T/C - G A CT - Tdurum_contig8348_831 chr5A 700443596 T/C + C T CT + Tdurum_contig81113_401 chr5A 700620138 A/G + A G CT - Excalibur_c77910_272 chr5A 701999747 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c42255_425 chr5A 702166708 A/C + A C GT - BS00068108_51 chr5A 702461365 A/G + A G CT - CAP12_rep_c5184_99 chr5A 702753127 A/G + G A CT - BS00069245_51 chr5A 703398417 T/C + C T CT + IACX5640 chr5A 704344878 T/C - G A AG + CAP12_c1272_334 chr5A 704515225 A/G + G A AG + IAAV3048 chr5A 705571373 A/G + A G AG + BS00000006_51 chr5A 706240306 T/G + G T AC - GENE-2673_1010 chr5A 706538694 A/C + A C AC + BobWhite_c11539_336 chr5A 706540817 T/C + T C CT + TA003462-0942 chr5A 707823663 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c13693_87 chr5A 708439001 A/G + A G CT - Excalibur_c2171_2728 chr5A 708441455 T/C + T C CT + RAC875_c39430_181 chr5B 87538 T/C + C T CT + BS00032003_51 chr5B 2559430 T/C - G A AG + BS00091518_51 chr5B 6648547 T/C + C T CT + BS00091519_51 chr5B 6648567 A/G + G A AG + BS00079166_51 chr5B 7706212 A/G - C T CT + IACX5872 chr5B 7706212 T/C + C T AG - BS00024992_51 chr5B 7937876 T/C - G A CT - tplb0060p09_735 chr5B 8343408 T/C + C T CT + Excalibur_c32189_941 chr5B 8344077 A/G + G A CT - Excalibur_c32189_998 chr5B 8344134 T/C + T C AG - BS00102828_51 chr5B 8353214 A/C + C A GT - BS00010153_51 chr5B 8905311 A/G + G A AG + Excalibur_c6967_1233 chr5B 8911807 T/C + T C CT + Kukri_c65921_274 chr5B 8917489 T/C + T C AG - RFL_Contig4979_965 chr5B 8918212 T/C - A G CT - BS00009810_51 chr5B 10265123 T/C - A G CT - Tdurum_contig14130_315 chr5B 10444723 A/G - T C CT + Tdurum_contig14130_245 chr5B 10444793 T/C - A G CT - BS00022525_51 chr5B 10444933 T/C - G A AG + BS00083715_51 chr5B 10445103 A/G - C T AG - RAC875_c79649_582 chr5B 11457617 T/C - A G CT - Excalibur_rep_c102143_58 chr5B 12573446 T/C + C T CT + RFL_Contig1899_2863 chr5B 12577524 A/G + A G AG + Kukri_c37061_649 chr5B 12849252 A/G + G A AG + BobWhite_c26680_62 chr5B 13179540 T/G - C A AC + Tdurum_contig44048_276 chr5B 13428167 T/G + T G GT + Tdurum_contig53796_360 chr5B 13724854 T/C + C T AG - RAC875_c29907_293 chr5B 15321551 A/C - T G AC - BS00011095_51 chr5B 15321611 T/G - C A GT - BS00100183_51 chr5B 15321664 A/G - T C CT + RAC875_c29907_115 chr5B 15321828 A/G NA NA NA AG NA flanks do not match reference at this position BS00079185_51 chr5B 15553223 A/G NA NA NA CT NA flanks do not match reference at this position BS00022336_51 chr5B 15553300 T/C + T C CT + BS00065543_51 chr5B 17575060 A/G + A G AG + RAC875_c54701_277 chr5B 17943882 T/C + C T AG - Excalibur_c11605_156 chr5B 17945079 A/C - T G AC - BobWhite_c29857_228 chr5B 17979804 A/G + A G AG + BS00065442_51 chr5B 19551659 A/G + G A AG + TA015732-1144 chr5B 21035432 A/C + A C AC + Tdurum_contig71099_245 chr5B 21182737 A/G + G A AG + Ex_c68034_498 chr5B 21535004 A/G - T C AG - Tdurum_contig44127_202 chr5B 21535004 T/C + T C AG - BobWhite_c5887_1277 chr5B 21536610 A/G + G A AG + BS00062617_51 chr5B 21538528 T/C + C T CT + Kukri_c29969_543 chr5B 21636271 T/G + T G GT + Kukri_c10970_573 chr5B 21749409 T/C - A G CT - RAC875_rep_c111261_94 chr5B 21749691 A/G + G A AG + Ra_c15638_858 chr5B 24918121 T/C + T C AG - BobWhite_c7400_194 chr5B 26450053 T/C + T C CT + CAP8_c909_312 chr5B 26450119 T/G - A C GT - BobWhite_c7400_334 chr5B 26450193 A/G + G A AG + Kukri_rep_c103150_398 chr5B 26915141 A/G - C T CT + Ra_c19198_137 chr5B 26916277 T/C + C T CT + CAP7_c5481_96 chr5B 26950989 T/C + C T CT + Excalibur_c58520_78 chr5B 27136067 A/G + A G AG + BS00106043_51 chr5B 27460048 T/C - G A AG + IAAV7594 chr5B 27806205 A/G - T C CT + BS00022773_51 chr5B 27821030 A/G - C T CT + Ex_c8962_467 chr5B 31113926 T/C - G A CT - Excalibur_c13536_202 chr5B 34039872 T/G + G T AC - BS00022602_51 chr5B 34253053 T/C + T C CT + BS00022107_51 chr5B 34719414 A/G + A G AG + BS00033612_51 chr5B 34764676 T/G - C A AC + RAC875_rep_c116173_605 chr5B 35290028 T/C + T C CT + Excalibur_c45323_708 chr5B 35529881 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c14594_182 chr5B 38157656 A/G + G A AG + Tdurum_contig49841_618 chr5B 38166746 T/C - A G AG + IAAV3362 chr5B 40784715 A/G + A G AG + Excalibur_c34426_723 chr5B 40784867 T/C - G A CT - RAC875_rep_c74170_236 chr5B 40784942 T/C - G A AG + BS00021873_51 chr5B 40784984 A/G - NA NA CT NA reference base G not among SNP alleles Excalibur_c23426_1581 chr5B 40786629 T/C + T C CT + BS00060015_51 chr5B 41275987 T/C - A G CT - Kukri_c50283_267 chr5B 42391760 A/C - G T GT + Excalibur_c22825_61 chr5B 42945675 T/C - A G CT - Excalibur_c32422_152 chr5B 44466521 A/G + A G CT - Tdurum_contig16267_354 chr5B 44626887 T/G + G T GT + Tdurum_contig81708_212 chr5B 44655619 A/G + G A CT - BS00063769_51 chr5B 47586797 A/G + A G CT - RAC875_c16827_292 chr5B 50469708 T/C + T C CT + Tdurum_contig25068_259 chr5B 51156459 T/C + T C CT + Ra_c439_1537 chr5B 52005323 T/G - A C GT - IAAV3261 chr5B 53024049 T/C + T C AG - Kukri_s113060_116 chr5B 53662599 A/C NA NA NA GT NA flanks do not match reference at this position Kukri_c2827_439 chr5B 53662722 T/C + C T AG - IACX20330 chr5B 55492409 A/C + A C AC + RAC875_c31197_62 chr5B 55549637 A/G - C T AG - RAC875_c49044_445 chr5B 55623185 T/C - A G CT - Ra_c19837_1031 chr5B 55624387 T/C + C T CT + Kukri_c43113_136 chr5B 55768213 A/G - T C CT + GENE-0782_747 chr5B 56565812 A/G - T C CT + BS00024717_51 chr5B 58331978 T/C + T C AG - Excalibur_c10669_143 chr5B 58563916 T/G + T G GT + RAC875_c62202_161 chr5B 58564001 T/C - A G CT - Excalibur_c10669_997 chr5B 58565866 A/G + G A AG + Kukri_c51_98 chr5B 59158340 A/G NA NA NA CT NA flanks do not match reference at this position Tdurum_contig62320_141 chr5B 59160099 A/C - T G AC - BS00074315_51 chr5B 61381261 A/G + G A CT - JD_c16284_736 chr5B 63362149 T/C - G A CT - IAAV2507 chr5B 63363412 A/G - C T AG - Kukri_rep_c106665_549 chr5B 63470061 A/G + G A CT - BobWhite_c10954_467 chr5B 64732536 T/G - A C GT - RAC875_c2440_755 chr5B 64732536 A/C + A C GT - BS00050709_51 chr5B 64733291 A/G - C T AG - Ku_c439_1308 chr5B 64736478 T/C - G A CT - Kukri_c439_857 chr5B 64736929 A/G - C T AG - RAC875_c104514_534 chr5B 65073011 T/C - A G CT - RAC875_rep_c91778_96 chr5B 65076998 T/C + T C AG - IAAV4252 chr5B 65243608 T/C - A G AG + Excalibur_c5540_1197 chr5B 68359640 A/G + A G CT - Excalibur_c92223_97 chr5B 68366086 A/G - C T CT + Tdurum_contig4708_1648 chr5B 68840985 T/C - G A AG + Ex_c226_499 chr5B 68844636 A/G - T C CT + BobWhite_c15585_87 chr5B 68846530 A/G - T C CT + Tdurum_contig28482_427 chr5B 68926853 A/G + G A AG + BS00103625_51 chr5B 69143466 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_c4383_143 chr5B 69562759 A/G + G A AG + Excalibur_c15838_305 chr5B 69648167 T/C - G A CT - Ku_c4349_1890 chr5B 74336208 T/C - A G AG + Ku_c4349_1791 chr5B 74336307 A/G - T C CT + Kukri_c18702_1234 chr5B 74996822 A/G - T C CT + Kukri_c18702_132 chr5B 74999904 A/G - C T AG - BobWhite_c2479_214 chr5B 78420589 T/G + T G GT + Tdurum_contig56973_413 chr5B 78708064 A/G + G A AG + Kukri_c73901_100 chr5B 78732535 T/C + T C CT + RAC875_c14769_1918 chr5B 78735622 A/G + G A CT - Excalibur_c24614_1203 chr5B 79787922 T/C - A G AG + BobWhite_rep_c55336_265 chr5B 79803766 A/C + A C AC + Kukri_c12490_766 chr5B 79813165 T/C - G A CT - Tdurum_contig93270_1008 chr5B 81180465 T/C + C T CT + RAC875_rep_c71474_66 chr5B 82462682 T/C - A G AG + Tdurum_contig17230_542 chr5B 82858886 A/C + A C GT - BobWhite_c1372_133 chr5B 84627481 A/G + G A AG + RAC875_c51478_173 chr5B 84951879 A/G + A G CT - Tdurum_contig52439_196 chr5B 86255525 T/C + C T AG - Kukri_c13224_551 chr5B 87230065 A/C + A C AC + TA005344-0744 chr5B 105777504 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c96137_101 chr5B 106155726 T/C + T C AG - Tdurum_contig354_149 chr5B 106155726 A/G - T C AG - BS00064515_51 chr5B 114434105 T/C + T C CT + Excalibur_c26226_458 chr5B 117939920 A/G + A G CT - Kukri_c40388_844 chr5B 118530566 A/G + G A AG + RFL_Contig2458_2536 chr5B 118647656 T/C - G A CT - RFL_Contig2458_805 chr5B 118650311 A/G - C T CT + Kukri_c43180_124 chr5B 120213576 A/G + A G AG + tplb0033o15_919 chr5B 120213678 A/G + A G AG + Kukri_rep_c97610_170 chr5B 120215820 A/G - T C CT + BobWhite_rep_c60287_356 chr5B 121556642 T/G + G T GT + BS00033460_51 chr5B 122100231 T/C - G A CT - BobWhite_c5456_805 chr5B 122423091 A/G - T C AG - CAP8_rep_c5411_249 chr5B 123755378 A/G - C T AG - BS00068205_51 chr5B 123758055 T/C - G A CT - BS00045740_51 chr5B 123760296 T/C - A G CT - BS00041689_51 chr5B 128854481 T/C - A G AG + Kukri_c27207_1662 chr5B 130726099 T/C - A G AG + IAAV4269 chr5B 130910684 A/G - C T AG - Excalibur_c16326_399 chr5B 131315575 A/G + G A CT - Kukri_rep_c106832_353 chr5B 133595184 A/G + A G CT - BS00082312_51 chr5B 133660289 T/C + T C CT + IAAV5071 chr5B 136627946 A/G + A G CT - IACX3026 chr5B 138346617 A/G + A G CT - IAAV3972 chr5B 141454855 T/C + T C AG - RAC875_c6409_476 chr5B 141454950 A/G + A G AG + Excalibur_c17915_346 chr5B 141902883 T/C - A G AG + Kukri_c8428_403 chr5B 143720792 A/C + A C GT - BobWhite_rep_c65244_502 chr5B 144239002 A/C - T G AC - Ku_c1470_49 chr5B 149002540 T/G + T G AC - tplb0045a04_2309 chr5B 153174975 A/G - T C AG - CAP8_c2487_181 chr5B 155281766 T/C + C T CT + TA004987-0866 chr5B 162491750 T/C + T C CT + Ku_c2042_923 chr5B 163070210 T/C + C T CT + JD_c12263_436 chr5B 163070657 A/G - C T AG - TA006114-0909 chr5B 166704924 T/C - A G AG + BobWhite_c7630_82 chr5B 173034953 A/G + A G CT - IAAV2983 chr5B 173034953 T/C - A G CT - IAAV7821 chr5B 181477772 A/G + G A CT - Excalibur_c52165_93 chr5B 185721076 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_c44641_134 chr5B 188800592 T/C - A G CT - IAAV4790 chr5B 194190493 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Ex_c22908_270 chr5B 195147206 T/C - G A AG + RAC875_c36684_56 chr5B 196471633 A/C - T G GT + Kukri_c18348_1025 chr5B 203511900 T/C + C T CT + Kukri_c34874_506 chr5B 204612744 A/G - T C CT + IAAV1764 chr5B 211147750 T/C + C T CT + IAAV8912 chr5B 218221819 A/G + A G CT - BS00032443_51 chr5B 221103322 A/G + G A CT - IAAV328 chr5B 221847216 A/G + G A CT - BS00063621_51 chr5B 232214885 A/G + G A CT - BS00063266_51 chr5B 232295563 T/C - G A CT - BS00015473_51 chr5B 234905972 T/G - C A AC + Kukri_c23836_1043 chr5B 234906700 A/C + A C AC + Excalibur_c97201_294 chr5B 234907100 T/G + T G GT + Ku_c8743_872 chr5B 236074626 T/G - A C GT - RAC875_c8988_568 chr5B 236258687 T/G - A C AC + Kukri_c34263_296 chr5B 236259881 A/G NA NA NA AG NA flanks do not match reference at this position BS00050778_51 chr5B 236260503 T/C - G A AG + RAC875_c1589_268 chr5B 236261429 T/C - G A AG + Ku_c1696_1153 chr5B 236286233 T/G - A C GT - Ku_c3121_1332 chr5B 236288407 A/G + G A AG + Ku_c3121_1368 chr5B 236288443 T/C + C T CT + Ku_c3121_1685 chr5B 236288760 T/G + T G GT + IAAV4164 chr5B 236289184 A/G + G A AG + Excalibur_c17132_2581 chr5B 238658962 T/C - G A CT - Kukri_c20360_726 chr5B 239396155 T/C + T C CT + Kukri_c20360_1390 chr5B 239397278 A/G + A G AG + Excalibur_rep_c101657_1126 chr5B 239427166 T/C + C T CT + BS00075030_51 chr5B 239428999 A/C + C A GT - Ex_c41873_341 chr5B 239434286 A/G - T C AG - Ex_c41873_329 chr5B 239434298 T/C - G A CT - BS00082081_51 chr5B 239437316 T/C - G A AG + Kukri_c58739_242 chr5B 240821489 T/C - A G CT - IAAV5612 chr5B 243848665 T/G - C A AC + Kukri_c859_793 chr5B 243849152 T/C - A G CT - Excalibur_c59976_360 chr5B 244120315 A/G + G A AG + BobWhite_rep_c49783_60 chr5B 244411456 T/C + T C AG - Kukri_rep_c105119_190 chr5B 249582175 T/C - G A CT - CAP11_c2008_278 chr5B 267113157 T/C - A G AG + Ku_c33217_323 chr5B 278884031 T/C - A G CT - BobWhite_c36054_53 chr5B 279097462 A/C - G T AC - IACX4548 chr5B 279097538 A/T + T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles tplb0050e20_730 chr5B 281634772 A/G - T C CT + Kukri_c31961_630 chr5B 281675472 T/C - G A CT - Kukri_rep_c113387_369 chr5B 283236052 A/G + A G CT - TA003665-0980 chr5B 284160880 A/G NA NA NA AG NA flanks do not match reference at this position Ra_c53208_433 chr5B 288305555 A/G - T C AG - Excalibur_c54077_129 chr5B 288482642 T/C - A G CT - BS00007437_51 chr5B 289567049 T/C + T C AG - Kukri_c34434_1037 chr5B 294562042 A/G + A G CT - Excalibur_rep_c69724_463 chr5B 306444090 T/C - A G CT - Excalibur_rep_c113602_93 chr5B 308923664 T/G + G T GT + RFL_Contig707_2297 chr5B 309814777 T/C + C T CT + Ra_c44540_304 chr5B 311850923 T/G - NA NA GT NA reference base G not among SNP alleles JD_c8050_978 chr5B 315815039 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c53009_237 chr5B 316379690 T/C + T C AG - Kukri_c44284_80 chr5B 317697095 T/C + T C CT + BS00092354_51 chr5B 318393565 T/C - G A CT - IAAV2293 chr5B 321217900 A/G + A G CT - IAAV6189 chr5B 321416555 T/C - A G AG + Jagger_c5539_105 chr5B 322290107 T/C + T C CT + Jagger_c249_279 chr5B 322553219 A/G - T C AG - CAP12_c2009_335 chr5B 322553428 A/G - C T AG - BS00110489_51 chr5B 323883060 T/C - A G CT - Kukri_c6633_674 chr5B 323884095 A/G - T C CT + BS00077423_51 chr5B 325093204 A/G + A G AG + BS00064891_51 chr5B 326912909 A/G - T C AG - BS00045447_51 chr5B 327080423 A/C - T G AC - BS00045446_51 chr5B 327080439 A/G - C T CT + CAP11_c2503_103 chr5B 327604898 A/C - T G GT + TA005820-0277 chr5B 327607174 T/C NA NA NA CT NA flanks do not match reference at this position JG_c1889_344 chr5B 327786180 A/G + A G AG + BS00065390_51 chr5B 328199928 T/G - C A AC + BS00065376_51 chr5B 329677410 A/G + G A AG + TA004465-1336 chr5B 332427748 A/C + A C AC + Kukri_c10632_1388 chr5B 332966733 A/G + A G AG + IAAV2526 chr5B 335947780 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c31482_513 chr5B 340633082 A/G - C T AG - Excalibur_c24828_1288 chr5B 346299983 T/C - A G AG + BS00023803_51 chr5B 350158170 A/G + A G CT - TA008675-0589 chr5B 353039065 T/C + T C CT + BS00002191_51 chr5B 354292020 A/G + A G AG + RAC875_c42518_57 chr5B 354987614 T/C + T C CT + Kukri_c36789_230 chr5B 355618351 T/C - G A CT - Ex_c5632_778 chr5B 356185972 T/C + C T AG - Kukri_c17783_58 chr5B 356187517 A/G + G A CT - BS00022086_51 chr5B 357103383 A/G - C T AG - RAC875_c47060_61 chr5B 357104872 A/G - T C CT + Kukri_rep_c105540_177 chr5B 357106634 A/C - T G GT + Ex_c40022_873 chr5B 357121156 A/G - T C CT + BS00022662_51 chr5B 357122469 A/G - C T CT + IAAV3825 chr5B 357552836 A/C + A C AC + BobWhite_c8764_219 chr5B 357552957 A/C - G T AC - CAP12_c1419_574 chr5B 362518088 T/C - G A CT - CAP8_c1968_64 chr5B 369153224 A/G NA NA NA CT NA flanks do not match reference at this position GENE-3370_463 chr5B 373679857 A/G + A G AG + BS00002208_51 chr5B 378816535 T/C + T C AG - Tdurum_contig84745_267 chr5B 378816535 A/G - T C AG - BS00022652_51 chr5B 378851382 A/G - T C AG - CAP11_c919_204 chr5B 387173377 A/C - T G AC - BS00064333_51 chr5B 387896205 A/G + G A AG + BS00056147_51 chr5B 387904098 T/C - G A CT - Excalibur_c30346_54 chr5B 388393869 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c29431_1849 chr5B 395633001 T/C - G A AG + BS00048572_51 chr5B 397435150 T/G - C A AC + IAAV6616 chr5B 397673282 T/C - A G CT - Kukri_c27568_1763 chr5B 397678573 A/G + A G AG + BS00068390_51 chr5B 399810451 A/G - C T AG - BS00092953_51 chr5B 400523616 A/G + G A CT - Kukri_c98694_120 chr5B 400533268 A/G + G A AG + BS00049793_51 chr5B 402843784 A/C - G T GT + BobWhite_c8048_663 chr5B 403182590 A/G - T C AG - RFL_Contig3811_3709 chr5B 403547313 T/G + G T GT + IACX8091 chr5B 403547912 T/C - A G CT - IACX6007 chr5B 403714015 A/G + A G AG + RAC875_rep_c105322_99 chr5B 403782889 T/C + C T CT + Jagger_c505_141 chr5B 403855544 A/G + A G CT - RAC875_c99618_116 chr5B 403855748 T/C - G A CT - BobWhite_c45340_368 chr5B 404184096 T/C - G A CT - Excalibur_c631_219 chr5B 404187320 A/G NA NA NA AG NA flanks do not match reference at this position BS00040350_51 chr5B 404189730 T/C + C T AG - BS00023161_51 chr5B 405725847 T/C + T C CT + BS00079914_51 chr5B 410532740 A/C - G T GT + RAC875_rep_c69785_196 chr5B 410535460 T/C - G A CT - BS00089969_51 chr5B 410852493 A/G + G A AG + IAAV5873 chr5B 411813961 A/G + A G AG + IAAV850 chr5B 411929668 A/T - A T AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00009789_51 chr5B 411929890 T/C - G A AG + Excalibur_c753_1556 chr5B 411947504 T/C - A G AG + IAAV1835 chr5B 414834892 T/G NA NA NA GT NA flanks do not match reference at this position Tdurum_contig48658_802 chr5B 415649292 T/C - A G AG + Kukri_c28117_583 chr5B 415649300 T/C + T C CT + Tdurum_contig48658_794 chr5B 415649300 A/G - T C AG - Kukri_c49151_139 chr5B 415801183 T/C + C T CT + tplb0033f11_1381 chr5B 417438359 T/C - A G AG + Tdurum_contig31131_198 chr5B 417443595 T/G - C A GT - IAAV10 chr5B 419725928 A/G + A G CT - BS00063423_51 chr5B 421643627 A/G - T C AG - RFL_Contig3192_1291 chr5B 422940287 T/C + T C AG - Kukri_c22967_1272 chr5B 424335769 A/G + A G AG + Kukri_c57830_63 chr5B 425671696 A/C NA NA NA GT NA flanks do not match reference at this position BobWhite_c40449_189 chr5B 426087381 A/C + A C GT - BobWhite_c34650_141 chr5B 427248295 T/C - G A CT - BS00023081_51 chr5B 427332291 T/C + T C AG - Kukri_c11240_332 chr5B 428125793 A/G + A G CT - BS00041704_51 chr5B 428129713 T/G + T G AC - Kukri_c12219_112 chr5B 430466215 A/G + G A CT - IAAV4074 chr5B 430467213 T/C - G A CT - Excalibur_c2433_324 chr5B 430469121 A/G NA NA NA AG NA flanks do not match reference at this position BS00028183_51 chr5B 431061084 T/C - A G CT - IAAV5469 chr5B 431076208 T/C - A G CT - Ex_c66350_322 chr5B 431798187 A/G - T C AG - JD_c3499_551 chr5B 431798207 T/C + T C AG - BobWhite_c14223_602 chr5B 431799474 A/G + A G AG + Excalibur_c49271_183 chr5B 431800194 A/G + A G AG + RAC875_c25756_279 chr5B 432155448 T/C + C T AG - Kukri_c2621_610 chr5B 432155872 T/C + T C AG - Tdurum_contig57742_400 chr5B 432156324 T/C - A G CT - Excalibur_c63344_424 chr5B 432175187 T/C - A G AG + BS00065788_51 chr5B 434700664 A/C + C A AC + BS00108019_51 chr5B 435158703 T/C + C T CT + BS00108020_51 chr5B 435158995 T/C + T C AG - Tdurum_contig10987_800 chr5B 436210354 T/C - A G AG + BS00070507_51 chr5B 437623048 A/C - T G GT + BS00064767_51 chr5B 438169956 A/G + G A CT - Kukri_c35659_250 chr5B 438219543 T/C - A G CT - Ra_c44756_929 chr5B 438220280 A/G - C T AG - GENE-3303_14 chr5B 438220601 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c44756_381 chr5B 438221031 A/G - C T AG - Tdurum_contig42092_281 chr5B 439653577 T/C + T C AG - Kukri_c9468_831 chr5B 442374779 A/G - T C CT + IACX5818 chr5B 442376761 A/T + T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles GENE-3440_199 chr5B 445453334 A/G + A G CT - BS00031411_51 chr5B 455735483 T/C - G A AG + Kukri_c36317_305 chr5B 455737258 A/G - T C AG - BS00001101_51 chr5B 455738675 T/G - A C GT - IACX3288 chr5B 455738675 A/C + A C GT - Tdurum_contig52447_814 chr5B 456507522 A/G - C T CT + GENE-3506_53 chr5B 457122696 A/G - T C AG - IAAV2421 chr5B 457123832 T/C + C T CT + IAAV4188 chr5B 457132518 T/C - G A CT - BobWhite_c47103_205 chr5B 457342490 T/C - A G CT - BobWhite_c47103_84 chr5B 457342612 T/C - G A CT - Ex_c1583_1138 chr5B 457396613 A/G - C T AG - Excalibur_c47321_138 chr5B 457963933 T/C + T C CT + RAC875_c9150_2945 chr5B 459477456 T/C - A G CT - Kukri_c9520_288 chr5B 460195022 T/G - A C GT - Kukri_c10530_1044 chr5B 460678285 T/C - A G CT - Tdurum_contig10911_155 chr5B 461137606 T/G - C A AC + Tdurum_contig10911_117 chr5B 461137644 A/G - C T AG - BS00022716_51 chr5B 461137742 T/C + C T CT + Kukri_c40046_237 chr5B 461289337 T/C - A G CT - BS00022993_51 chr5B 461291676 A/G + G A CT - BS00032235_51 chr5B 461303496 A/C - G T GT + BS00067152_51 chr5B 461545223 A/G - C T AG - BS00069867_51 chr5B 461829067 T/G - A C GT - BS00069866_51 chr5B 461829096 T/G - C A GT - Ra_c15623_1791 chr5B 461829993 T/C + T C AG - BS00009531_51 chr5B 462127501 A/G + G A AG + BobWhite_c27885_197 chr5B 462127639 A/G + A G AG + IAAV2246 chr5B 462144261 T/G + G T GT + Excalibur_rep_c110067_199 chr5B 462730877 A/G - C T AG - TA004677-0674 chr5B 463403141 T/C NA NA NA AG NA flanks do not match reference at this position BS00094480_51 chr5B 464327601 A/G + A G CT - Ra_c35412_1057 chr5B 464595187 A/G + A G AG + Excalibur_c25661_1177 chr5B 466000036 T/C + T C CT + IAAV5974 chr5B 466006228 T/C + C T AG - BobWhite_c12229_182 chr5B 466171778 A/G + G A CT - Ku_c1031_670 chr5B 466172715 A/G + G A AG + Kukri_c2181_291 chr5B 466172922 A/G + A G AG + Kukri_c2181_677 chr5B 466174035 A/G + A G CT - RAC875_c28078_871 chr5B 467513521 A/G + A G CT - RAC875_c56330_993 chr5B 469825126 A/G - C T CT + Kukri_rep_c81356_289 chr5B 469827606 A/G + A G CT - Kukri_rep_c69727_102 chr5B 469827764 A/C - T G GT + RAC875_c5704_412 chr5B 469827933 A/C + C A GT - Excalibur_rep_c107257_528 chr5B 469830068 A/C - T G AC - RAC875_c2491_916 chr5B 469830282 A/G - T C AG - Kukri_c37275_94 chr5B 470208521 A/G - T C CT + Excalibur_c38625_172 chr5B 470209763 A/G + A G AG + BobWhite_c23037_241 chr5B 472680489 A/C - G T GT + IAAV8847 chr5B 473114356 A/G - T C AG - RAC875_rep_c116598_137 chr5B 473115672 A/G + G A CT - Ku_c11172_1085 chr5B 473178587 T/C + T C CT + Tdurum_contig41335_181 chr5B 473637834 A/C + C A AC + TA005387-0575 chr5B 473642332 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_c5897_607 chr5B 473662007 A/G - C T AG - RFL_Contig773_790 chr5B 473740412 A/C - T G AC - RAC875_c32768_440 chr5B 473871399 A/G - C T AG - Kukri_c10296_1512 chr5B 473878667 A/G - T C AG - Tdurum_contig63161_121 chr5B 473878721 A/G - T C CT + BobWhite_rep_c63648_306 chr5B 473878759 A/G + A G CT - Kukri_c10296_1074 chr5B 473879105 A/C - T G GT + Excalibur_rep_c104800_795 chr5B 475996038 A/G - T C CT + IACX2883 chr5B 476012472 T/C - A G CT - Ra_c8939_653 chr5B 476797802 A/C - G T AC - RAC875_c38511_91 chr5B 476805550 T/C + T C AG - Ku_c1083_1261 chr5B 478130052 A/G + G A CT - Ku_c1083_1314 chr5B 478130105 A/G + G A CT - BobWhite_s67247_276 chr5B 478743928 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c2437_1569 chr5B 479025051 T/C - A G AG + Kukri_c33299_519 chr5B 479193598 A/C - T G AC - RAC875_c24376_704 chr5B 479197716 T/C + C T AG - Tdurum_contig68472_291 chr5B 479200222 A/C - G T AC - Tdurum_contig68472_115 chr5B 479200398 T/G - A C AC + Tdurum_contig57403_589 chr5B 479389439 A/G - C T CT + Kukri_c46476_551 chr5B 479389713 A/G + G A CT - Kukri_c46476_647 chr5B 479389809 T/C + T C CT + Tdurum_contig57403_311 chr5B 479389809 A/G - T C CT + BS00066289_51 chr5B 479390876 A/G + G A CT - RAC875_c4287_2984 chr5B 479500768 T/C - A G AG + Excalibur_c10444_2056 chr5B 479500839 T/C - G A CT - RAC875_c39141_55 chr5B 479501818 T/C - G A CT - BS00021949_51 chr5B 479635138 T/C + C T CT + Kukri_c45713_151 chr5B 479716557 A/G - T C CT + Tdurum_contig77275_259 chr5B 480163680 T/C - A G AG + BS00066138_51 chr5B 485074366 T/C + T C CT + Kukri_c62247_248 chr5B 485997910 T/G + G T AC - GENE-3397_535 chr5B 486733480 T/C - A G AG + BobWhite_rep_c49058_130 chr5B 487223443 T/C - G A AG + CAP12_rep_c4520_171 chr5B 487462496 A/G + A G AG + GENE-3573_962 chr5B 487610329 T/C - A G AG + Ku_c11150_773 chr5B 487831488 A/C - G T GT + CAP12_c7929_116 chr5B 488016289 T/C + T C AG - RAC875_c10174_268 chr5B 488016483 T/C + C T AG - BS00009607_51 chr5B 488106488 T/C NA NA NA AG NA flanks do not match reference at this position IACX7928 chr5B 488106488 A/G NA NA NA AG NA flanks do not match reference at this position BS00009311_51 chr5B 488106761 A/G NA NA NA CT NA flanks do not match reference at this position Jagger_c3991_101 chr5B 488820772 T/C + T C AG - GENE-3437_68 chr5B 489280646 A/G + G A CT - GENE-3437_148 chr5B 489280722 T/C + T C CT + BS00065313_51 chr5B 489845892 A/G + G A AG + Kukri_c63163_141 chr5B 490759424 T/C - G A CT - Kukri_c63093_241 chr5B 491817672 T/C + T C CT + Tdurum_contig42636_995 chr5B 491957899 T/C - A G CT - CAP7_c11553_123 chr5B 497756692 T/C - A G CT - CAP7_rep_c8461_106 chr5B 497905006 A/C - T G AC - BS00068173_51 chr5B 498266165 T/C - G A CT - IAAV1826 chr5B 498883364 C/G - C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Excalibur_rep_c68017_636 chr5B 498883635 T/C NA NA NA AG NA flanks do not match reference at this position BS00022694_51 chr5B 498886862 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_rep_c68017_140 chr5B 498886946 T/C - A G CT - RAC875_c34910_173 chr5B 499128463 A/C + A C AC + Kukri_c8983_459 chr5B 499168605 A/G + A G CT - BS00010837_51 chr5B 499385268 T/G + T G GT + IACX9571 chr5B 499385268 A/C - T G GT + Excalibur_c96334_93 chr5B 501238086 T/G - A C GT - RAC875_c15929_628 chr5B 501477592 A/G + G A AG + RAC875_c33738_654 chr5B 501478043 A/G - T C CT + BS00064660_51 chr5B 501480761 A/C + A C GT - BS00064661_51 chr5B 501480779 A/G + G A CT - BS00022040_51 chr5B 501957843 T/C + C T CT + Excalibur_c36525_679 chr5B 501958103 T/C + T C AG - BobWhite_c31565_664 chr5B 501958268 T/C + T C AG - BS00022763_51 chr5B 501958268 T/C + T C AG - BS00093122_51 chr5B 501958341 T/C + C T CT + RAC875_c60520_164 chr5B 502502977 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c26263_2071 chr5B 503093828 A/C - T G AC - Kukri_c7760_1210 chr5B 503094268 A/G - C T AG - Kukri_rep_c112991_207 chr5B 503097940 A/G - T C CT + IACX9371 chr5B 503101574 T/C - G A AG + IAAV6876 chr5B 503101731 A/G - T C AG - Excalibur_rep_c70952_72 chr5B 503218459 A/G + A G AG + RAC875_c97163_563 chr5B 503326464 T/C - A G CT - BS00095389_51 chr5B 505481957 T/C - G A AG + Excalibur_c9846_458 chr5B 505482257 A/G + A G AG + Tdurum_contig30483_335 chr5B 505484161 A/C - T G AC - Excalibur_c9846_1996 chr5B 505484231 T/C NA NA NA CT NA flanks do not match reference at this position Jagger_c6390_111 chr5B 505805757 T/C - A G AG + BobWhite_c20692_123 chr5B 505805867 A/C - T G GT + BS00087680_51 chr5B 505806432 T/G - C A AC + Excalibur_c4031_1227 chr5B 505806528 A/G - T C AG - Kukri_c22631_462 chr5B 505807306 A/C - G T AC - Excalibur_c8675_1638 chr5B 506269933 T/C - A G CT - Excalibur_c8675_1550 chr5B 506270125 T/C NA NA NA CT NA flanks do not match reference at this position RFL_Contig2885_1150 chr5B 506271207 A/G + A G CT - BobWhite_rep_c61555_115 chr5B 506274026 T/C - A G AG + Kukri_c14245_895 chr5B 506274446 A/G - C T AG - IACX7596 chr5B 506275619 A/C + A C AC + GENE-3466_653 chr5B 506506081 T/G + T G GT + RAC875_c14963_1579 chr5B 506511195 A/G + A G CT - BS00088186_51 chr5B 506513414 A/C + A C AC + BS00088187_51 chr5B 506513457 A/C + C A GT - BS00005092_51 chr5B 506781442 A/G + A G AG + Excalibur_rep_c67473_264 chr5B 506789656 A/G - C T CT + Excalibur_rep_c67473_197 chr5B 506789723 T/C - G A AG + BS00011006_51 chr5B 506952435 A/G - T C CT + BS00091774_51 chr5B 506953473 T/C - G A AG + BS00099648_51 chr5B 507588168 T/G + T G AC - BS00022960_51 chr5B 507588247 A/G + A G AG + BobWhite_c11861_557 chr5B 507706045 T/C + T C CT + BS00098821_51 chr5B 507873235 A/G - T C CT + BobWhite_c43683_388 chr5B 507937784 A/G - T C CT + BS00067615_51 chr5B 508256849 A/G - T C AG - RAC875_c52809_168 chr5B 508257900 T/G + G T AC - Ku_c28054_204 chr5B 508267419 T/C - G A CT - BobWhite_rep_c50822_462 chr5B 508795404 A/G - C T CT + Kukri_c7306_187 chr5B 510375129 A/G + A G CT - BS00106103_51 chr5B 510558974 A/G + G A CT - Excalibur_c54386_136 chr5B 510559105 A/G - T C CT + Excalibur_c54386_103 chr5B 510559138 T/G - C A GT - tplb0060m15_1174 chr5B 510730006 T/C - G A AG + tplb0060m15_1025 chr5B 510730155 A/G - T C CT + IAAV6078 chr5B 510883128 T/C + T C CT + TA001114-0926 chr5B 510883689 T/C + T C CT + BS00065697_51 chr5B 511307311 A/G - C T AG - BobWhite_c10247_316 chr5B 511361051 A/G + A G AG + tplb0049b14_1104 chr5B 511696169 T/C + T C AG - Excalibur_c84332_397 chr5B 511696499 A/G - T C CT + tplb0049b14_1542 chr5B 511696607 T/C + T C AG - Excalibur_c11613_213 chr5B 511696922 A/G + A G CT - Kukri_c29829_421 chr5B 512990524 A/G + A G CT - BS00085890_51 chr5B 513326036 T/C - G A AG + GENE-3155_183 chr5B 513605731 A/G + G A AG + Kukri_c8237_1973 chr5B 513605898 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_rep_c70220_288 chr5B 513607981 A/G + A G CT - Kukri_c66814_100 chr5B 514932464 T/C - G A AG + Excalibur_c28850_166 chr5B 515184173 T/C - A G AG + Excalibur_c54806_1116 chr5B 515185462 T/C + C T AG - CAP11_c506_72 chr5B 515186993 A/G - C T AG - BS00098227_51 chr5B 515193645 A/G - C T CT + IACX5859 chr5B 515193909 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles IAAV6818 chr5B 516030823 T/C - G A CT - RFL_Contig2357_185 chr5B 516042561 A/G - T C CT + BS00088558_51 chr5B 516469101 A/C NA NA NA AC NA flanks do not match reference at this position RAC875_c38382_625 chr5B 517650687 A/G - T C AG - BobWhite_c16398_128 chr5B 517679204 T/C + T C AG - RAC875_rep_c87796_223 chr5B 517679335 T/C - G A CT - BS00066903_51 chr5B 517776467 A/G - T C AG - Excalibur_c21847_53 chr5B 517866126 A/G - T C CT + RAC875_c66955_439 chr5B 517867213 T/C - A G CT - Excalibur_c2727_124 chr5B 517867702 A/G - T C AG - BobWhite_c10126_263 chr5B 518078580 A/G - C T CT + BS00065996_51 chr5B 518490161 T/G - A C AC + Excalibur_c35797_615 chr5B 518682396 T/C - A G AG + Excalibur_c35797_547 chr5B 518682464 A/G - T C CT + GENE-3574_643 chr5B 519148901 A/G + G A CT - RAC875_c19099_308 chr5B 519153210 A/G + G A AG + RFL_Contig487_1286 chr5B 519742306 A/G + A G AG + BS00042014_51 chr5B 520552412 T/C + T C CT + BS00083511_51 chr5B 520875654 A/G - C T AG - BS00022520_51 chr5B 520875758 A/G - C T AG - RAC875_c5995_94 chr5B 520875863 T/C - G A AG + CAP7_c1155_57 chr5B 520875886 A/C - T G AC - Ex_c5594_2818 chr5B 520885115 T/C - A G AG + BS00076835_51 chr5B 520898529 A/G - T C AG - BS00076833_51 chr5B 520898541 A/G - T C AG - BS00069601_51 chr5B 521138327 T/C - A G CT - BS00015205_51 chr5B 521160333 A/C + NA NA AC NA reference base G not among SNP alleles BS00069741_51 chr5B 521427116 A/G + A G CT - Kukri_c35480_647 chr5B 522077632 T/C - A G AG + Ex_c24477_484 chr5B 523185706 T/C - G A CT - Ra_c1726_1071 chr5B 523186514 A/C + A C AC + Ra_c1726_3210 chr5B 523188650 A/G + A G AG + IACX3059 chr5B 523198820 T/G + G T AC - Excalibur_c45471_81 chr5B 523215282 A/G + A G CT - RAC875_c44706_164 chr5B 525811964 A/G + G A AG + BS00010863_51 chr5B 526576590 T/G + T G GT + TA002629-0202 chr5B 526576590 A/C NA NA NA AC NA flanks do not match reference at this position IAAV2002 chr5B 526589433 A/G - T C AG - BS00063099_51 chr5B 526589704 A/G + A G AG + GENE-0209_733 chr5B 526590135 T/C - A G AG + Kukri_c82296_367 chr5B 527050928 T/C + C T CT + RAC875_c18335_443 chr5B 527256246 A/G - C T AG - RAC875_c42009_247 chr5B 527257362 A/G + A G AG + BS00077667_51 chr5B 527339308 A/G + A G AG + BS00068480_51 chr5B 527342497 T/C + T C CT + Excalibur_c22958_433 chr5B 527342503 A/G - C T CT + IACX17304 chr5B 527609092 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles IAAV659 chr5B 527609262 A/G + A G AG + BS00070613_51 chr5B 528574798 A/C + A C GT - RFL_Contig2304_1569 chr5B 528705016 A/G - T C AG - RFL_Contig4472_2387 chr5B 529491356 T/G + T G GT + RAC875_c98401_90 chr5B 529492713 T/C + C T AG - RFL_Contig4472_3405 chr5B 529492930 A/C + C A AC + Tdurum_contig100174_60 chr5B 530189366 T/C - A G CT - Excalibur_c97089_263 chr5B 530231402 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c68097_62 chr5B 530233602 T/C - A G AG + BS00046512_51 chr5B 530234102 A/G + A G AG + BobWhite_c4773_85 chr5B 530334953 T/G - C A AC + BobWhite_rep_c65835_277 chr5B 530622713 A/G - C T AG - Excalibur_rep_c104876_277 chr5B 531152629 T/C + T C CT + RAC875_c7585_1097 chr5B 531152967 A/G + G A CT - RAC875_rep_c70643_107 chr5B 531153235 T/C + T C AG - BobWhite_rep_c62475_70 chr5B 531199441 A/G + A G CT - BS00022999_51 chr5B 531219762 T/C + C T AG - Kukri_c46932_65 chr5B 531538475 T/C + C T CT + Kukri_c34173_518 chr5B 531540203 T/C - G A AG + TA003435-0313 chr5B 531543026 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_c6633_395 chr5B 531599324 T/C - A G CT - BobWhite_c6633_240 chr5B 531599479 T/C - G A CT - IAAV1358 chr5B 531599479 A/G + G A CT - BobWhite_c16987_106 chr5B 531642256 A/G - T C AG - IAAV8195 chr5B 532601220 T/C + T C CT + Excalibur_c36377_615 chr5B 533494506 T/C - G A AG + Kukri_c14564_1108 chr5B 533495358 A/G + A G AG + Excalibur_c7968_2218 chr5B 533507877 T/G - C A AC + BS00075815_51 chr5B 536047002 T/C - G A CT - BS00093591_51 chr5B 536051794 T/C + C T AG - BobWhite_c47456_121 chr5B 536054396 T/C - A G AG + Tdurum_contig67535_391 chr5B 536323831 T/G + G T AC - Tdurum_contig75960_546 chr5B 536513256 A/G + G A AG + Kukri_c2346_1102 chr5B 536515457 A/G - T C CT + GENE-3619_539 chr5B 536680666 A/G - T C CT + Kukri_c29267_215 chr5B 539460175 T/C + C T CT + BS00067209_51 chr5B 541286850 T/C + C T AG - Excalibur_c17055_1451 chr5B 541343196 A/G + A G AG + TA001786-1535 chr5B 541500342 A/C + A C AC + TA003468-0770 chr5B 541500342 A/C NA NA NA GT NA flanks do not match reference at this position IAAV7226 chr5B 542952954 T/C - A G CT - Excalibur_c6649_304 chr5B 543612787 T/C + T C CT + Excalibur_c6649_769 chr5B 543613398 T/C + C T AG - Excalibur_c6649_794 chr5B 543613423 A/C + A C GT - RAC875_c1565_1098 chr5B 543620696 T/C - G A CT - IACX2901 chr5B 544610911 A/T + T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles IACX9261 chr5B 546704021 A/C + C A GT - tplb0027f13_1493 chr5B 546827787 T/C - A G CT - Ra_c10633_2155 chr5B 547406906 A/C + A C GT - Excalibur_rep_c105399_213 chr5B 548196507 T/C + T C AG - BobWhite_c27244_211 chr5B 548196994 T/C + T C CT + Kukri_c22607_242 chr5B 548197625 T/G + T G GT + BobWhite_c19327_314 chr5B 548528429 A/G + A G CT - Tdurum_contig61623_129 chr5B 549673256 A/G + G A CT - Ex_c26924_745 chr5B 549948395 T/C - A G AG + BS00017264_51 chr5B 550152789 A/G + A G CT - IAAV2426 chr5B 550152789 T/C - A G CT - BS00000592_51 chr5B 550156642 T/C + C T AG - IACX2796 chr5B 550156642 A/G - C T AG - Kukri_c37692_347 chr5B 550211476 A/G - T C AG - BS00099782_51 chr5B 550211728 T/C + C T AG - RAC875_c10139_92 chr5B 550225896 A/C + A C AC + Excalibur_c56310_57 chr5B 550229479 T/C + C T AG - BS00044388_51 chr5B 550229557 T/C + C T CT + BS00087043_51 chr5B 550235487 A/G - C T CT + RAC875_c8757_589 chr5B 550236110 T/C - G A CT - BS00049083_51 chr5B 550321223 A/G + G A CT - CAP12_c703_150 chr5B 550377824 T/C - G A CT - GENE-3383_710 chr5B 550393681 A/G + G A AG + RAC875_c32320_88 chr5B 550395376 A/G + A G CT - BS00020982_51 chr5B 550732849 A/G + A G CT - Tdurum_contig31075_260 chr5B 550732849 T/C - A G AG + BS00087696_51 chr5B 550732855 T/C + T C CT + Excalibur_c33675_201 chr5B 550847442 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c33675_410 chr5B 550847823 A/G + A G CT - RAC875_c23289_303 chr5B 550851192 T/C + C T CT + Tdurum_contig63997_587 chr5B 550851215 T/C + T C AG - BS00012038_51 chr5B 550851278 A/G - T C CT + Ex_c29928_1020 chr5B 550928276 T/G + G T GT + BS00068805_51 chr5B 551499538 T/G + G T AC - BS00082101_51 chr5B 551659161 T/C - G A AG + BS00021971_51 chr5B 551659264 A/C - G T AC - BS00000137_51 chr5B 551663099 A/G + A G AG + Excalibur_c45297_316 chr5B 553351420 A/G + A G CT - BS00029869_51 chr5B 554212726 A/C - T G AC - Ku_c11429_519 chr5B 554212807 T/C + C T CT + Kukri_c30643_112 chr5B 554821658 T/C - G A AG + Kukri_c6113_189 chr5B 554822450 T/C - G A AG + RAC875_c2105_740 chr5B 555011224 A/G + A G CT - RAC875_c985_387 chr5B 555177099 T/C - A G AG + Tdurum_contig44635_759 chr5B 555177099 A/G + A G AG + RAC875_c103988_92 chr5B 555177293 A/G + A G CT - BS00076169_51 chr5B 555179343 A/G + G A AG + BS00073015_51 chr5B 555181754 T/C - G A AG + BS00066345_51 chr5B 555185091 T/C - G A CT - BS00109560_51 chr5B 556182641 T/C + T C CT + Tdurum_contig53072_1935 chr5B 556639522 A/G - C T CT + Excalibur_c81014_100 chr5B 556785893 A/G NA NA NA AG NA flanks do not match reference at this position BS00068710_51 chr5B 558120029 T/C + C T AG - TA002756-0960 chr5B 558342508 T/C NA NA NA CT NA flanks do not match reference at this position BS00105054_51 chr5B 558625399 T/C - A G AG + Tdurum_contig12995_792 chr5B 559771991 T/C - A G AG + Tdurum_contig12995_722 chr5B 559772168 T/C NA NA NA CT NA flanks do not match reference at this position BS00067331_51 chr5B 562968766 T/C - G A CT - BS00010311_51 chr5B 562969733 A/C - T G GT + Kukri_rep_c103366_421 chr5B 565768900 A/G - C T AG - Ra_c11667_324 chr5B 565898778 A/G + G A AG + Excalibur_c874_1479 chr5B 566686004 A/G + A G AG + IAAV2296 chr5B 566686138 T/C + T C AG - Kukri_c66357_357 chr5B 566687926 T/C - A G CT - RAC875_c20785_1219 chr5B 566973104 T/C + T C AG - Ku_c4240_216 chr5B 567152784 T/C + C T CT + Excalibur_c18492_249 chr5B 567152814 T/C + C T CT + BS00008767_51 chr5B 567153179 A/G + A G CT - Kukri_c29560_156 chr5B 567156775 T/C - A G CT - Ra_c6906_2125 chr5B 568404334 A/G - T C CT + Excalibur_c20766_802 chr5B 568418403 A/G + A G AG + Ra_c22730_460 chr5B 570579213 T/C + T C AG - Ra_c7619_526 chr5B 570894409 T/C + C T AG - IACX6034 chr5B 570926030 T/G + T G GT + Ku_c55173_549 chr5B 570927467 A/G + A G AG + IAAV5992 chr5B 571185926 A/G - C T AG - Kukri_c12910_908 chr5B 571203522 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c12910_214 chr5B 571204757 A/G - C T CT + IAAV475 chr5B 571231266 T/C - A G AG + RAC875_c30011_426 chr5B 571475214 T/C - A G AG + BS00062731_51 chr5B 571616182 A/C + A C GT - BS00065936_51 chr5B 571635916 T/C + C T CT + BS00011514_51 chr5B 572547199 T/C - A G AG + RAC875_rep_c102342_470 chr5B 573495731 A/G - C T CT + BS00084096_51 chr5B 577228776 A/G + A G AG + RAC875_c50755_244 chr5B 577302293 T/G - A C AC + IAAV2160 chr5B 577302397 T/C - A G AG + TA006199-1015 chr5B 577303116 T/G NA NA NA GT NA flanks do not match reference at this position BobWhite_c3552_1303 chr5B 577304193 A/G - C T CT + GENE-2239_795 chr5B 577304193 A/G NA NA NA AG NA flanks do not match reference at this position IAAV8463 chr5B 577305479 T/G + G T AC - Excalibur_c12048_1756 chr5B 577308453 T/C + T C CT + Kukri_rep_c102237_122 chr5B 578368514 A/G - T C AG - RFL_Contig5461_683 chr5B 580366047 T/C - G A CT - Excalibur_c5329_1335 chr5B 580686304 T/C - G A CT - BobWhite_c45848_120 chr5B 580733081 A/G - T C AG - BS00065128_51 chr5B 582582356 T/C - A G CT - Kukri_rep_c108378_52 chr5B 583178283 T/C - A G CT - RAC875_c7011_435 chr5B 583178310 T/C + C T AG - Kukri_c52257_991 chr5B 583179136 A/G + A G CT - RFL_Contig539_1789 chr5B 583577794 T/C - A G CT - BobWhite_c11495_120 chr5B 584072434 A/G - T C AG - BS00022673_51 chr5B 584127508 T/C + C T AG - GENE-2689_215 chr5B 584612037 A/G - C T AG - Excalibur_c3165_730 chr5B 584853852 T/C + T C CT + Kukri_c59540_137 chr5B 586352468 T/C - A G AG + Kukri_c26747_211 chr5B 587069486 T/C - G A CT - Kukri_c2955_281 chr5B 587126794 A/G + G A CT - IACX9238 chr5B 587127059 A/C + A C GT - RFL_Contig2832_2410 chr5B 587127305 T/C + T C CT + Tdurum_contig10086_387 chr5B 587342807 A/G + A G CT - Kukri_c29739_91 chr5B 587344279 A/G + A G AG + BS00005860_51 chr5B 587344633 A/G + A G CT - Tdurum_contig28768_250 chr5B 587471662 T/G + G T AC - BS00079321_51 chr5B 587600648 T/C + T C CT + BS00021736_51 chr5B 587600726 T/C + C T CT + BobWhite_c17445_83 chr5B 588160550 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c6176_1400 chr5B 588508469 A/G + G A CT - BS00080474_51 chr5B 588681985 T/C - A G AG + RAC875_rep_c114200_428 chr5B 588682736 A/G - T C CT + Tdurum_contig98569_290 chr5B 589120307 A/C - T G AC - Tdurum_contig98569_56 chr5B 589120541 A/C - G T GT + CAP12_c2189_159 chr5B 589228287 T/C + T C AG - Excalibur_c4189_124 chr5B 589373385 T/C NA NA NA AG NA flanks do not match reference at this position BS00049213_51 chr5B 589581887 A/G - C T CT + Excalibur_rep_c106165_238 chr5B 591144413 A/G NA NA NA CT NA flanks do not match reference at this position Tdurum_contig10669_1621 chr5B 591192039 A/G - T C AG - Tdurum_contig10669_1557 chr5B 591192103 T/G - C A AC + Tdurum_contig10669_1535 chr5B 591192125 T/C - A G CT - RAC875_rep_c104919_902 chr5B 591193186 T/G - C A GT - GENE-4085_443 chr5B 591482917 A/G + G A AG + Kukri_c4581_737 chr5B 591653032 T/C + T C CT + BS00080495_51 chr5B 591654414 T/G + T G GT + CAP11_c6746_112 chr5B 591829842 A/C + A C AC + BS00021735_51 chr5B 593943053 A/G - T C AG - RAC875_c47696_532 chr5B 593943223 A/G - T C AG - BobWhite_rep_c50349_139 chr5B 594745426 A/G - T C AG - RAC875_c16536_80 chr5B 594868020 T/C + C T AG - BS00017233_51 chr5B 594871885 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_rep_c113786_110 chr5B 594875902 A/C - T G AC - BS00022689_51 chr5B 594913732 A/G - T C CT + RAC875_c60758_623 chr5B 597220536 A/G - T C AG - RAC875_c60758_585 chr5B 597220574 T/G - A C GT - Kukri_c87104_125 chr5B 597220702 T/C NA NA NA CT NA flanks do not match reference at this position BS00033487_51 chr5B 597289555 T/C + C T CT + Excalibur_c35398_114 chr5B 597290674 A/G + A G CT - BS00026679_51 chr5B 597300851 T/C + C T AG - IACX7945 chr5B 597864929 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Tdurum_contig47071_1322 chr5B 600187586 T/C + T C AG - Tdurum_contig52688_476 chr5B 600496907 A/G - T C CT + IACX6070 chr5B 600496921 A/G - C T CT + BS00041911_51 chr5B 601326850 T/C + C T AG - Tdurum_contig47491_258 chr5B 601336308 T/C + C T AG - BS00066039_51 chr5B 601338205 A/G - C T AG - RFL_Contig3885_1183 chr5B 601405824 A/G - C T CT + Tdurum_contig85945_281 chr5B 601418670 A/G - T C CT + BS00037487_51 chr5B 601419385 A/G + A G AG + Tdurum_contig19615_188 chr5B 601419385 T/C - A G AG + BobWhite_rep_c60245_107 chr5B 602138808 A/G + A G CT - Tdurum_contig82077_336 chr5B 602138808 T/C - A G CT - RFL_Contig1265_515 chr5B 602139015 T/C + T C AG - Tdurum_contig82077_129 chr5B 602139015 A/G - T C AG - Tdurum_contig14326_597 chr5B 603881987 T/C + T C CT + BS00022065_51 chr5B 603884073 A/G - T C CT + BS00022852_51 chr5B 604022655 A/G + G A CT - Excalibur_c82693_359 chr5B 604022736 T/C + C T CT + Tdurum_contig43078_437 chr5B 604023029 T/C - A G CT - BS00095092_51 chr5B 604023041 A/G + G A CT - RFL_Contig2772_1693 chr5B 605480942 A/C - G T AC - GENE-2344_73 chr5B 605826923 T/C - G A CT - BS00003655_51 chr5B 606021046 T/C + T C AG - IACX5792 chr5B 606021046 A/G - T C CT + RAC875_rep_c108082_333 chr5B 606850571 T/C - A G CT - RFL_Contig3835_2474 chr5B 607876265 T/C + T C CT + RFL_Contig3835_2578 chr5B 607876369 T/C + C T CT + BS00054946_51 chr5B 611385423 A/G + G A AG + Excalibur_c35561_309 chr5B 612682449 T/C - A G CT - Kukri_c36018_985 chr5B 612982119 T/C + T C CT + Kukri_rep_c101622_604 chr5B 615198853 T/C - G A CT - Kukri_c836_513 chr5B 615704107 A/G + A G AG + RAC875_c28645_455 chr5B 616652623 A/G - T C CT + Kukri_c10508_253 chr5B 617137928 A/G + A G CT - Kukri_c10508_438 chr5B 617139993 A/G + A G AG + Tdurum_contig57696_133 chr5B 617141991 T/C + C T AG - BobWhite_c22036_399 chr5B 617142065 T/C + C T AG - Tdurum_contig85060_121 chr5B 617819247 T/C + T C AG - Kukri_c25613_1347 chr5B 617826553 T/C - G A CT - BobWhite_c22572_782 chr5B 618123503 T/C + T C CT + CAP7_c1274_206 chr5B 618475693 T/G - C A AC + RAC875_c49291_156 chr5B 620018484 T/C - G A AG + Tdurum_contig82473_67 chr5B 620827474 A/G - T C CT + Tdurum_contig51422_127 chr5B 621237112 A/G + A G CT - BS00016757_51 chr5B 621263173 A/G - T C AG - BS00015015_51 chr5B 621263180 T/C - A G CT - BS00049548_51 chr5B 621841095 T/C - A G AG + BobWhite_rep_c63253_215 chr5B 622040405 T/C + T C AG - BS00037104_51 chr5B 622390978 A/C + A C GT - Tdurum_contig25692_435 chr5B 622396307 A/G - T C AG - RAC875_rep_c91630_132 chr5B 622555946 T/C + T C AG - Tdurum_contig24416_284 chr5B 622626415 A/G - T C CT + BobWhite_c17845_132 chr5B 631026825 T/C + T C AG - BobWhite_c21482_192 chr5B 631029058 T/C + T C AG - BS00021960_51 chr5B 631951975 T/C - A G CT - IAAV265 chr5B 635091963 A/G - T C AG - Excalibur_c4169_2488 chr5B 635092002 A/C - G T AC - Tdurum_contig5017_993 chr5B 635358632 T/C + C T CT + Tdurum_contig5017_1015 chr5B 635358654 T/G + G T AC - BS00028492_51 chr5B 635808733 T/C - G A CT - RAC875_rep_c109658_614 chr5B 636598120 T/G - A C AC + RAC875_rep_c109658_382 chr5B 636598352 T/C - G A CT - Kukri_c17933_943 chr5B 636653281 A/G - C T CT + Excalibur_c21238_532 chr5B 636655468 A/G + G A AG + Excalibur_c92906_314 chr5B 637128828 A/G + G A AG + Excalibur_c39478_137 chr5B 637898002 A/G - C T CT + BS00100707_51 chr5B 638508166 T/C + C T AG - BS00022991_51 chr5B 638508602 T/C + T C AG - BS00025795_51 chr5B 638833499 T/G + G T GT + Tdurum_contig42069_208 chr5B 639094563 T/G - C A GT - BS00022433_51 chr5B 639737446 T/C + T C CT + BS00066231_51 chr5B 639973140 A/G - T C CT + BobWhite_rep_c64277_490 chr5B 640149787 A/G + A G AG + Kukri_c82145_51 chr5B 640543468 T/C - A G AG + BobWhite_c39214_164 chr5B 641412149 A/G - C T AG - CAP7_c180_95 chr5B 642276667 T/C - G A CT - Kukri_rep_c105748_630 chr5B 642833447 T/C + T C CT + BS00111093_51 chr5B 643167976 A/C + C A GT - BobWhite_c41609_107 chr5B 643462537 T/C - A G CT - Kukri_c7966_93 chr5B 643469456 T/G - C A AC + Excalibur_rep_c109685_107 chr5B 643667314 T/C NA NA NA CT NA flanks do not match reference at this position RFL_Contig320_681 chr5B 644855367 T/C + C T CT + Tdurum_contig47627_442 chr5B 644888669 A/C - T G AC - Excalibur_c8724_348 chr5B 647913053 A/G - T C AG - BobWhite_c12883_272 chr5B 647940744 A/G - T C AG - Tdurum_contig32745_228 chr5B 647992950 A/G - C T AG - RFL_Contig4520_749 chr5B 649402795 A/G + A G CT - BobWhite_c31268_254 chr5B 649870648 A/G - C T AG - IACX546 chr5B 650010690 T/C + C T AG - Tdurum_contig92805_192 chr5B 650016116 T/C - A G CT - BobWhite_c10245_305 chr5B 650346429 A/G - C T CT + IACX757 chr5B 650558811 A/G - C T CT + BS00022899_51 chr5B 652477863 A/G - T C CT + BS00022477_51 chr5B 652632812 A/G - C T AG - BS00029852_51 chr5B 652634943 T/G - A C AC + Tdurum_contig59606_2411 chr5B 652634943 A/C + A C GT - BS00022956_51 chr5B 653433467 A/G - T C CT + BS00022231_51 chr5B 653655623 A/G + A G CT - BS00037023_51 chr5B 654494343 T/C - A G CT - BobWhite_c11038_312 chr5B 654750310 T/C + C T AG - BobWhite_c11038_605 chr5B 654751510 T/C + T C AG - tplb0057d20_531 chr5B 654954572 A/G - T C CT + Tdurum_contig15047_186 chr5B 655149053 T/C - G A AG + BS00093743_51 chr5B 656232706 T/C + C T AG - RAC875_rep_c105761_317 chr5B 656232736 A/G - C T AG - BS00093746_51 chr5B 656232891 T/C + T C CT + Excalibur_c39672_90 chr5B 656255204 T/C + T C CT + Excalibur_c39672_189 chr5B 656255405 T/G + T G GT + Excalibur_c4083_731 chr5B 656256864 T/G + T G AC - BS00021868_51 chr5B 656257298 A/G - C T CT + Kukri_rep_c103049_96 chr5B 656258314 A/G - C T AG - Kukri_c16006_431 chr5B 656258669 T/C + T C AG - BS00064272_51 chr5B 656713588 A/G + G A AG + BS00064274_51 chr5B 656713704 A/G + A G AG + Excalibur_c23661_1712 chr5B 656905462 T/G - C A GT - IACX6116 chr5B 657711708 A/G + A G AG + Kukri_c11272_486 chr5B 657714245 T/C + C T AG - BS00084106_51 chr5B 657714453 A/G + A G CT - RAC875_c56438_114 chr5B 657884215 T/C - A G AG + BS00050054_51 chr5B 658370047 T/C + C T AG - BS00050057_51 chr5B 658370121 T/G + G T GT + BS00097105_51 chr5B 658454282 A/G + A G AG + Tdurum_contig8171_1548 chr5B 658454330 A/C + C A GT - BobWhite_c38408_71 chr5B 658454384 T/C + T C AG - Tdurum_contig8171_1602 chr5B 658454384 T/C + T C CT + Tdurum_contig8171_1680 chr5B 658454462 A/G + A G AG + Tdurum_contig8171_1712 chr5B 658454494 T/C + T C AG - Tdurum_contig8171_1783 chr5B 658454565 T/C + T C AG - IACX7841 chr5B 658740013 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c4096_220 chr5B 659973318 A/G + A G CT - Ra_c6374_1984 chr5B 662028562 T/C + C T AG - Tdurum_contig45588_730 chr5B 662030433 A/G - C T CT + tplb0057b23_1134 chr5B 662034879 T/C - G A AG + BS00012140_51 chr5B 662455799 T/C + C T CT + tplb0029o19_1172 chr5B 662829791 A/G + A G CT - BS00062409_51 chr5B 662851468 T/C - G A CT - Kukri_c41_858 chr5B 663115905 A/G + A G CT - Kukri_c46570_214 chr5B 663135505 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c24226_1356 chr5B 663137019 A/C + A C GT - BobWhite_c43_86 chr5B 663516563 A/G - C T CT + RAC875_c29488_56 chr5B 663522311 T/C + C T CT + Kukri_c91279_125 chr5B 663522410 T/C - G A CT - Excalibur_c25522_755 chr5B 663523081 T/C - G A AG + Tdurum_contig35470_227 chr5B 663798945 T/C + T C CT + RAC875_c12293_588 chr5B 664021432 A/G - C T CT + GENE-2890_482 chr5B 664025483 A/G - C T CT + GENE-2890_50 chr5B 664025680 T/C - G A AG + Kukri_c5739_276 chr5B 664682459 A/G - T C CT + GENE-2932_119 chr5B 664950791 T/C - A G CT - BS00098520_51 chr5B 665810490 A/G - T C AG - Tdurum_contig47033_241 chr5B 666202377 A/G + G A AG + Tdurum_contig47033_367 chr5B 666202503 T/C + C T CT + BS00078784_51 chr5B 668198283 T/C - A G AG + RAC875_c45135_184 chr5B 668474049 A/G - C T CT + Excalibur_c45488_148 chr5B 668474076 T/C - G A AG + BS00028082_51 chr5B 668582697 A/G + G A CT - RFL_Contig6156_727 chr5B 669451565 A/C - T G AC - Kukri_c40099_249 chr5B 669483230 A/G + G A AG + Tdurum_contig8210_317 chr5B 669483437 A/G - C T AG - RAC875_rep_c111379_703 chr5B 669550599 T/C + C T AG - Tdurum_contig77918_477 chr5B 669672832 A/G - C T CT + BS00088733_51 chr5B 669896568 T/C + C T CT + Tdurum_contig44115_132 chr5B 669896568 T/C + C T AG - RAC875_c62400_267 chr5B 669896712 T/C + C T AG - Tdurum_contig44115_561 chr5B 669897438 T/G + G T GT + RAC875_c62400_639 chr5B 669897740 T/C + C T AG - Tdurum_contig44115_720 chr5B 669897812 T/C + C T CT + RAC875_c62400_840 chr5B 669897941 T/C + C T CT + RAC875_c62400_924 chr5B 669898025 T/C + C T AG - Tdurum_contig92938_632 chr5B 670020276 T/C + C T CT + BS00022886_51 chr5B 670081444 A/C - T G AC - BS00095157_51 chr5B 670246157 T/C - A G CT - BS00062971_51 chr5B 670541156 T/G + T G AC - BS00062972_51 chr5B 670541188 T/G + G T GT + BS00084907_51 chr5B 670828747 A/G - T C CT + Excalibur_c17489_804 chr5B 670829766 T/C - A G CT - Excalibur_c17489_769 chr5B 670829801 T/C - A G AG + GENE-2307_865 chr5B 671094245 T/C + T C CT + IACX1947 chr5B 671094762 A/G - C T AG - Ku_c22523_598 chr5B 671192861 T/C - NA NA AG NA reference base C not among SNP alleles Excalibur_c19001_809 chr5B 671192979 A/G - C T CT + BS00021948_51 chr5B 671196095 A/G - C T CT + BS00024814_51 chr5B 671301137 T/G - C A GT - Kukri_c35405_256 chr5B 671353518 T/C - G A CT - BS00077685_51 chr5B 671356275 A/G - C T CT + Kukri_c87328_116 chr5B 671360339 T/C + C T AG - CAP12_c2231_114 chr5B 672594691 A/C - G T GT + IAAV5014 chr5B 672594740 A/G + A G AG + BS00039874_51 chr5B 672953298 A/G - T C AG - Tdurum_contig58293_582 chr5B 673126150 T/C + T C AG - BobWhite_c23141_92 chr5B 674269213 T/C - A G CT - RFL_Contig3029_487 chr5B 674270105 A/C - T G GT + Excalibur_c54134_84 chr5B 674661069 A/G NA NA NA CT NA flanks do not match reference at this position BobWhite_rep_c66326_95 chr5B 674892390 A/G - T C AG - Excalibur_rep_c106003_475 chr5B 674894337 A/G + A G AG + BobWhite_rep_c66196_464 chr5B 675080455 T/C + T C CT + Kukri_c24292_390 chr5B 675882510 T/C + T C CT + Excalibur_rep_c102533_116 chr5B 677154676 A/G - C T AG - BS00010582_51 chr5B 677875563 A/C - T G GT + BobWhite_c17737_911 chr5B 677876449 T/C - G A CT - BS00062618_51 chr5B 678515535 T/G - C A GT - Excalibur_rep_c108404_225 chr5B 678621027 A/C NA NA NA AC NA flanks do not match reference at this position BS00029348_51 chr5B 678659619 T/C + T C AG - GENE-4868_140 chr5B 678663769 T/C - G A CT - Excalibur_c9969_98 chr5B 678917284 A/G - C T AG - Excalibur_c37910_276 chr5B 678917541 T/C + C T CT + RAC875_c17575_2549 chr5B 679132639 T/C - A G AG + BS00011633_51 chr5B 679133566 A/G + A G AG + Kukri_c27433_2206 chr5B 679134189 T/C + T C AG - Kukri_c27433_2333 chr5B 679134316 A/G + A G AG + BobWhite_c6685_1922 chr5B 679347871 T/C - A G CT - RAC875_c19660_1530 chr5B 679348886 T/C - G A CT - BS00078870_51 chr5B 679354789 T/G + T G GT + BS00048316_51 chr5B 679687636 T/C + C T AG - RAC875_c33791_320 chr5B 679804124 T/C + C T CT + Kukri_rep_c109463_264 chr5B 679815220 T/C - A G CT - RAC875_c38873_1118 chr5B 680358790 A/G - C T AG - RAC875_c2260_232 chr5B 680603510 T/C + C T AG - BS00088624_51 chr5B 680612328 T/G - A C AC + IACX751 chr5B 681079730 A/G + A G CT - BobWhite_c15241_604 chr5B 682536858 A/G + G A CT - Excalibur_c21971_522 chr5B 682698867 T/C - A G CT - IAAV8023 chr5B 682699266 T/C - A G CT - Tdurum_contig49583_669 chr5B 682839475 T/C - G A CT - RFL_Contig5337_1453 chr5B 682839856 A/G - T C CT + RAC875_c278_2934 chr5B 683141923 T/C - A G AG + RAC875_c278_1801 chr5B 683143170 A/G - C T AG - tplb0033c09_1345 chr5B 683342122 T/C + C T AG - BS00022438_51 chr5B 683517370 A/G + G A CT - Excalibur_c46000_203 chr5B 684494483 T/C - A G CT - Kukri_c67054_123 chr5B 684612648 A/G + A G AG + Kukri_c16864_398 chr5B 684615889 T/C + C T CT + Tdurum_contig65330_190 chr5B 684615889 A/G - C T CT + Excalibur_c78724_434 chr5B 684762928 A/G - C T AG - BS00069416_51 chr5B 685069742 A/C + C A AC + BS00069417_51 chr5B 685069797 A/G + G A CT - BobWhite_c26082_239 chr5B 685431645 A/G + G A AG + Ex_c9543_935 chr5B 685638351 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c5120_938 chr5B 687738216 T/C - G A AG + Excalibur_c32894_327 chr5B 687798146 A/G - C T CT + CAP12_c5949_104 chr5B 689851858 A/C + A C AC + BobWhite_c20282_164 chr5B 689853919 T/G - A C GT - BS00092233_51 chr5B 690703760 A/G - T C CT + BS00048425_51 chr5B 691152095 T/C - G A AG + BS00033185_51 chr5B 691434482 A/G + G A AG + BS00059847_51 chr5B 691860628 A/G + A G CT - BobWhite_c10921_1183 chr5B 692213259 T/C + T C CT + Excalibur_c23452_401 chr5B 692509160 A/G - T C CT + RFL_Contig5616_1779 chr5B 692564892 T/C + C T CT + Kukri_c1214_544 chr5B 692633948 A/C + A C AC + Kukri_c1214_825 chr5B 692634229 T/C + T C CT + Kukri_c1214_948 chr5B 692634352 T/C + T C AG - Kukri_c1214_1488 chr5B 692634892 A/G + G A AG + Kukri_c1214_2316 chr5B 692635833 T/C + T C CT + Kukri_c1214_2686 chr5B 692636203 A/G + G A AG + Kukri_c5588_1726 chr5B 693205970 T/C + C T AG - BS00024829_51 chr5B 693612491 T/G NA NA NA GT NA flanks do not match reference at this position RAC875_c22722_671 chr5B 693614130 T/C + C T CT + Kukri_c50720_397 chr5B 693670789 T/G - A C GT - RAC875_c18094_69 chr5B 693679867 A/C + C A GT - BS00077733_51 chr5B 693874441 T/C - A G AG + RAC875_rep_c96433_140 chr5B 694519309 A/G - C T AG - RAC875_c20161_821 chr5B 695484265 T/G - A C GT - Kukri_c7546_3035 chr5B 695657438 T/G - A C AC + Excalibur_rep_c100012_1145 chr5B 695659880 A/G + A G CT - Ku_c7546_861 chr5B 695659996 A/G - C T CT + tplb0031m13_1902 chr5B 695705144 T/C - A G AG + Kukri_c10913_480 chr5B 695775859 T/C + C T CT + Ku_c10913_2542 chr5B 695778622 A/G + A G AG + Kukri_c2735_626 chr5B 695990254 T/C + C T CT + Excalibur_rep_c68362_135 chr5B 695992865 A/G + G A AG + Ku_c2735_2959 chr5B 695992955 A/C + A C AC + Excalibur_c24511_1282 chr5B 696023088 T/C + T C AG - RAC875_c79095_311 chr5B 696176278 A/G - C T CT + BobWhite_c3488_386 chr5B 696188817 T/C - A G CT - RFL_Contig3285_1009 chr5B 696189453 A/C - G T AC - Tdurum_contig5522_455 chr5B 696193535 A/G - C T AG - BS00109754_51 chr5B 696420736 T/C - G A CT - Tdurum_contig10030_364 chr5B 696420895 T/C + C T CT + Tdurum_contig10100_230 chr5B 696490959 A/G - T C AG - RFL_Contig2911_406 chr5B 697115712 T/C NA NA NA CT NA flanks do not match reference at this position Jagger_c5071_425 chr5B 697118032 A/G + A G CT - Kukri_c88397_242 chr5B 697377370 T/C + T C CT + BS00068775_51 chr5B 697614394 A/G + G A AG + Excalibur_c146_92 chr5B 697680103 A/G + G A CT - Excalibur_c146_170 chr5B 697680299 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c18410_193 chr5B 697682441 A/G + A G CT - Tdurum_contig60189_855 chr5B 697682441 T/C - A G CT - Kukri_c18410_349 chr5B 697682951 T/C + C T CT + Kukri_c18410_409 chr5B 697683011 T/C + T C AG - Tdurum_contig60189_310 chr5B 697683429 A/G - C T CT + Excalibur_c23801_115 chr5B 700232256 T/C + T C AG - Tdurum_contig66604_927 chr5B 700232256 A/G - T C AG - Jagger_c8121_167 chr5B 700234628 A/G + A G AG + RAC875_c82589_246 chr5B 700236129 T/C - G A AG + Kukri_c7866_1387 chr5B 700330587 T/C - G A AG + IACX20775 chr5B 701152852 A/T + A T AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Kukri_c45387_380 chr5B 701153065 T/C - A G AG + Excalibur_c2618_1412 chr5B 701155202 T/C + T C CT + Excalibur_c2618_1723 chr5B 701155513 T/C + C T AG - Tdurum_contig97942_51 chr5B 701174270 A/G + A G AG + Excalibur_c48802_286 chr5B 701174465 A/C - G T AC - BS00031338_51 chr5B 701189732 T/C + C T AG - RAC875_c20429_101 chr5B 701457927 T/C - A G CT - Tdurum_contig84832_110 chr5B 701461843 T/C + C T CT + BS00024766_51 chr5B 702376333 T/C - G A CT - BobWhite_c10956_71 chr5B 702376619 A/G NA NA NA CT NA flanks do not match reference at this position IAAV7110 chr5B 702941393 A/G - T C AG - Tdurum_contig59631_198 chr5B 702941540 A/G + A G CT - BobWhite_c24484_240 chr5B 702941592 T/C - G A AG + Tdurum_contig59631_417 chr5B 702941759 T/C + C T CT + Tdurum_contig59965_403 chr5B 703088678 T/C NA NA NA AG NA flanks do not match reference at this position Ku_c36367_203 chr5B 704240009 T/G - C A GT - Excalibur_c72294_134 chr5B 704865063 A/G - T C AG - RAC875_c17214_958 chr5B 704883555 T/G + T G AC - Excalibur_c8658_1144 chr5B 706165385 T/C - A G CT - Kukri_c3070_72 chr5B 706305448 A/C + A C AC + Tdurum_contig28552_88 chr5B 707131652 T/C + C T CT + RAC875_rep_c106589_784 chr5B 707131775 T/C - A G CT - Tdurum_contig28552_211 chr5B 707131775 A/G + A G AG + RAC875_rep_c106589_650 chr5B 707131909 A/G - T C AG - RAC875_rep_c106589_184 chr5B 707133141 T/C NA NA NA AG NA flanks do not match reference at this position Tdurum_contig92922_58 chr5B 707134581 A/C - T G GT + Tdurum_contig44271_1220 chr5B 708222957 A/G + A G CT - Kukri_c5318_380 chr5B 709159885 T/G + T G GT + RAC875_c30241_331 chr5B 710625170 T/C - A G CT - Excalibur_c71602_591 chr5B 711582630 T/C - A G AG + Excalibur_c71602_420 chr5B 711582801 T/C - A G CT - Kukri_c637_517 chr5B 711702429 T/C - A G CT - Excalibur_c2207_1060 chr5B 712600972 A/G + G A AG + Kukri_c91538_610 chr5B 712696868 A/G - C T CT + tplb0048o03_953 chr5B 712697171 T/C + C T AG - IAAV4618 chr5B 712850724 A/T + NA NA AT NA reference base G not among SNP alleles RAC875_c37988_243 chr5B 712851567 A/G + G A CT - BS00021993_51 chr5B 712902514 T/C - G A CT - BS00009777_51 chr5B 712905714 T/C - G A AG + JG_c1426_201 chr5B 712907134 A/G - T C CT + BS00034658_51 chr5D 1614313 A/C + A C GT - GENE-3111_152 chr5D 7412338 T/G - A C GT - TA006089-0703 chr5D 8530760 T/C + T C CT + Kukri_rep_c70770_1937 chr5D 8535949 T/C + C T CT + Excalibur_c1110_328 chr5D 9732032 T/G - C A GT - RFL_Contig4911_357 chr5D 10522417 T/C + T C CT + RAC875_c103396_446 chr5D 13893187 A/G - T C AG - Kukri_c16994_1482 chr5D 18181125 T/C - A G AG + Excalibur_c29975_333 chr5D 21463055 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_c30273_138 chr5D 23298067 T/C - G A AG + Excalibur_c3948_1315 chr5D 26790958 T/C - A G CT - Excalibur_c17904_437 chr5D 29609763 A/G + A G AG + Excalibur_c3730_2098 chr5D 30115847 A/G - T C CT + IAAV7134 chr5D 30116079 A/T + A T AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles TA002772-0920 chr5D 30116335 A/G - C T AG - Excalibur_c3730_546 chr5D 30117528 T/C - A G CT - Excalibur_rep_c66392_1299 chr5D 43210977 A/G + G A AG + GENE-1265_290 chr5D 43213569 A/G - C T AG - Kukri_c24627_122 chr5D 51840719 T/C + T C CT + RAC875_c49044_335 chr5D 52615389 A/G - T C AG - RAC875_c17427_270 chr5D 59033266 A/G + G A CT - JD_c947_819 chr5D 59042623 T/C + T C CT + Jagger_c6508_51 chr5D 59042827 T/C - A G AG + Kukri_c644_305 chr5D 69350188 T/C NA NA NA AG NA flanks do not match reference at this position BS00065783_51 chr5D 69456350 T/C - A G CT - Excalibur_c33031_1755 chr5D 71914616 T/C + C T CT + RAC875_c5518_1401 chr5D 74464537 T/C + T C CT + CAP7_c1403_70 chr5D 74464714 T/C + T C AG - GENE-3524_570 chr5D 77054976 T/G - C A AC + D_F5MV3MU01ARH30_116 chr5D 78011824 A/G + A G CT - GENE-3606_315 chr5D 84902243 A/C - G T AC - Ku_c6501_507 chr5D 95291466 A/G + G A AG + Excalibur_rep_c69282_651 chr5D 101700367 A/G + A G AG + TA002565-0478 chr5D 107584042 T/G - A C AC + RAC875_c68368_99 chr5D 114807994 A/G - T C AG - Ra_c70331_779 chr5D 132880061 T/C - A G CT - GENE-3609_447 chr5D 154539123 T/C + C T AG - RAC875_rep_c70595_321 chr5D 154539793 A/G + G A CT - Excalibur_c10046_579 chr5D 160064709 A/G - T C CT + Excalibur_c37257_681 chr5D 169244131 T/C - A G CT - BS00065882_51 chr5D 175639248 A/C + C A AC + RAC875_c26265_146 chr5D 188337693 T/C - A G CT - RAC875_c26265_117 chr5D 188337722 A/C - T G GT + Kukri_c10780_511 chr5D 192269747 T/C - A G AG + GENE-3460_57 chr5D 212567784 T/C + T C CT + BS00065401_51 chr5D 230944850 T/C + T C AG - Kukri_c13045_302 chr5D 241250896 T/G - C A AC + RFL_Contig2012_2777 chr5D 249789682 T/G - C A GT - GENE-3478_202 chr5D 255685303 A/G + G A CT - RAC875_c92929_92 chr5D 276710447 T/C - A G CT - IAAV7187 chr5D 278311956 T/C + C T AG - Kukri_rep_c73094_348 chr5D 278625735 T/C - G A CT - GENE-3499_134 chr5D 280790487 A/C - G T AC - Excalibur_c13516_146 chr5D 287305338 A/G - T C AG - BS00001085_51 chr5D 304163637 T/G + G T GT + Kukri_c31786_657 chr5D 322959521 A/G - T C AG - GENE-3583_319 chr5D 341566392 T/C - A G AG + IACX2960 chr5D 347482700 T/C - A G CT - BS00000615_51 chr5D 354269559 T/G + G T AC - RAC875_c62685_520 chr5D 360545419 T/C + C T AG - IACX11633 chr5D 364396265 A/G - T C AG - GENE-3591_126 chr5D 365324412 A/G + A G AG + RAC875_c19105_498 chr5D 365698586 T/C + C T AG - Excalibur_c8082_478 chr5D 367414250 A/G + A G CT - BS00068414_51 chr5D 368331380 A/C - G T AC - RAC875_c63892_604 chr5D 369388338 T/C + C T AG - RAC875_c63892_678 chr5D 369388412 T/C + C T CT + BobWhite_c6244_144 chr5D 369720825 A/G - C T AG - BS00066349_51 chr5D 369727577 T/C + C T CT + BS00067895_51 chr5D 370450747 T/C - A G CT - BobWhite_c48301_178 chr5D 370468355 A/G + G A AG + RAC875_c7186_1147 chr5D 370468405 T/C - A G AG + GENE-4720_278 chr5D 381412960 A/C - G T GT + GENE-4720_236 chr5D 381412998 T/C - G A CT - Excalibur_c23709_938 chr5D 384069073 A/G - T C CT + Kukri_c10530_1013 chr5D 384070240 A/G - T C AG - Excalibur_c15578_73 chr5D 386732910 A/G + G A AG + BobWhite_c7263_337 chr5D 389934906 A/G - C T AG - Excalibur_c15835_86 chr5D 390257401 A/G + G A AG + IAAV7514 chr5D 391736720 A/G + G A AG + RAC875_rep_c78046_324 chr5D 393455810 A/G + G A CT - Kukri_c11815_706 chr5D 396808868 T/C - A G AG + RFL_Contig658_1166 chr5D 399148904 T/C + C T AG - Kukri_c24295_437 chr5D 399290099 T/C NA NA NA CT NA flanks do not match reference at this position BS00011318_51 chr5D 403075900 A/G + G A CT - BobWhite_c14323_288 chr5D 408776414 T/C + C T CT + IACX7890 chr5D 413073476 T/C + T C AG - RFL_Contig79_332 chr5D 413073725 A/G - T C CT + IACX5869 chr5D 413757350 T/G - A C GT - CAP11_c5629_55 chr5D 413761298 A/G - T C CT + GENE-3639_127 chr5D 414220823 T/G + T G AC - GENE-3206_268 chr5D 414247585 T/C - A G AG + GENE-3206_154 chr5D 414247695 A/G - C T CT + BS00011931_51 chr5D 415616884 T/C + C T AG - RAC875_c32587_186 chr5D 415680906 A/G + A G CT - Kukri_c26289_1242 chr5D 416213837 T/C - A G AG + IAAV4110 chr5D 418872791 T/C + T C AG - JD_c61555_640 chr5D 418872800 A/G - C T AG - Excalibur_c26312_475 chr5D 418874509 A/G + A G CT - Kukri_c55914_256 chr5D 418875766 A/G + A G CT - GENE-3641_40 chr5D 420874028 A/G + A G CT - BobWhite_c10764_251 chr5D 420919311 T/C - G A AG + D_GBB4FNX02JJ4FT_425 chr5D 421421630 T/C - A G CT - Kukri_c24933_538 chr5D 421844494 A/G + A G AG + JG_c1749_345 chr5D 422018148 A/G + A G CT - IAAV8416 chr5D 422462674 T/C + T C CT + Kukri_c26137_300 chr5D 423071174 A/G + G A CT - RAC875_c42095_237 chr5D 423071473 A/C + A C GT - IAAV3804 chr5D 423071612 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles D_GBB4FNX02HRJ2H_262 chr5D 423270304 T/C - A G CT - Kukri_c6477_696 chr5D 423502759 T/C - A G AG + GENE-3155_15 chr5D 424350182 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_rep_c103557_293 chr5D 424351685 T/C - G A AG + BS00021869_51 chr5D 424352416 A/C - G T AC - Excalibur_c30606_424 chr5D 425719525 A/G + A G AG + BobWhite_c8422_189 chr5D 425841738 A/C - G T GT + GENE-3189_137 chr5D 425847931 T/C - G A AG + Jagger_c6210_187 chr5D 426168157 A/G - C T AG - BobWhite_c7070_196 chr5D 426168185 T/C - A G AG + BobWhite_c17735_254 chr5D 429713700 T/G + T G AC - Kukri_c65301_127 chr5D 429909640 A/C + A C GT - TA003502-1375 chr5D 432525447 A/C NA NA NA GT NA flanks do not match reference at this position IAAV8929 chr5D 435274039 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Excalibur_c560_180 chr5D 435777580 A/G + G A CT - Excalibur_c14753_899 chr5D 436191311 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_rep_c101527_180 chr5D 436582775 T/C + T C CT + IAAV1706 chr5D 436801771 A/C + NA NA AC NA reference base G not among SNP alleles BS00065609_51 chr5D 436983359 T/G + G T GT + Kukri_c46932_155 chr5D 437342230 T/C + T C CT + RFL_Contig5739_641 chr5D 437342323 A/G + A G AG + RFL_Contig5739_1542 chr5D 437344051 T/C + T C CT + Kukri_c34173_169 chr5D 437344179 A/G - T C CT + IAAV6140 chr5D 437456909 A/T + A T AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Kukri_c9522_622 chr5D 438105855 T/C + T C AG - BS00023103_51 chr5D 439785994 T/C + T C CT + BS00024761_51 chr5D 439787007 T/C - A G CT - GENE-3619_813 chr5D 441104725 T/C - A G CT - Jagger_c5859_114 chr5D 441104852 T/C - A G CT - BobWhite_c19443_131 chr5D 442701407 T/C - G A CT - BobWhite_c6782_180 chr5D 443009451 A/G - C T AG - Kukri_c52_298 chr5D 443012753 A/G + G A AG + BS00009335_51 chr5D 443013136 T/C + C T AG - IACX7649 chr5D 443014302 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Kukri_rep_c95876_493 chr5D 444728644 T/C - A G CT - IAAV8572 chr5D 445109829 T/C + C T AG - Kukri_c1137_411 chr5D 445313019 T/G + G T AC - RAC875_c4792_754 chr5D 445315748 T/C + C T CT + Excalibur_c11929_1019 chr5D 446278510 A/C + C A GT - Kukri_rep_c113115_261 chr5D 446911141 A/G + A G AG + BS00010590_51 chr5D 447776528 T/G - A C GT - IAAV2323 chr5D 448816302 T/C + C T AG - Excalibur_rep_c106979_146 chr5D 448816356 T/C - A G AG + CAP7_c12729_232 chr5D 449850960 T/C + T C AG - IAAV4104 chr5D 450206572 T/C + T C CT + BS00067841_51 chr5D 451132521 T/C + T C AG - Kukri_c5967_586 chr5D 452679463 T/C + C T AG - IAAV8258 chr5D 453816280 T/C + C T AG - Kukri_c46526_103 chr5D 454111197 T/C - G A AG + Kukri_rep_c69276_59 chr5D 454119558 T/G + G T GT + RAC875_c28667_516 chr5D 458907611 T/C + C T AG - Tdurum_contig42008_7461 chr5D 461080602 T/C + T C AG - Kukri_c8495_616 chr5D 464088272 A/C + A C AC + BS00011453_51 chr5D 464090069 A/G + G A CT - Tdurum_contig27797_654 chr5D 464991041 T/G + T G AC - Excalibur_c26671_57 chr5D 471047858 T/C - A G CT - Excalibur_c24051_1028 chr5D 473342325 A/G - T C AG - GENE-2794_534 chr5D 473794656 T/C - G A CT - BobWhite_c28333_454 chr5D 479361053 T/C + T C AG - RAC875_c30867_515 chr5D 479452914 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_rep_c72553_368 chr5D 482107783 A/G + G A AG + Excalibur_c11840_1722 chr5D 482298667 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c41209_71 chr5D 482564069 A/G + A G AG + RAC875_c10323_90 chr5D 486243124 T/G + T G GT + Jagger_c3819_70 chr5D 489350836 T/C - A G CT - Kukri_rep_c70662_486 chr5D 489356502 A/G - T C CT + BS00082423_51 chr5D 489775906 T/C + T C AG - Excalibur_c9868_1206 chr5D 491447163 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_rep_c112275_315 chr5D 492721570 T/C - A G CT - RAC875_rep_c109097_771 chr5D 492728711 T/C - A G CT - BS00064691_51 chr5D 496067119 T/G + T G GT + RAC875_c54692_357 chr5D 496908774 A/G - C T AG - BobWhite_c6017_1147 chr5D 500674162 A/G - T C AG - BobWhite_c6017_1096 chr5D 500674213 A/G - T C AG - Kukri_c45951_367 chr5D 500675839 A/G + G A AG + GENE-2702_73 chr5D 505544092 T/C - G A CT - Tdurum_contig29090_280 chr5D 506074431 T/C - A G CT - BobWhite_c2730_245 chr5D 507775647 A/G - C T CT + RAC875_c8787_915 chr5D 512539650 T/C - A G CT - RAC875_c10436_793 chr5D 512772585 T/C + T C AG - BobWhite_c1562_369 chr5D 513526322 A/G - C T CT + IACX6288 chr5D 519343514 T/C - G A AG + RFL_Contig4167_1164 chr5D 519651444 T/C - A G CT - GENE-2855_121 chr5D 520782322 T/C + C T CT + Excalibur_c3328_227 chr5D 520783607 T/C + T C AG - Kukri_c7815_2958 chr5D 520897774 T/C + T C CT + BS00067651_51 chr5D 521522831 T/G - C A AC + Excalibur_c55589_258 chr5D 525081715 T/G + T G GT + Kukri_c21269_757 chr5D 526689071 T/C + T C AG - IAAV1779 chr5D 528403379 A/G - C T CT + BobWhite_c8264_515 chr5D 528973258 T/C - A G AG + Excalibur_c7613_789 chr5D 528980282 A/G + A G CT - Kukri_c32825_95 chr5D 529218679 T/C + T C CT + Kukri_rep_c110039_95 chr5D 529539957 T/C + C T CT + D_contig16027_318 chr5D 530405290 T/C - A G CT - GENE-2559_63 chr5D 530429925 A/G - C T AG - Kukri_c3576_1212 chr5D 530645764 A/G - T C CT + Excalibur_c8168_226 chr5D 531888441 A/G + A G CT - CAP7_c1979_79 chr5D 531893232 A/G + G A AG + RAC875_s117042_147 chr5D 534867023 A/G - T C CT + Excalibur_c74925_338 chr5D 535199813 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c4699_215 chr5D 537675150 T/C - A G CT - Excalibur_c4699_147 chr5D 537675218 T/C - A G CT - Kukri_c27433_947 chr5D 538164715 A/G + A G AG + BobWhite_c38741_305 chr5D 538165858 A/C - T G AC - BobWhite_c38741_143 chr5D 538166020 T/C - A G CT - BobWhite_c38741_108 chr5D 538166055 A/G - T C CT + JD_c2888_218 chr5D 538166112 T/C + T C CT + Excalibur_rep_c107626_110 chr5D 538166148 A/G + A G CT - RAC875_c2260_1700 chr5D 539026615 A/G + A G CT - BobWhite_c43731_313 chr5D 540347176 A/G - T C CT + BS00065864_51 chr5D 541944743 T/C + T C AG - Excalibur_c91745_337 chr5D 541945313 T/C - A G AG + Excalibur_c36048_410 chr5D 542694754 A/G - T C AG - Excalibur_c22576_108 chr5D 542699062 T/G + T G AC - D_GB5Y7FA02JRQ1I_101 chr5D 542991675 A/G - C T AG - BobWhite_c13718_682 chr5D 543058038 A/G - T C AG - Kukri_c34435_265 chr5D 543058308 T/C + C T AG - D_GCE8AKX02J2BYY_249 chr5D 543237654 A/C + A C AC + CAP7_c756_531 chr5D 544614760 T/C + C T AG - Excalibur_c1289_927 chr5D 544698157 A/G + G A AG + Excalibur_c99753_273 chr5D 546081734 T/C + T C AG - BobWhite_c13030_406 chr5D 546086647 A/G + A G AG + BS00079676_51 chr5D 546652117 A/G - C T AG - RAC875_c13169_459 chr5D 546652723 T/C + T C AG - D_GA8KES401AL4GG_122 chr5D 546653556 T/C + T C CT + BS00105939_51 chr5D 546679766 A/G - C T CT + Excalibur_c687_886 chr5D 546688598 A/G + A G AG + Kukri_c7786_81 chr5D 546689237 T/C + C T CT + BS00088587_51 chr5D 546689952 T/G - A C GT - IACX10520 chr5D 546690038 T/C + C T AG - D_GDS7LZN01CBWNE_99 chr5D 546700476 T/C - G A AG + Kukri_c5528_603 chr5D 546703116 T/C + T C CT + Kukri_c22934_766 chr5D 546779518 T/C - G A AG + BS00073116_51 chr5D 546864069 T/G + G T GT + Excalibur_c42190_383 chr5D 546906350 A/G - C T AG - Excalibur_c28592_377 chr5D 546909954 T/C - G A AG + Excalibur_c28592_173 chr5D 546910383 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c14043_548 chr5D 546910464 T/C - A G CT - CAP8_c145_89 chr5D 547273518 T/C + C T CT + CAP7_rep_c12715_390 chr5D 547273572 T/C - A G CT - BS00011794_51 chr5D 547273607 T/C - G A CT - BS00022036_51 chr5D 547273811 A/G - C T CT + RAC875_c50750_234 chr5D 548354017 T/C + T C AG - Kukri_c5228_1011 chr5D 548367072 T/C - A G CT - Excalibur_rep_c104791_725 chr5D 548367544 T/C + C T CT + Ku_c5228_417 chr5D 548367666 A/C - T G AC - Ku_c5228_402 chr5D 548367681 A/G - T C AG - Excalibur_c13901_98 chr5D 548368169 T/G - A C GT - Ra_c2279_718 chr5D 548368505 T/C + C T CT + Ra_c2279_730 chr5D 548368517 T/C + C T CT + Kukri_c14692_75 chr5D 548368912 A/G - T C AG - D_GCE8AKX02IXEFJ_281 chr5D 548869242 A/G - T C CT + BS00022688_51 chr5D 548879230 T/C - A G CT - Kukri_rep_c106820_591 chr5D 548880858 T/C + C T AG - D_GDS7LZN02I3554_251 chr5D 548942210 A/G + G A CT - Ku_c45387_733 chr5D 549576055 A/G - T C AG - IAAV1981 chr5D 549579200 A/G + A G AG + Excalibur_c50584_358 chr5D 549770546 T/C - G A AG + Kukri_c14878_97 chr5D 549806447 A/C + A C AC + IAAV1320 chr5D 549806945 A/G + A G AG + Kukri_c11140_323 chr5D 549855154 T/C - G A AG + Excalibur_c63110_92 chr5D 549867662 A/G + G A CT - Kukri_c28182_129 chr5D 549891152 T/C - A G AG + D_GB5Y7FA01DGNQR_235 chr5D 550153597 A/G + A G AG + BobWhite_c7604_254 chr5D 550206088 A/G - T C AG - BobWhite_c7604_181 chr5D 550206161 T/C - G A AG + Kukri_rep_c101796_71 chr5D 550438855 A/G + A G AG + BS00084133_51 chr5D 550441953 T/C - A G CT - BS00022537_51 chr5D 550441963 T/C - A G CT - IAAV1744 chr5D 550443455 A/G + A G CT - BS00013077_51 chr5D 550509820 A/G - T C AG - BS00009821_51 chr5D 550509823 T/C - A G CT - BS00022267_51 chr5D 550511075 T/C + T C CT + BS00074353_51 chr5D 550925008 T/C - G A CT - BS00025017_51 chr5D 551059358 T/C - G A CT - Excalibur_c30378_344 chr5D 552711321 T/G - A C AC + RAC875_c3672_705 chr5D 552711400 A/G + A G AG + Jagger_c8037_96 chr5D 553793879 A/G - C T AG - IACX7488 chr5D 554472730 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00032035_51 chr5D 555065425 T/G - A C GT - BobWhite_c20748_123 chr5D 555501739 A/G - T C AG - Excalibur_c46394_762 chr5D 555931943 A/G + G A CT - RAC875_rep_c70257_1346 chr5D 556232637 T/C + T C AG - BobWhite_c8037_778 chr5D 556232658 T/C - G A CT - RAC875_c16419_585 chr5D 556553215 T/G - A C GT - IACX5957 chr5D 557038046 T/G + G T GT + GENE-3006_294 chr5D 558441139 A/C + A C GT - BS00078603_51 chr5D 559481621 T/C + T C AG - RAC875_c93365_200 chr5D 559731784 A/G - T C AG - IACX5717 chr5D 559896067 A/C - T G AC - BobWhite_c33778_146 chr5D 559901489 A/G + G A AG + BS00011935_51 chr5D 559922067 T/C + C T CT + BS00058709_51 chr5D 559933771 T/C + T C CT + D_GDS7LZN02F4FP5_176 chr5D 559959298 A/G - T C AG - BS00010322_51 chr5D 560228200 T/C - G A CT - tplb0031c19_924 chr5D 560263400 A/G - C T AG - RAC875_c8100_163 chr5D 560503313 T/C + T C CT + RAC875_c8100_245 chr5D 560503395 A/G + G A AG + RAC875_c34968_514 chr5D 561673718 A/G - C T AG - Excalibur_c30778_271 chr5D 561675601 A/G - T C AG - Kukri_c21384_1758 chr5D 561676112 T/C + T C AG - Excalibur_c15405_808 chr5D 561704589 T/C - A G AG + BS00012069_51 chr5D 561707164 A/G + G A CT - RAC875_c14078_561 chr5D 561707179 A/G - C T AG - Ra_c105060_1855 chr5D 561795330 T/C - A G CT - Excalibur_c24145_1643 chr5D 561796615 A/G - T C AG - BS00079664_51 chr5D 561797031 T/C + C T CT + RFL_Contig617_1357 chr5D 562062929 T/C - G A AG + BS00021991_51 chr5D 562094170 A/G + G A AG + BS00085191_51 chr5D 562094493 T/C + T C CT + BobWhite_c47158_89 chr5D 562121483 T/C - G A AG + Kukri_rep_c104865_57 chr5D 562121967 T/C + T C CT + BS00011561_51 chr5D 562338720 T/C + T C CT + Excalibur_c1559_913 chr5D 562651160 A/G + A G AG + RAC875_rep_c78258_214 chr5D 562652154 T/C + C T CT + BobWhite_c22752_182 chr5D 562652370 A/C + A C AC + Kukri_c7827_1168 chr5D 562722865 T/C - A G CT - Kukri_c17093_1099 chr5D 562726475 A/G + G A AG + RAC875_c3988_3479 chr5D 562726606 T/C + C T AG - RAC875_c18090_752 chr5D 563754715 A/G + A G CT - RAC875_c29987_507 chr5D 563856217 A/G + A G AG + BobWhite_c31_2478 chr5D 565719244 T/C + C T AG - BobWhite_c15849_189 chr6A 287397 T/C + T C CT + BS00024901_51 chr6A 287786 T/C + T C CT + Tdurum_contig44853_1083 chr6A 631382 T/C + T C CT + BobWhite_c6527_222 chr6A 636793 A/G - T C CT + BS00082812_51 chr6A 639383 A/C + A C AC + RFL_Contig2815_1764 chr6A 796360 T/C - G A AG + BS00010580_51 chr6A 943142 T/C + T C CT + Kukri_c11737_1241 chr6A 943894 A/G - C T CT + RAC875_c13610_822 chr6A 1497480 T/C + C T CT + RAC875_c13610_1239 chr6A 1497897 A/G + G A AG + RAC875_c13610_1599 chr6A 1498868 A/G + A G AG + RAC875_c13610_1836 chr6A 1499962 T/C + T C CT + Excalibur_c19430_1066 chr6A 1500411 A/C - T G GT + RAC875_c13610_2646 chr6A 1500772 A/G + A G CT - BS00070384_51 chr6A 1831952 A/C + C A AC + Ku_c3650_1548 chr6A 1877200 A/G - C T CT + BS00071571_51 chr6A 1879563 T/C + C T CT + Excalibur_c50323_215 chr6A 1889151 T/C + T C CT + BS00093036_51 chr6A 2178229 T/C - G A CT - BS00074429_51 chr6A 2221151 A/G + A G AG + RAC875_c87324_202 chr6A 2233741 A/G + G A AG + Kukri_c80373_786 chr6A 2247864 T/C + C T AG - BS00093317_51 chr6A 2248435 A/G - C T AG - RAC875_c6135_95 chr6A 2402533 T/C + C T AG - Kukri_c143_1116 chr6A 2402669 A/G + G A AG + BS00022232_51 chr6A 3358999 A/G + G A AG + Kukri_rep_c97145_758 chr6A 3634498 A/G - T C CT + Excalibur_c15851_590 chr6A 3746516 T/G + G T GT + BS00109922_51 chr6A 4678762 A/G - C T AG - BS00109919_51 chr6A 4678786 T/C - G A CT - BS00067630_51 chr6A 5221726 A/G - C T CT + Excalibur_c431_1130 chr6A 5326425 T/C - A G AG + RAC875_c4668_771 chr6A 5326725 A/G - C T CT + Tdurum_contig12045_613 chr6A 5326956 A/G - C T AG - Tdurum_contig12045_246 chr6A 5327323 T/C - A G CT - TA005787-0140 chr6A 5363950 T/C + T C CT + BS00083630_51 chr6A 5604366 T/G + G T GT + Tdurum_contig55193_296 chr6A 6596867 A/G + A G CT - Excalibur_c20597_569 chr6A 6725061 T/C - G A CT - Excalibur_c20597_509 chr6A 6725121 A/G - C T AG - RFL_Contig5170_330 chr6A 6728251 A/G + G A AG + Kukri_c3009_1374 chr6A 6732787 T/C + T C CT + RFL_Contig5170_1904 chr6A 6733051 T/C + C T AG - IAAV9150 chr6A 6733115 A/G - C T CT + Kukri_c3009_1702 chr6A 6733115 T/C + C T CT + Tdurum_contig63703_1237 chr6A 6733400 T/C - A G CT - Tdurum_contig63703_1143 chr6A 6733494 T/C - A G AG + BS00082191_51 chr6A 7595547 T/G - C A AC + BobWhite_c3714_659 chr6A 8002498 T/C + T C CT + Tdurum_contig97611_150 chr6A 8791427 T/C + C T CT + Tdurum_contig54957_624 chr6A 9053137 T/C - G A AG + Excalibur_rep_c110867_88 chr6A 9327785 T/C - A G CT - BobWhite_c22086_444 chr6A 9327986 A/G - T C CT + GENE-0345_707 chr6A 10493680 A/G - C T CT + Kukri_rep_c101615_148 chr6A 10560366 A/G - C T CT + RAC875_c2145_92 chr6A 10919252 A/G + A G CT - Kukri_c89274_86 chr6A 11157695 T/C - G A AG + Kukri_rep_c70457_607 chr6A 11274085 T/C + C T CT + BS00065069_51 chr6A 11500009 A/G + G A AG + BS00098857_51 chr6A 11555419 A/G + G A CT - RFL_Contig1622_1259 chr6A 11589659 T/C - G A AG + RFL_Contig1622_923 chr6A 11589995 T/C - A G AG + Excalibur_c64989_250 chr6A 12392199 T/C + C T CT + IACX8154 chr6A 12392796 C/G - G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Kukri_c49017_75 chr6A 12393235 A/G + G A AG + CAP7_rep_c5315_221 chr6A 12836364 A/C + A C GT - BS00105910_51 chr6A 13071834 T/C - A G CT - RAC875_c28122_475 chr6A 13071986 T/C + C T CT + Excalibur_c4202_1326 chr6A 13072516 T/C - A G CT - BS00030455_51 chr6A 13072586 T/C - A G CT - RAC875_rep_c97032_73 chr6A 13075634 A/G + A G AG + Ra_c4286_1000 chr6A 13076609 A/G + G A AG + Ex_c3530_106 chr6A 13076622 T/C + C T AG - Jagger_c9118_62 chr6A 13382953 A/G - T C CT + Tdurum_contig45243_188 chr6A 13382953 T/C + T C CT + Kukri_c21443_482 chr6A 14354277 A/G - C T CT + RAC875_c6137_562 chr6A 15734681 T/G - A C AC + RAC875_c23552_1354 chr6A 15747995 A/G - C T AG - Kukri_c18874_1239 chr6A 15748739 T/C + T C AG - Excalibur_rep_c105463_330 chr6A 15766570 A/G + A G CT - GENE-4050_396 chr6A 16565175 T/C - G A AG + RAC875_c2253_2011 chr6A 16566127 T/C - G A CT - Ra_c2253_1271 chr6A 16566982 T/C - A G AG + RAC875_c2253_1255 chr6A 16566998 T/C - A G AG + BS00077789_51 chr6A 16569121 T/G - C A GT - Kukri_c10377_376 chr6A 16570585 A/G - T C AG - Excalibur_c5442_1691 chr6A 16571261 A/G + G A CT - CAP11_c1594_271 chr6A 17638471 T/C - A G AG + tplb0060j17_1091 chr6A 17638551 A/G - T C CT + tplb0060j17_879 chr6A 17638763 T/C - A G CT - RAC875_c38136_199 chr6A 18705995 T/C + C T AG - Kukri_c24705_248 chr6A 18706665 T/G + T G GT + Excalibur_c7044_243 chr6A 18706958 T/C - G A CT - RAC875_c62325_320 chr6A 20507528 A/C + A C AC + BS00011591_51 chr6A 21141961 A/G - T C AG - Excalibur_c98315_309 chr6A 21441818 T/G - A C GT - BS00085980_51 chr6A 21520723 A/G + A G AG + Tdurum_contig75595_886 chr6A 21521450 T/C - A G CT - BS00025084_51 chr6A 21707016 A/G - C T AG - GENE-4235_196 chr6A 22023199 T/C + C T CT + BobWhite_c36070_89 chr6A 22023522 A/C - T G AC - Excalibur_c39390_303 chr6A 22444025 A/G + A G CT - Kukri_c17618_874 chr6A 22524400 A/C - T G GT + IACX7801 chr6A 22524617 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Kukri_c37241_513 chr6A 22528192 A/G + G A AG + BS00044360_51 chr6A 22693950 A/G - C T CT + BS00022292_51 chr6A 23356743 A/G - T C CT + Excalibur_c23748_1233 chr6A 23357337 A/C + C A AC + BS00062894_51 chr6A 23371179 A/G - T C AG - BS00065076_51 chr6A 23372062 A/G + G A AG + BS00022660_51 chr6A 23410200 T/C + C T CT + Kukri_c11106_292 chr6A 23410275 A/G + G A AG + BS00093145_51 chr6A 23411709 T/C - G A CT - BobWhite_c24848_219 chr6A 23602321 T/C + C T AG - Kukri_c7458_1132 chr6A 23723080 A/G - C T CT + RAC875_rep_c106371_205 chr6A 23723284 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig50062_934 chr6A 23723284 A/G NA NA NA CT NA flanks do not match reference at this position BS00012023_51 chr6A 23876308 T/C + C T AG - BS00090073_51 chr6A 23877937 A/G + A G AG + RAC875_c52504_215 chr6A 24332134 A/G - C T AG - JD_c12608_191 chr6A 24772191 T/C NA NA NA CT NA flanks do not match reference at this position BS00003861_51 chr6A 24828633 T/C + C T CT + RAC875_c53520_103 chr6A 24830093 T/G + G T AC - Tdurum_contig11414_478 chr6A 25635242 T/C + T C CT + BS00110201_51 chr6A 25692998 A/G - T C AG - Excalibur_c35324_183 chr6A 25696409 T/C - A G CT - RAC875_rep_c113205_124 chr6A 26932282 T/C + C T AG - Excalibur_c18333_711 chr6A 27083831 A/G + A G AG + CAP7_rep_c8019_110 chr6A 27519940 T/C + C T CT + Tdurum_contig47463_615 chr6A 27781065 T/C + C T CT + BobWhite_c9330_499 chr6A 27781458 T/G - A C AC + Kukri_c2357_152 chr6A 27785692 A/G - T C AG - Tdurum_contig33313_101 chr6A 28412812 A/G - T C AG - Kukri_c264_438 chr6A 29558070 A/G + G A AG + Kukri_c264_539 chr6A 29558171 A/G + A G AG + Excalibur_c1708_1975 chr6A 29559295 A/G + A G CT - Tdurum_contig42015_2187 chr6A 29559719 T/G + G T GT + IAAV4117 chr6A 29610301 T/C + T C CT + BS00066661_51 chr6A 29967261 A/G - T C AG - IACX8337 chr6A 30030973 A/G - T C CT + Tdurum_contig64407_187 chr6A 30190310 A/G + A G AG + Tdurum_contig64407_219 chr6A 30190342 T/G + T G AC - Tdurum_contig64407_297 chr6A 30190420 A/G + A G AG + Tdurum_contig25770_254 chr6A 30464300 T/C + C T AG - Tdurum_contig25770_308 chr6A 30464354 A/G + G A CT - Excalibur_c60006_83 chr6A 30465677 T/C - A G AG + Excalibur_c17274_263 chr6A 30467684 T/C + T C AG - RAC875_rep_c106439_1097 chr6A 30467762 T/C + C T AG - Tdurum_contig64854_527 chr6A 30557829 A/G - T C CT + BS00091666_51 chr6A 31354418 T/C + T C AG - BS00091668_51 chr6A 31354458 A/C + C A GT - Kukri_c100884_175 chr6A 31355454 A/G - C T CT + Tdurum_contig61934_167 chr6A 31383099 A/G + A G AG + Tdurum_contig42906_732 chr6A 32658939 A/C + A C GT - Tdurum_contig9544_978 chr6A 32660585 T/C + T C AG - Tdurum_contig9544_2126 chr6A 32662304 T/C + C T CT + GENE-1530_1075 chr6A 32670121 T/G + T G AC - GENE-1530_594 chr6A 32670292 A/G NA NA NA CT NA flanks do not match reference at this position BS00076530_51 chr6A 32794680 T/C - G A CT - Tdurum_contig62141_496 chr6A 33953232 T/C - A G AG + Kukri_c35661_63 chr6A 33954717 T/C - A G AG + Kukri_rep_c104648_106 chr6A 33954865 A/C + A C AC + Kukri_rep_c104648_439 chr6A 33955363 T/G + G T AC - Tdurum_contig102404_127 chr6A 34972823 A/G - T C AG - RAC875_c34617_143 chr6A 34982359 A/G - T C CT + Tdurum_contig42729_433 chr6A 35637050 T/C - A G AG + Tdurum_contig42729_380 chr6A 35637103 T/C - G A CT - Tdurum_contig42729_242 chr6A 35637241 T/G - C A GT - Tdurum_contig76911_950 chr6A 36922033 A/G + G A AG + Excalibur_c97022_396 chr6A 37415157 A/G - C T CT + Kukri_rep_c105789_163 chr6A 37445517 A/G + G A AG + Tdurum_contig57672_482 chr6A 37700603 T/G + T G AC - Kukri_c20831_800 chr6A 38432389 A/G + A G CT - Excalibur_c8399_344 chr6A 38442504 A/C + C A AC + Excalibur_c8399_398 chr6A 38442558 A/G + G A CT - Excalibur_c8399_516 chr6A 38442676 A/G + A G AG + Excalibur_c8399_584 chr6A 38442744 T/C + T C AG - Excalibur_c8399_616 chr6A 38442776 A/C + C A AC + Kukri_c56638_212 chr6A 38452876 A/G + A G CT - BobWhite_c62620_150 chr6A 38470584 A/G - T C AG - Kukri_c17868_516 chr6A 38473833 A/G + A G AG + BobWhite_c534_837 chr6A 38474820 T/G + T G AC - Excalibur_rep_c94617_226 chr6A 38552092 A/G + A G AG + tplb0060o04_767 chr6A 39144401 T/C + C T AG - Excalibur_c25335_306 chr6A 41080294 A/C - T G GT + Kukri_c14765_1655 chr6A 41083892 A/C + C A AC + Kukri_rep_c112782_72 chr6A 43275763 T/C + T C AG - BobWhite_rep_c65857_65 chr6A 43276364 A/G - T C CT + GENE-0221_350 chr6A 47902386 T/G + G T GT + BS00023627_51 chr6A 48551333 A/G + A G AG + Excalibur_c9713_247 chr6A 48563698 A/G + A G CT - Jagger_c2853_75 chr6A 51399093 T/G - C A AC + Tdurum_contig92819_647 chr6A 51408240 A/G - C T CT + BS00031178_51 chr6A 51409080 T/C - G A AG + Kukri_c27958_334 chr6A 51507980 T/C + C T AG - IAAV3806 chr6A 52019801 A/C + C A AC + Excalibur_c10263_218 chr6A 52019883 A/G + G A AG + BobWhite_c4872_97 chr6A 52296237 A/G + G A CT - Tdurum_contig58912_605 chr6A 53508683 A/C + C A GT - BS00029282_51 chr6A 53785332 T/G + T G AC - BS00063109_51 chr6A 57763772 A/G - T C AG - RAC875_c27962_61 chr6A 60022663 A/G + A G AG + Excalibur_c48569_78 chr6A 60022996 T/C + C T CT + RAC875_c49875_405 chr6A 60168056 A/G - C T CT + Tdurum_contig17126_1477 chr6A 60431021 T/C - G A CT - RAC875_c33523_648 chr6A 60431498 A/G + G A CT - Excalibur_rep_c82397_137 chr6A 60431746 A/G + G A CT - Tdurum_contig55124_310 chr6A 60435864 T/C - A G CT - IAAV8577 chr6A 60442847 T/C - A G AG + Tdurum_contig16290_156 chr6A 60736012 T/G - C A AC + BS00079942_51 chr6A 61024089 A/G - T C AG - RAC875_rep_c73850_589 chr6A 61024279 T/C - A G CT - BS00023847_51 chr6A 61028461 A/G - T C AG - BobWhite_c18017_209 chr6A 61030200 A/G - T C AG - RAC875_c28637_1004 chr6A 61035305 A/G + A G CT - Kukri_rep_c68344_627 chr6A 61037728 T/C - A G CT - BS00021747_51 chr6A 61385214 T/G - C A AC + Kukri_c22149_276 chr6A 61386483 T/C - G A CT - Kukri_c45898_147 chr6A 61388308 T/C - G A CT - CAP7_c900_114 chr6A 61401403 T/C - A G AG + RAC875_rep_c107081_918 chr6A 61408816 T/C - G A AG + CAP7_c2381_149 chr6A 61418826 T/C + T C AG - Tdurum_contig83190_441 chr6A 61813444 T/C - G A AG + tplb0052b07_577 chr6A 61888248 A/G - C T CT + BS00011607_51 chr6A 63105338 T/C + T C AG - RAC875_rep_c81239_73 chr6A 63563014 T/C + C T AG - Excalibur_c6057_281 chr6A 63775383 A/G - T C CT + BS00021999_51 chr6A 65066575 A/G + G A CT - RAC875_c31973_225 chr6A 65072590 T/C + T C AG - BS00022704_51 chr6A 65073763 T/G - C A AC + RFL_Contig1038_942 chr6A 65140102 T/C - A G CT - BS00090928_51 chr6A 65434444 T/C + C T AG - RAC875_c4632_1681 chr6A 65553522 T/C - G A CT - Excalibur_c53686_249 chr6A 65553629 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c8610_408 chr6A 65553629 T/C + T C CT + Kukri_c66040_207 chr6A 65555359 A/G + A G AG + RAC875_c4632_934 chr6A 65556888 A/G - T C CT + Ex_c102862_798 chr6A 65860744 T/C - A G CT - TA004440-0664 chr6A 65861877 T/C NA NA NA CT NA flanks do not match reference at this position TA005243-1174 chr6A 66432067 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_c12641_1185 chr6A 67538430 A/G + G A AG + Excalibur_c38928_307 chr6A 67642427 A/G + G A CT - RAC875_rep_c99895_112 chr6A 67642933 A/G + G A AG + Kukri_c48959_337 chr6A 68622549 A/C - T G GT + Kukri_c21943_466 chr6A 70419977 A/G - T C CT + BS00067619_51 chr6A 71089044 A/C - G T GT + Tdurum_contig32619_202 chr6A 71447487 T/C - A G AG + RAC875_rep_c75251_505 chr6A 71450874 A/G + G A CT - Kukri_rep_c117390_70 chr6A 71539367 A/G + A G CT - JD_c5418_941 chr6A 71704211 A/G - T C CT + Tdurum_contig61970_835 chr6A 71704248 A/G - C T AG - Ku_c11950_931 chr6A 72432957 T/C + T C CT + Excalibur_c33724_303 chr6A 72434643 A/G + A G CT - GENE-3983_99 chr6A 73571981 A/G - C T AG - IAAV1234 chr6A 73576061 T/C + C T AG - Ku_c14907_456 chr6A 73576162 A/C + A C GT - Excalibur_c30324_564 chr6A 73642353 A/G + G A AG + CAP11_c3827_198 chr6A 73723587 T/C + C T CT + BS00046964_51 chr6A 73724747 A/G - C T AG - Tdurum_contig14559_477 chr6A 73994642 A/G - T C AG - RAC875_c17297_341 chr6A 73995107 A/G - C T CT + IAAV5188 chr6A 74025854 A/G - T C AG - Kukri_c67_1504 chr6A 74497975 T/C - A G AG + IAAV3046 chr6A 74499272 T/C - A G CT - BS00010811_51 chr6A 77513440 T/C + C T AG - Tdurum_contig51717_1582 chr6A 77514020 A/G + G A AG + RAC875_rep_c114561_587 chr6A 77532867 A/G - C T AG - Ra_c28284_223 chr6A 77538645 A/G - C T CT + GENE-4231_195 chr6A 80646014 A/G - T C CT + RFL_Contig5958_1142 chr6A 85020160 A/G + G A CT - IACX508 chr6A 85020357 A/G + G A AG + Kukri_c9595_242 chr6A 85756445 T/C + C T CT + BS00022554_51 chr6A 86118974 T/C + C T CT + BS00084846_51 chr6A 86118999 A/G + A G AG + BS00039145_51 chr6A 87296989 T/C - G A CT - RFL_Contig2605_693 chr6A 87297147 A/G - C T AG - RFL_Contig2605_672 chr6A 87297168 A/G - C T AG - Kukri_c50910_866 chr6A 87651032 T/C + C T AG - Kukri_c7794_1247 chr6A 87652173 T/C + C T CT + RAC875_c767_4007 chr6A 88093440 T/C + C T AG - BS00004377_51 chr6A 88094858 A/G + A G CT - IACX6453 chr6A 88094858 T/C - A G AG + Kukri_c16463_584 chr6A 88774064 T/C + T C CT + BS00093995_51 chr6A 88855161 T/C + C T CT + BS00092676_51 chr6A 90033865 T/C + C T AG - IAAV612 chr6A 91427584 A/G - T C CT + tplb0028p11_1104 chr6A 91866229 T/C + T C CT + Tdurum_contig15238_972 chr6A 91886378 T/C + T C AG - BS00065870_51 chr6A 91900694 A/G - T C AG - BS00012297_51 chr6A 93818299 A/C - T G AC - BS00026558_51 chr6A 94231857 T/C + T C CT + BS00063608_51 chr6A 96443875 A/G - C T AG - BS00066636_51 chr6A 99014191 T/C - G A AG + Tdurum_contig66802_343 chr6A 100232441 A/C + A C AC + Kukri_c77911_260 chr6A 100238738 T/C - G A AG + GENE-3659_162 chr6A 101302744 T/G + T G AC - tplb0032i10_420 chr6A 103760156 A/G + G A AG + BS00034886_51 chr6A 103958719 A/G + G A CT - BS00039515_51 chr6A 105558784 A/C + C A AC + RFL_Contig916_683 chr6A 106985479 T/G - C A GT - BobWhite_c20782_697 chr6A 107113248 A/G + A G AG + BS00044311_51 chr6A 107113578 T/C - G A AG + Kukri_c49417_141 chr6A 107175749 A/G - T C AG - RAC875_c83532_305 chr6A 108069382 T/C - A G CT - RAC875_c25029_554 chr6A 108070335 A/G + G A CT - Ra_c22700_943 chr6A 108077249 A/G - T C AG - Ra_c22700_818 chr6A 108077374 A/G - T C CT + RAC875_c75884_249 chr6A 111565794 T/C - A G CT - Ku_c8125_1049 chr6A 112584823 T/C - A G CT - IACX14305 chr6A 113517456 A/G + A G AG + RAC875_rep_c74600_377 chr6A 115020871 A/G NA NA NA CT NA flanks do not match reference at this position GENE-2561_69 chr6A 115409836 T/C - A G CT - Ku_c32392_967 chr6A 116709866 T/C + C T AG - BS00046046_51 chr6A 143376666 T/C - A G AG + BS00027313_51 chr6A 151492080 A/G - C T AG - Excalibur_c95665_51 chr6A 153353587 A/C - T G GT + IACX170 chr6A 157134836 A/G + G A CT - BS00041481_51 chr6A 176574357 T/C + C T AG - Jagger_c5227_133 chr6A 184826335 T/C - A G AG + Excalibur_rep_c102619_754 chr6A 192204971 A/G + A G CT - RAC875_rep_c70378_1464 chr6A 201552566 A/G + G A AG + BS00064654_51 chr6A 209895756 A/G - C T CT + Excalibur_c60816_99 chr6A 225313080 A/G + G A AG + Kukri_rep_c70185_854 chr6A 228535896 A/G + G A AG + Ku_c42436_461 chr6A 230701197 A/G - C T CT + BS00043715_51 chr6A 230706426 A/G - C T AG - BS00063977_51 chr6A 233343130 T/C + C T CT + Excalibur_c61509_69 chr6A 233345803 T/C + T C AG - IAAV5536 chr6A 233959213 T/G - C A AC + Ra_c28538_971 chr6A 249158525 A/G + G A CT - Excalibur_s105534_234 chr6A 252846711 T/C NA NA NA CT NA flanks do not match reference at this position TA004097-0977 chr6A 255325658 T/G - A C AC + BS00023089_51 chr6A 270610287 T/C - A G AG + IAAV5967 chr6A 273168266 T/C + T C AG - BS00088375_51 chr6A 286320473 A/G - C T AG - BS00068469_51 chr6A 288411615 T/C - G A CT - RAC875_c13778_650 chr6A 297711316 A/G - T C AG - IAAV894 chr6A 311856582 T/C - A G AG + Ku_c71238_1537 chr6A 322060754 A/G + A G CT - IAAV6535 chr6A 324286919 T/G + T G GT + BS00089169_51 chr6A 333957304 T/G + T G GT + Kukri_c16868_1062 chr6A 335779960 T/C - A G CT - BS00013851_51 chr6A 342527012 A/G + A G AG + BS00066748_51 chr6A 352604248 A/G - T C AG - BobWhite_c20706_135 chr6A 352662865 A/G - C T AG - Kukri_c33967_97 chr6A 356201731 A/G + G A CT - Excalibur_c99271_71 chr6A 359076160 T/C + C T AG - Tdurum_contig11951_212 chr6A 363516970 T/G - C A AC + BS00065079_51 chr6A 367145698 A/C - G T GT + Excalibur_c37358_676 chr6A 369172152 T/C - G A CT - Excalibur_c29213_372 chr6A 377853483 T/C + T C AG - BS00024191_51 chr6A 381025610 A/G - C T CT + Ex_c50864_326 chr6A 381032912 A/G + A G AG + JD_c6195_347 chr6A 381033715 T/G - A C GT - Ra_c41794_1690 chr6A 387065054 A/G - C T AG - RAC875_c60707_1852 chr6A 387067797 A/G - T C AG - IACX3317 chr6A 388059029 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles IAAV1385 chr6A 388213961 A/G + A G AG + BS00022120_51 chr6A 396301431 A/G - C T CT + RAC875_c5819_1450 chr6A 399834020 A/G - T C AG - BobWhite_rep_c64054_499 chr6A 399879102 T/C - A G CT - IAAV6992 chr6A 401890392 T/C + C T AG - Tdurum_contig17318_413 chr6A 404697458 T/G + G T GT + BS00022913_51 chr6A 409092614 T/C - A G AG + tplb0047k12_1370 chr6A 411095177 A/G - T C AG - Ra_c5250_567 chr6A 411936343 A/C - T G AC - BS00064820_51 chr6A 414867914 T/C + T C CT + IACX4889 chr6A 417444341 A/C + C A AC + IAAV6837 chr6A 421527450 A/G - C T AG - GENE-0659_105 chr6A 421753640 A/G + A G AG + BS00078715_51 chr6A 424093750 T/C - A G CT - BS00086046_51 chr6A 425277756 A/G - T C CT + Kukri_c56494_585 chr6A 425737454 A/C - T G AC - Excalibur_c4579_979 chr6A 427616757 T/C + T C CT + BS00066047_51 chr6A 430279313 T/C - G A CT - Kukri_c30819_246 chr6A 431144281 T/C - A G AG + BS00087178_51 chr6A 432246904 T/C - A G AG + BS00022605_51 chr6A 432248086 T/C - G A AG + Kukri_c38882_391 chr6A 433970968 T/C + C T CT + Excalibur_c1492_1282 chr6A 435778508 T/G NA NA NA AC NA flanks do not match reference at this position TA004032-0298 chr6A 437498220 T/C NA NA NA AG NA flanks do not match reference at this position BS00022553_51 chr6A 437702676 A/G - T C CT + BS00099290_51 chr6A 438579488 T/C + T C CT + BS00072945_51 chr6A 439668219 A/G + A G AG + Excalibur_c49239_97 chr6A 439668825 A/G - T C CT + RAC875_c58848_60 chr6A 440057065 A/G - T C CT + IACX203 chr6A 440234074 T/C + T C AG - RAC875_c49166_240 chr6A 440255621 A/G - C T AG - CAP11_c1206_301 chr6A 441806792 T/C - A G AG + Ku_c13637_545 chr6A 446728696 A/G - T C AG - BS00062823_51 chr6A 447421299 T/G + T G AC - Excalibur_c15844_1470 chr6A 447833898 A/C + C A AC + TA003858-0637 chr6A 451663617 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c23305_563 chr6A 452097334 A/C - T G AC - TA005690-1190 chr6A 452638226 A/G NA NA NA CT NA flanks do not match reference at this position BS00021689_51 chr6A 454638528 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig78006_158 chr6A 454638908 A/G - C T CT + IAAV7384 chr6A 454649374 T/G - A C GT - Tdurum_contig53138_302 chr6A 454649374 A/C + A C AC + IACX2250 chr6A 456752280 A/G - T C CT + GENE-4081_644 chr6A 484276131 T/G + T G GT + RAC875_c43536_193 chr6A 490496147 T/C + C T CT + Kukri_rep_c106170_174 chr6A 495426977 T/G - A C GT - IAAV622 chr6A 496841056 A/C - T G GT + GENE-3709_393 chr6A 496844226 A/G - C T CT + tplb0025i05_1985 chr6A 497462168 A/C - T G AC - TA004297-0876 chr6A 497791940 T/C - A G AG + GENE-4154_365 chr6A 498951610 A/C - T G GT + RAC875_c62614_191 chr6A 498953690 T/C - G A CT - Excalibur_rep_c69275_346 chr6A 499007758 A/G - C T CT + Ex_c1911_649 chr6A 499793749 A/C + A C GT - IACX5753 chr6A 500508436 T/C - G A CT - BS00010221_51 chr6A 501176793 T/C + C T CT + IACX7439 chr6A 501176875 T/G + G T GT + BS00040124_51 chr6A 501222263 A/G - T C AG - Kukri_c16199_886 chr6A 501485939 T/C + T C CT + BS00067934_51 chr6A 501801411 T/C - G A CT - RAC875_rep_c91575_101 chr6A 502712024 A/G - T C CT + Kukri_rep_c71164_191 chr6A 503729422 T/C + T C AG - Excalibur_c10352_911 chr6A 517892965 A/G - T C CT + BS00037006_51 chr6A 520354827 A/C + A C AC + BS00005019_51 chr6A 530046844 T/C + T C AG - BS00071708_51 chr6A 530218666 A/G + A G CT - BS00071706_51 chr6A 530218937 A/G + A G AG + Ku_c45494_267 chr6A 531002799 A/G + A G AG + BS00074752_51 chr6A 531101136 T/G - A C AC + BS00037223_51 chr6A 531278379 A/C - T G GT + IAAV7790 chr6A 531388441 A/C - T G AC - BS00084251_51 chr6A 531394562 A/C + C A GT - BS00084250_51 chr6A 531394648 T/G + T G AC - GENE-4052_338 chr6A 531516786 A/G + A G CT - BS00073872_51 chr6A 531522343 T/C - G A CT - Ku_c18430_1287 chr6A 532318211 A/C + A C GT - IAAV8493 chr6A 532318905 A/G + A G AG + RAC875_c691_1486 chr6A 533256714 A/G - C T AG - Excalibur_c53981_77 chr6A 533258521 T/C NA NA NA CT NA flanks do not match reference at this position BS00010780_51 chr6A 533259295 T/C - A G AG + Kukri_c19612_514 chr6A 533412588 T/C NA NA NA AG NA flanks do not match reference at this position BS00022836_51 chr6A 534962059 A/G - T C CT + BobWhite_c2568_115 chr6A 535402702 A/G + G A CT - IACX3586 chr6A 536254462 A/G + G A AG + IACX6046 chr6A 538056697 T/C - A G CT - CAP11_rep_c6843_59 chr6A 542232386 T/C - A G AG + CAP8_rep_c9395_153 chr6A 542828422 A/G - C T AG - IAAV4239 chr6A 542934428 A/G - C T AG - Tdurum_contig9835_664 chr6A 542934428 T/C + C T AG - BS00077448_51 chr6A 543378546 A/G - C T AG - BS00071732_51 chr6A 543397781 A/C - T G AC - Kukri_c8148_2719 chr6A 543937896 A/G - C T AG - Excalibur_c12748_2822 chr6A 543938205 T/C - G A AG + BS00036397_51 chr6A 543941067 T/C + C T CT + Excalibur_c11578_324 chr6A 544151490 A/C - T G GT + BS00072903_51 chr6A 544175959 A/G - C T AG - IAAV1652 chr6A 544204877 A/G - T C AG - JD_c12038_441 chr6A 544206710 A/C - T G AC - GENE-3726_78 chr6A 545112436 T/G + T G AC - Tdurum_contig81516_69 chr6A 545112860 A/C - T G GT + Kukri_c18260_345 chr6A 545124465 T/C + T C CT + Kukri_c2700_1137 chr6A 545811764 T/C NA NA NA AG NA flanks do not match reference at this position Tdurum_contig42125_5692 chr6A 545828569 A/G + G A AG + Tdurum_contig42125_5972 chr6A 545828849 T/C + C T CT + Tdurum_contig13240_523 chr6A 545832531 T/G + G T GT + Kukri_c44260_577 chr6A 546548035 T/C - A G AG + Kukri_c9262_401 chr6A 546552530 T/G + T G AC - Ku_c9262_902 chr6A 546553031 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c26057_1049 chr6A 547739853 T/C + T C CT + BobWhite_c1082_134 chr6A 548411495 A/C - T G AC - BobWhite_c19820_129 chr6A 548419475 T/C + T C AG - Ra_c16143_1157 chr6A 548600505 A/G - C T AG - Ra_c2370_1278 chr6A 549231231 T/C + T C CT + Tdurum_contig42858_1256 chr6A 550073974 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig42858_1352 chr6A 550074156 T/G + G T AC - RAC875_c29455_79 chr6A 550282493 A/G + G A CT - tplb0035a03_368 chr6A 550284054 A/G + G A CT - IACX5813 chr6A 550738391 T/C - G A AG + BS00063096_51 chr6A 551654256 A/G + G A AG + BobWhite_c6950_269 chr6A 552763328 A/G - C T AG - Excalibur_c37474_242 chr6A 553858501 A/C + C A AC + tplb0057g20_780 chr6A 555318099 T/C + T C CT + BS00047388_51 chr6A 555669562 T/C - G A CT - Excalibur_rep_c111263_307 chr6A 557672061 A/G - T C AG - BS00023893_51 chr6A 557933700 A/C + C A GT - CAP12_c2701_221 chr6A 559526507 T/C + T C CT + Kukri_rep_c105296_156 chr6A 559864316 T/C - G A CT - BS00023020_51 chr6A 560815424 T/C + C T CT + Kukri_c14906_220 chr6A 561599905 A/G - T C CT + Tdurum_contig61574_645 chr6A 562931621 A/G - T C CT + Tdurum_contig28847_322 chr6A 563126585 A/C - G T GT + RAC875_rep_c90952_205 chr6A 563131011 A/G - T C AG - Tdurum_contig29974_90 chr6A 563558658 A/G + G A CT - RAC875_c104548_369 chr6A 563742315 A/C NA NA NA AC NA flanks do not match reference at this position Tdurum_contig55363_297 chr6A 563742729 T/C + T C AG - Kukri_c6128_373 chr6A 564271936 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c6128_319 chr6A 564272561 T/C - G A CT - Tdurum_contig69065_319 chr6A 564515617 T/C + C T CT + BS00081699_51 chr6A 564717875 T/C - G A CT - BS00042195_51 chr6A 564723645 T/C - A G CT - GENE-4204_738 chr6A 564974982 T/C + T C AG - Ku_c44079_365 chr6A 565473384 T/C NA NA NA AG NA flanks do not match reference at this position BobWhite_c2143_229 chr6A 567091432 T/C + C T CT + BobWhite_c13845_195 chr6A 567933365 A/C + C A GT - IAAV5761 chr6A 567933456 A/G - C T CT + Tdurum_contig30416_144 chr6A 568050071 T/G - A C GT - Excalibur_c17905_126 chr6A 568494248 T/C + T C AG - IAAV8730 chr6A 568494376 A/G - T C CT + BS00022489_51 chr6A 568503437 T/C + C T AG - BS00082640_51 chr6A 568505010 T/C + T C CT + BobWhite_c32372_186 chr6A 568506927 T/C - G A CT - Kukri_rep_c69713_250 chr6A 569124147 T/C - A G CT - IAAV5585 chr6A 570378542 T/G - C A GT - GENE-3980_221 chr6A 570379811 A/G + G A CT - Kukri_c15096_4174 chr6A 570381184 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_rep_c113731_95 chr6A 573128867 T/C - A G CT - Kukri_c34083_349 chr6A 573492957 A/C - T G GT + Kukri_c12602_861 chr6A 573497130 A/G - T C AG - Ku_c3895_2991 chr6A 573506870 T/C NA NA NA CT NA flanks do not match reference at this position IAAV2501 chr6A 573507699 T/C - A G CT - Kukri_c3895_1286 chr6A 573508575 T/C - A G AG + Kukri_c3895_530 chr6A 573509857 A/G - T C AG - Kukri_c669_259 chr6A 574473364 A/G + G A AG + Excalibur_rep_c104696_400 chr6A 574475881 T/C NA NA NA AG NA flanks do not match reference at this position IAAV151 chr6A 574479896 T/C + T C CT + Excalibur_c32726_279 chr6A 574486229 A/G - T C AG - BobWhite_c47143_592 chr6A 574486839 T/G - A C AC + BS00058929_51 chr6A 580280921 T/G - A C AC + BobWhite_c17385_55 chr6A 581733581 T/C + T C AG - CAP7_c4283_67 chr6A 581746429 T/C + T C CT + CAP7_c4283_232 chr6A 581746594 A/G + G A AG + Kukri_c9763_115 chr6A 581747079 A/G + A G AG + Excalibur_c25898_434 chr6A 581796030 T/C - A G CT - Kukri_c20107_74 chr6A 581894810 A/G - C T AG - Tdurum_contig75084_965 chr6A 581977359 T/C + C T AG - IACX4309 chr6A 581977577 A/G + G A CT - Tdurum_contig54311_256 chr6A 582086903 T/C - A G CT - BobWhite_s67148_292 chr6A 582253754 A/G + G A CT - BobWhite_s67148_324 chr6A 582253786 A/G + G A AG + BS00063378_51 chr6A 582960918 A/G - T C AG - BobWhite_c26503_61 chr6A 583268917 T/C + C T CT + Tdurum_contig41947_720 chr6A 583814512 A/G - T C AG - Kukri_rep_c69627_954 chr6A 584678686 T/C - G A AG + RAC875_rep_c92223_1022 chr6A 584680389 A/C - T G GT + BS00066475_51 chr6A 584987784 A/G + G A AG + IACX473 chr6A 585192973 T/G + G T AC - Excalibur_c10372_1256 chr6A 585429518 T/C - G A AG + IAAV7168 chr6A 587778152 A/G - C T CT + RAC875_c7630_1383 chr6A 591017769 T/C + T C AG - Excalibur_c2737_309 chr6A 591732069 T/C + T C CT + Excalibur_c3432_98 chr6A 591733011 A/C - T G GT + Tdurum_contig62188_499 chr6A 592033735 A/G - C T AG - Kukri_c11266_1036 chr6A 592467833 A/C - T G GT + TA001855-0472 chr6A 592475421 T/C NA NA NA AG NA flanks do not match reference at this position RFL_Contig5037_560 chr6A 594748659 T/C + T C AG - RAC875_c93959_96 chr6A 594959438 A/G + G A CT - Excalibur_c52196_235 chr6A 595479797 A/G + A G AG + BS00099074_51 chr6A 595627707 T/G + T G GT + BS00003185_51 chr6A 596165675 T/C + T C AG - Excalibur_c24825_539 chr6A 596170405 T/C + T C CT + Ra_c3533_880 chr6A 596383482 T/C + T C CT + Kukri_c57452_1040 chr6A 596521164 A/C - G T AC - RAC875_c103443_475 chr6A 596903227 A/G - T C CT + BS00103442_51 chr6A 597351302 T/C - A G AG + RAC875_rep_c74051_276 chr6A 597351418 T/G - A C GT - Kukri_rep_c95718_868 chr6A 597356658 T/C - A G AG + RFL_Contig6053_3082 chr6A 597790267 T/C - G A AG + RFL_Contig6053_2072 chr6A 597791360 A/C - T G AC - Tdurum_contig28802_213 chr6A 597833088 T/C + T C CT + BS00022372_51 chr6A 598155213 T/C - G A CT - BobWhite_c27145_731 chr6A 598635440 T/C - G A CT - Tdurum_contig75700_411 chr6A 598635440 A/G + G A AG + BS00011202_51 chr6A 599033838 A/C + A C GT - BS00004466_51 chr6A 599035194 T/C + T C CT + Tdurum_contig8166_2257 chr6A 599042788 T/C - G A AG + BS00000750_51 chr6A 599046188 T/C + T C CT + IACX2946 chr6A 599046599 A/G + G A AG + GENE-4118_142 chr6A 599050301 A/G + G A CT - Tdurum_contig46670_1262 chr6A 599050478 A/G - T C AG - RAC875_c1998_1744 chr6A 599050945 T/C + T C CT + Tdurum_contig46670_911 chr6A 599050945 A/G - T C CT + RAC875_c1998_2067 chr6A 599051353 T/C + T C AG - BS00096240_51 chr6A 600406158 T/C + T C AG - IAAV5088 chr6A 600672607 T/C + T C AG - Tdurum_contig33799_172 chr6A 600817833 T/C - G A AG + Kukri_c9406_337 chr6A 601224125 A/G - T C AG - RAC875_c35946_481 chr6A 601226562 T/C + T C AG - Excalibur_c7002_314 chr6A 601472969 A/G + A G CT - BobWhite_c53978_99 chr6A 601473116 A/G - T C CT + BobWhite_rep_c60354_274 chr6A 601950883 A/G - T C CT + IACX1130 chr6A 602452538 A/C + A C AC + Tdurum_contig30262_75 chr6A 602623230 A/G + A G AG + RAC875_rep_c70106_1236 chr6A 602706392 T/C - A G CT - RAC875_rep_c70106_1175 chr6A 602706453 A/G - C T CT + RAC875_c40653_612 chr6A 602708877 A/G + A G AG + Tdurum_contig9503_575 chr6A 603136636 T/C + C T AG - RAC875_c10648_86 chr6A 603194123 A/C - T G GT + BobWhite_c2296_94 chr6A 603194161 T/C - G A AG + BS00095206_51 chr6A 603208282 T/G + T G AC - BS00090829_51 chr6A 603282460 T/C + C T AG - Tdurum_contig49511_330 chr6A 603282460 A/G - C T AG - RFL_Contig3175_1271 chr6A 604877104 T/C - A G CT - RFL_Contig3175_1217 chr6A 604877158 T/C - A G CT - RFL_Contig3175_482 chr6A 604878982 T/G - A C AC + RFL_Contig2765_669 chr6A 604884350 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c15525_271 chr6A 604886748 T/C + C T CT + BS00088274_51 chr6A 604887176 T/C + C T CT + CAP11_c2649_327 chr6A 604887200 A/G + A G CT - BS00022729_51 chr6A 605229804 T/C - G A AG + RAC875_rep_c105861_454 chr6A 605231081 T/C + T C AG - Excalibur_c25390_2483 chr6A 605231918 A/G + A G AG + Tdurum_contig30953_142 chr6A 605376001 A/G + A G AG + Excalibur_c16590_1536 chr6A 605380209 A/G + A G AG + Tdurum_contig42418_2618 chr6A 605552753 T/C + T C CT + IAAV6777 chr6A 605564404 T/C + T C AG - Excalibur_rep_c105389_309 chr6A 605564686 A/G + G A CT - Kukri_c30754_271 chr6A 606762616 A/G - C T AG - Kukri_c30754_229 chr6A 606762658 T/C - A G CT - BobWhite_c12032_371 chr6A 606764327 T/C + T C CT + Excalibur_c19182_226 chr6A 606766764 T/C + C T AG - RAC875_c28339_128 chr6A 606766833 A/G + G A AG + BS00080394_51 chr6A 606767635 A/G - C T CT + BS00022362_51 chr6A 606768061 A/G - C T CT + tplb0026o20_691 chr6A 606964649 A/G - C T CT + BS00093844_51 chr6A 606972908 A/C + A C AC + Excalibur_c79991_552 chr6A 606979768 T/C + C T AG - Tdurum_contig11275_461 chr6A 606985262 T/C NA NA NA AG NA flanks do not match reference at this position BS00003485_51 chr6A 606986775 T/C - G A AG + GENE-3948_357 chr6A 607053757 A/C + C A AC + BS00078214_51 chr6A 607452525 A/G - T C AG - RAC875_c77791_840 chr6A 607805901 T/C + T C AG - RAC875_c3312_1715 chr6A 607953273 A/G - C T AG - GENE-3933_586 chr6A 607954753 T/G + T G AC - BS00071855_51 chr6A 607955469 A/C + A C AC + Kukri_rep_c70994_104 chr6A 607956669 T/C - G A AG + Kukri_c45702_439 chr6A 607956733 A/G + A G AG + RAC875_c27781_591 chr6A 607958631 T/C + T C CT + BobWhite_c40602_313 chr6A 608077887 A/G - C T AG - RAC875_c13595_438 chr6A 608078628 A/G - T C CT + IAAV7160 chr6A 608090557 T/G - A C AC + tplb0037a05_913 chr6A 608093026 T/C - G A AG + Excalibur_c4261_342 chr6A 608115842 A/G + A G CT - Excalibur_rep_c103232_355 chr6A 608117593 A/G - T C AG - Kukri_c41482_311 chr6A 608500952 A/G - T C CT + Kukri_c29930_72 chr6A 608711649 T/C + T C AG - Excalibur_rep_c68035_128 chr6A 608901084 A/G - T C AG - BS00094893_51 chr6A 608969499 A/G + A G CT - IAAV5969 chr6A 609003517 A/G - C T AG - Kukri_c1468_1748 chr6A 609004632 T/C + T C AG - RFL_Contig5262_1500 chr6A 609035806 A/G - C T CT + Excalibur_rep_c90454_251 chr6A 609035945 A/G + G A CT - BS00009600_51 chr6A 609257626 T/C + C T CT + BS00046261_51 chr6A 609288327 A/G + G A AG + JD_c6831_221 chr6A 609379828 A/G + G A AG + Tdurum_contig29607_413 chr6A 609380011 T/C + C T AG - Excalibur_rep_c98042_438 chr6A 609451980 T/C + T C CT + Ex_c69054_723 chr6A 609452924 T/C + T C CT + Excalibur_rep_c69054_795 chr6A 609452996 T/C + T C CT + IACX5481 chr6A 609453528 T/C + C T CT + BS00063415_51 chr6A 609898500 T/C - A G AG + Kukri_c40994_61 chr6A 609972045 A/G NA NA NA CT NA flanks do not match reference at this position RFL_Contig4069_2628 chr6A 610198984 A/C - T G AC - RAC875_c76675_100 chr6A 610200064 T/C - G A CT - BobWhite_c10832_1131 chr6A 610200112 A/C + C A AC + BS00040814_51 chr6A 610348988 A/G - T C AG - BS00057487_51 chr6A 610406637 T/G - C A GT - Ex_c449_423 chr6A 610652650 T/C + T C AG - BobWhite_c10343_320 chr6A 610899344 A/G + A G AG + GENE-1205_484 chr6A 611313093 T/C + T C CT + Tdurum_contig83087_104 chr6A 611320373 A/G + G A AG + Jagger_c1423_102 chr6A 611326259 A/G - T C CT + Kukri_c47553_74 chr6A 611483364 T/C - G A AG + BS00011578_51 chr6A 611485398 A/G + G A CT - RAC875_c11876_120 chr6A 611487672 T/C - A G AG + Kukri_c21058_880 chr6A 611660898 A/C + A C AC + BS00042709_51 chr6A 611713191 T/C - G A AG + CAP8_c1237_68 chr6A 611808239 A/G - T C CT + Excalibur_rep_c76495_144 chr6A 611858999 A/C - T G GT + Kukri_c3164_802 chr6A 612108755 A/G - T C CT + BS00075346_51 chr6A 612112109 A/G - C T CT + Excalibur_c11769_2154 chr6A 612122933 T/C - A G CT - Excalibur_rep_c107705_351 chr6A 612124792 T/C + C T CT + Kukri_c37301_385 chr6A 612178824 A/G + A G AG + Kukri_c9805_696 chr6A 612291651 T/C + T C CT + IACX5958 chr6A 613245813 T/C - A G CT - BS00099407_51 chr6A 613257256 A/G + A G CT - BS00109913_51 chr6A 613482322 T/C + T C CT + Ex_c28973_947 chr6A 613486981 A/G + A G AG + RAC875_c4568_60 chr6A 613619246 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c41438_223 chr6A 613763762 T/C + T C CT + GENE-4008_83 chr6A 613990643 T/G - C A AC + BS00041200_51 chr6A 614007620 A/G - C T AG - BobWhite_c45410_242 chr6A 614009496 A/G - C T AG - RAC875_c6429_973 chr6A 614164658 A/G - T C AG - RAC875_c6429_132 chr6A 614165694 A/C - G T AC - RAC875_c6429_88 chr6A 614165738 T/C - A G CT - RAC875_c6429_55 chr6A 614165771 T/C - G A CT - BS00003723_51 chr6A 614445151 T/G + G T GT + Kukri_c74519_147 chr6A 614523183 A/G + A G AG + Excalibur_c18265_399 chr6A 614647638 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig10729_986 chr6A 615035834 A/G + G A AG + Tdurum_contig10729_989 chr6A 615035837 T/C + C T AG - RAC875_c12821_550 chr6A 615439057 T/C - G A CT - RAC875_c12821_466 chr6A 615439141 T/C - G A AG + IAAV1529 chr6A 615457218 A/C - T G AC - Kukri_rep_c71567_1037 chr6A 615457218 A/C - T G AC - Jagger_c9571_73 chr6A 615458459 A/C + C A AC + Kukri_c66671_183 chr6A 615466344 T/C - G A CT - RAC875_c17011_373 chr6A 615466367 T/C - G A AG + Kukri_c494_1479 chr6A 615468963 T/C - G A CT - Kukri_c494_1413 chr6A 615469029 A/G - T C CT + RAC875_c39433_564 chr6A 615588207 A/G + A G CT - BS00082460_51 chr6A 615589117 A/G - C T AG - BS00011404_51 chr6A 615780305 T/C - G A CT - Kukri_c15506_380 chr6A 615807386 T/C - A G AG + Kukri_c41157_315 chr6A 615809827 A/G - T C AG - Tdurum_contig42643_194 chr6A 615812907 T/C - A G AG + Tdurum_contig70819_393 chr6A 615821862 T/G - C A GT - Kukri_c14511_511 chr6A 615822319 T/C + C T AG - RAC875_c2254_1091 chr6A 615822700 A/G - T C CT + Kukri_c3570_1817 chr6A 615823670 T/C + C T AG - RFL_Contig2800_905 chr6A 616339013 A/G - T C AG - BobWhite_c8930_148 chr6A 616410023 T/C + T C AG - Excalibur_c6108_394 chr6A 616739647 A/G + A G AG + Kukri_c19426_1858 chr6A 616755354 T/C - A G CT - Kukri_c9940_695 chr6A 616818933 T/C NA NA NA AG NA flanks do not match reference at this position BS00011899_51 chr6A 616819394 T/C - A G CT - Tdurum_contig42489_1422 chr6A 616821751 A/G - T C CT + Excalibur_c31994_684 chr6A 616917665 T/G - C A AC + Excalibur_c98257_136 chr6A 616924042 T/C - A G AG + Tdurum_contig25624_227 chr6A 617043019 T/C + T C AG - Tdurum_contig68258_1773 chr6A 617055862 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c21405_1705 chr6B 166389 A/G + G A CT - Excalibur_c28854_1580 chr6B 167061 A/C + A C AC + BobWhite_c20959_229 chr6B 169531 A/G - C T CT + Ku_c5002_1518 chr6B 699721 T/C + T C AG - Ku_c5002_1541 chr6B 699744 A/C + A C AC + CAP7_rep_c7543_346 chr6B 3384268 T/G + G T AC - Excalibur_c15744_322 chr6B 3871404 A/G - C T AG - BobWhite_c18566_106 chr6B 3883636 A/C + A C GT - Tdurum_contig61178_618 chr6B 3883853 A/G - C T AG - BS00072387_51 chr6B 3884417 A/G - C T CT + RAC875_c82406_177 chr6B 3887315 A/C - T G GT + Tdurum_contig43538_648 chr6B 3887315 T/G + T G AC - Tdurum_contig43538_1111 chr6B 3888746 A/G + A G CT - Tdurum_contig43538_1306 chr6B 3888941 A/G + A G CT - Excalibur_c96134_182 chr6B 3889151 T/C + C T CT + Tdurum_contig43538_1582 chr6B 3889217 T/C + T C CT + Tdurum_contig43538_1687 chr6B 3889322 A/G + G A AG + Tdurum_contig43538_1812 chr6B 3889447 T/G + T G GT + BS00029434_51 chr6B 4518584 T/C + C T AG - IACX5923 chr6B 4875520 A/G + G A AG + BS00055174_51 chr6B 6009015 A/C + C A GT - Tdurum_contig41996_1823 chr6B 6801964 T/C - G A AG + RAC875_c31381_313 chr6B 6851179 T/C + T C AG - Excalibur_c12316_465 chr6B 6851782 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_rep_c74471_125 chr6B 7155633 A/C NA NA NA AC NA flanks do not match reference at this position BS00062956_51 chr6B 8387629 A/G + G A CT - IACX9205 chr6B 8388265 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles IACX9397 chr6B 8388403 A/G + G A AG + BS00028088_51 chr6B 8778718 T/G - A C GT - RAC875_c58425_331 chr6B 8781213 A/G - C T AG - RAC875_rep_c77197_202 chr6B 8781523 A/G + G A CT - RAC875_c1305_120 chr6B 8781840 A/G + G A AG + BobWhite_rep_c52979_181 chr6B 9002316 T/C + C T CT + BS00003622_51 chr6B 9003859 T/C + C T AG - Excalibur_c1988_276 chr6B 9036142 T/C - G A CT - Excalibur_c1988_181 chr6B 9036237 T/C - A G CT - Ex_c66287_325 chr6B 9036267 T/C + C T AG - RAC875_c44002_166 chr6B 9036267 T/C + C T AG - BS00063429_51 chr6B 10744813 A/G - C T CT + BS00092845_51 chr6B 11298665 T/G - C A AC + Excalibur_c30648_924 chr6B 11539107 T/C - G A CT - RAC875_rep_c105224_352 chr6B 11585106 A/G - C T CT + Tdurum_contig42655_703 chr6B 12672555 T/C - G A AG + CAP11_c7959_386 chr6B 15129406 A/G - C T CT + RAC875_c18689_1950 chr6B 15781125 T/C - G A CT - RAC875_c18689_1870 chr6B 15781205 A/G - C T CT + Tdurum_contig64467_233 chr6B 15781807 A/C + A C GT - RAC875_rep_c73081_330 chr6B 17226498 T/G + G T AC - Tdurum_contig52364_941 chr6B 17418556 T/C + C T AG - Excalibur_c50559_622 chr6B 17534370 A/G + G A AG + RAC875_c62256_904 chr6B 17703245 T/C - A G AG + Excalibur_c55093_143 chr6B 17703733 A/G + A G CT - Excalibur_c19747_53 chr6B 19057776 A/C + A C AC + RAC875_c38592_352 chr6B 20685956 T/C - G A CT - RAC875_rep_c105906_124 chr6B 20686826 A/G - T C AG - RAC875_rep_c70449_63 chr6B 21420567 A/G - C T AG - BS00010403_51 chr6B 21420887 A/G - T C AG - BS00030457_51 chr6B 21422927 A/G + A G CT - Tdurum_contig29162_378 chr6B 21785760 T/C + T C CT + Excalibur_c39830_862 chr6B 25261570 T/C + C T AG - RFL_Contig4853_1435 chr6B 25554767 A/G - C T CT + RAC875_c68849_153 chr6B 26633917 T/C - G A CT - BS00033641_51 chr6B 26650949 T/C + C T CT + BS00027942_51 chr6B 28116742 A/G - C T AG - Tdurum_contig50121_249 chr6B 28153588 T/C - A G AG + Excalibur_c100270_78 chr6B 31015044 A/G - T C CT + Ra_c5084_295 chr6B 35823405 A/G - T C CT + Tdurum_contig55083_623 chr6B 38879762 A/G + G A CT - Kukri_rep_c104879_103 chr6B 40282772 A/G - T C CT + Tdurum_contig62941_85 chr6B 40283285 T/C - A G AG + IACX9024 chr6B 40455359 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles IAAV8704 chr6B 40455471 T/C + C T CT + RAC875_c16962_288 chr6B 40455847 T/C - G A CT - RFL_Contig5693_807 chr6B 40456105 T/C - G A CT - Tdurum_contig9612_971 chr6B 40456105 A/G + G A AG + BS00110803_51 chr6B 41703651 A/G - C T AG - RAC875_rep_c107929_341 chr6B 41704411 T/C - G A AG + Excalibur_rep_c76289_85 chr6B 41706023 T/C - G A CT - RAC875_c26450_575 chr6B 41706367 T/C + T C AG - BS00090069_51 chr6B 41976041 A/C + C A AC + Ra_c27159_181 chr6B 41994339 A/G - T C CT + Kukri_c61725_545 chr6B 42510512 A/G - T C AG - Kukri_c61725_298 chr6B 42510759 T/C - A G AG + Kukri_c61725_199 chr6B 42510944 T/C - G A AG + Kukri_c24439_323 chr6B 46754457 T/C - A G CT - RAC875_c42372_853 chr6B 46766443 A/G - T C AG - RAC875_c42372_738 chr6B 46766558 T/G - A C GT - BobWhite_c41574_185 chr6B 46883810 A/C + A C GT - Ex_c61830_971 chr6B 47864386 A/G - C T AG - Kukri_c8343_228 chr6B 48348693 T/C + T C AG - tplb0024k14_1812 chr6B 48351934 T/C - A G AG + tplb0024k14_829 chr6B 48352916 A/C - G T GT + tplb0024k14_744 chr6B 48353001 T/G - A C GT - CAP7_rep_c6771_332 chr6B 49984647 A/G + A G AG + Excalibur_c57724_371 chr6B 49984871 T/C - A G CT - RAC875_c31280_122 chr6B 50124101 A/G - C T CT + Ku_c6663_1331 chr6B 50990146 A/G + G A CT - BobWhite_c23828_884 chr6B 50990975 A/G + A G AG + RAC875_c1215_1525 chr6B 51215838 T/C - A G CT - Kukri_rep_c107317_286 chr6B 52354159 A/G - T C AG - Kukri_c9424_195 chr6B 52354381 A/C + A C GT - Excalibur_c5999_312 chr6B 52354794 T/C - G A CT - BS00074183_51 chr6B 54419424 T/C + C T AG - Excalibur_c99745_169 chr6B 55349424 T/C - A G CT - BS00099998_51 chr6B 55997215 T/C - G A CT - Excalibur_c35713_106 chr6B 55997716 T/C - G A AG + Excalibur_c31375_558 chr6B 59010495 A/G - T C CT + IAAV7349 chr6B 64929800 A/G - C T AG - Tdurum_contig29033_75 chr6B 67938043 A/C + C A AC + Jagger_c286_219 chr6B 71150965 T/C + C T CT + Kukri_c31032_897 chr6B 75029242 A/G - C T AG - RAC875_c10650_90 chr6B 75032110 A/G - T C CT + Excalibur_c6876_523 chr6B 76003262 A/G + G A CT - RFL_Contig2024_600 chr6B 77011676 A/C + A C AC + RAC875_rep_c116755_285 chr6B 77457215 A/C + A C AC + BS00067590_51 chr6B 77749711 T/C + C T CT + BS00065680_51 chr6B 79928169 A/C - T G AC - RAC875_c6837_468 chr6B 79982810 A/C + A C AC + BS00010643_51 chr6B 84129364 T/C + C T AG - Excalibur_s111479_146 chr6B 84614233 T/C + T C CT + BS00063990_51 chr6B 85790501 A/C + C A GT - RAC875_c29042_1124 chr6B 88712997 T/C - A G CT - BobWhite_rep_c66748_215 chr6B 90278659 T/C + T C CT + BobWhite_rep_c66748_275 chr6B 90278804 T/C + T C AG - Tdurum_contig5486_1406 chr6B 90279029 A/G - C T CT + Tdurum_contig62803_286 chr6B 93562245 A/G + A G CT - BS00022823_51 chr6B 94000089 T/G + T G AC - RAC875_c23812_187 chr6B 96648749 T/G + G T GT + BS00036521_51 chr6B 100291191 T/C + T C AG - BobWhite_rep_c64102_331 chr6B 109143455 T/C + C T AG - Ex_c31970_673 chr6B 112885924 A/G + G A CT - Tdurum_contig43872_549 chr6B 112905745 T/C - A G CT - BS00066226_51 chr6B 113453322 T/G + T G GT + Kukri_c33668_877 chr6B 119529978 T/C + T C CT + BS00087190_51 chr6B 121486924 T/G + T G AC - BS00022607_51 chr6B 121489184 A/G NA NA NA CT NA flanks do not match reference at this position BS00082086_51 chr6B 121489788 T/G - C A AC + Kukri_c48571_361 chr6B 121782243 T/C - A G AG + BS00109541_51 chr6B 121783235 T/C - A G AG + IAAV8967 chr6B 121783506 A/C NA NA NA AC NA flanks do not match reference at this position Kukri_c39151_460 chr6B 121790155 A/C + C A AC + RAC875_c33034_408 chr6B 122294647 T/C - A G AG + RAC875_c55347_506 chr6B 122967840 T/C - G A AG + Kukri_c75566_265 chr6B 123747825 A/G - T C CT + BobWhite_c10614_157 chr6B 123910765 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig81911_179 chr6B 124632777 A/G + G A CT - RAC875_c2730_1330 chr6B 126135833 A/G - C T CT + RAC875_c2730_620 chr6B 126136933 T/C - G A AG + GENE-3798_1224 chr6B 126137359 A/C - T G AC - GENE-3798_1161 chr6B 126137418 A/G - T C CT + GENE-3798_1143 chr6B 126137432 T/C - G A CT - IAAV1673 chr6B 126138627 A/G - T C AG - RAC875_c20186_569 chr6B 126145213 A/G + A G CT - BS00045453_51 chr6B 126145369 T/C + C T CT + RAC875_c8954_425 chr6B 126220509 A/G + G A AG + RAC875_c8954_479 chr6B 126220673 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c64292_78 chr6B 126631619 A/G + A G CT - RAC875_c64292_194 chr6B 126631821 T/C + C T AG - RAC875_c33609_246 chr6B 127319263 T/G + T G GT + RAC875_c33609_381 chr6B 127319398 T/C + C T CT + Tdurum_contig62383_259 chr6B 127320325 T/C - A G CT - BobWhite_c11042_284 chr6B 127322391 T/G + G T GT + RAC875_rep_c111557_801 chr6B 127325540 A/C NA NA NA GT NA flanks do not match reference at this position Excalibur_c22223_188 chr6B 127325775 A/G - T C AG - Excalibur_rep_c104880_102 chr6B 127609030 T/C + T C AG - Tdurum_contig61970_499 chr6B 127751697 A/C - T G GT + RAC875_rep_c71306_97 chr6B 127752851 T/C - A G CT - BobWhite_c5418_82 chr6B 127753014 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c3044_188 chr6B 128732780 A/G + G A CT - Kukri_c3044_221 chr6B 128732813 T/C + C T CT + RAC875_rep_c104354_333 chr6B 128733226 T/C NA NA NA AG NA flanks do not match reference at this position Tdurum_contig45714_546 chr6B 128733226 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig8740_109 chr6B 128735552 T/C + C T CT + BS00028217_51 chr6B 128738347 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig75750_432 chr6B 128925521 T/G - C A GT - BobWhite_c30622_180 chr6B 129303374 T/C - A G CT - Tdurum_contig48689_514 chr6B 130078489 A/G - T C AG - Excalibur_c56606_75 chr6B 130829632 A/G + G A AG + BS00023168_51 chr6B 130829883 T/C - G A AG + Kukri_c8288_2063 chr6B 130943333 T/C + C T CT + Kukri_c8288_2819 chr6B 130946663 T/C + T C CT + BS00022897_51 chr6B 130946842 T/C + T C CT + BobWhite_c16635_331 chr6B 130968371 T/C - A G AG + BS00003897_51 chr6B 132118573 T/C - A G CT - Excalibur_c45952_256 chr6B 132345733 T/C - G A AG + Kukri_rep_c71420_511 chr6B 132440114 A/G - T C CT + Ra_c11763_604 chr6B 132443457 A/G + G A CT - BS00033008_51 chr6B 133996658 T/C + C T CT + Kukri_c17997_389 chr6B 134823490 T/G - A C AC + Tdurum_contig21737_203 chr6B 136111626 T/C + C T AG - Tdurum_contig41980_2722 chr6B 138704124 T/C - A G CT - Tdurum_contig41980_2293 chr6B 138704553 T/C - A G CT - Tdurum_contig41980_1727 chr6B 138705119 A/G - C T CT + Tdurum_contig41980_619 chr6B 138706227 A/G - C T CT + Tdurum_contig67567_93 chr6B 140362014 A/G + G A CT - GENE-3813_174 chr6B 140853374 A/G - C T AG - BS00069412_51 chr6B 143198823 A/G - C T CT + BS00003214_51 chr6B 143204314 T/C - G A CT - BobWhite_c1905_98 chr6B 144001431 A/G - C T AG - RFL_Contig5844_291 chr6B 144888091 T/G + G T AC - RAC875_c54818_481 chr6B 146144732 T/C + C T AG - RAC875_c54818_572 chr6B 146144823 T/C + T C CT + Excalibur_c36771_136 chr6B 146646555 A/G + A G CT - BS00062807_51 chr6B 147057891 A/G + A G CT - Excalibur_rep_c110812_495 chr6B 147579066 A/G - T C AG - Ra_c14171_2765 chr6B 147579698 T/C - A G CT - Kukri_c43406_2491 chr6B 147579850 T/C - A G CT - RAC875_c14171_2342 chr6B 147580121 T/G - C A AC + RAC875_c14171_664 chr6B 147582276 T/C - A G CT - BS00079100_51 chr6B 147962786 T/C - A G AG + Kukri_rep_c100676_151 chr6B 149038091 A/C - T G AC - RAC875_c79742_159 chr6B 149059029 T/C + T C AG - RAC875_c4254_334 chr6B 149416646 T/C NA NA NA CT NA flanks do not match reference at this position BS00066437_51 chr6B 149458463 T/C + T C CT + Kukri_c29591_1356 chr6B 149469981 A/G - T C AG - Tdurum_contig15238_240 chr6B 149470877 A/C + A C GT - Excalibur_c51910_530 chr6B 149547103 A/G NA NA NA AG NA flanks do not match reference at this position Ku_c18274_1139 chr6B 149547461 T/G - C A GT - RAC875_rep_c106022_126 chr6B 149547472 T/C + T C AG - Tdurum_contig11126_182 chr6B 149616948 T/C + T C CT + BS00046963_51 chr6B 150665070 A/G - T C CT + GENE-3716_393 chr6B 150773335 T/C - G A AG + Kukri_c38732_546 chr6B 151131066 A/G - T C CT + Kukri_c38732_246 chr6B 151131366 A/G - C T CT + Kukri_c38732_225 chr6B 151131387 T/C - G A CT - Tdurum_contig51676_120 chr6B 151133561 A/G + A G CT - RAC875_c4710_1109 chr6B 151134176 A/G - C T AG - BS00073879_51 chr6B 151375642 T/C - G A CT - Excalibur_rep_c106789_271 chr6B 153957925 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_c1693_225 chr6B 154508978 T/C NA NA NA CT NA flanks do not match reference at this position BS00014588_51 chr6B 155547614 T/C - G A CT - IAAV1319 chr6B 155547614 A/G + G A CT - Excalibur_c3259_379 chr6B 155549787 T/G - A C GT - BobWhite_c26504_163 chr6B 156219099 A/C - G T GT + RAC875_c14852_693 chr6B 156265774 T/C + C T CT + Ra_c14852_1487 chr6B 156266570 T/C + T C AG - BS00107795_51 chr6B 156267586 T/C + T C AG - RAC875_c14852_2171 chr6B 156267604 T/C + C T CT + Kukri_c3018_865 chr6B 156271187 T/C + T C CT + BobWhite_rep_c65994_267 chr6B 156525752 T/C + T C CT + Tdurum_contig6121_545 chr6B 157475097 A/G + A G AG + Tdurum_contig6121_907 chr6B 157475437 A/G + G A AG + Tdurum_contig6121_947 chr6B 157475477 A/G + G A CT - Excalibur_c63243_434 chr6B 157873511 A/G - T C CT + Kukri_rep_c68102_99 chr6B 158859675 A/G - C T CT + GENE-3659_104 chr6B 159699832 T/C + C T CT + BS00057297_51 chr6B 163229397 A/C + C A AC + BS00111399_51 chr6B 163951054 A/G + A G AG + BS00058774_51 chr6B 163951583 T/G - A C GT - BobWhite_c47659_100 chr6B 164373151 T/G + G T GT + BS00011624_51 chr6B 164394576 T/C - G A CT - BS00076397_51 chr6B 164871466 A/G + A G CT - RAC875_c17189_155 chr6B 165332553 T/C - G A CT - BS00073259_51 chr6B 165561783 T/C + T C CT + BS00051998_51 chr6B 166112341 T/C + T C CT + IACX9279 chr6B 166595251 T/C - A G CT - BobWhite_c686_387 chr6B 168465018 T/C + C T CT + BobWhite_c22767_189 chr6B 169316948 T/C + T C CT + RAC875_c81264_124 chr6B 170990404 T/G - A C GT - BobWhite_c10140_297 chr6B 171971500 T/C - G A AG + Tdurum_contig70639_196 chr6B 171971500 A/G + G A AG + BS00022117_51 chr6B 174556712 T/C + T C CT + BS00021686_51 chr6B 174566651 A/G + G A CT - RAC875_c12879_176 chr6B 174567139 T/C + C T AG - Kukri_c25377_106 chr6B 174567929 T/C NA NA NA CT NA flanks do not match reference at this position Ku_c2606_779 chr6B 175712115 A/G - C T CT + BS00078597_51 chr6B 175719158 T/C - G A AG + Kukri_c1982_1406 chr6B 176242498 T/C + C T CT + BS00022226_51 chr6B 176403382 A/G - T C CT + Ku_c22026_1410 chr6B 178013875 T/C + T C CT + BobWhite_c15653_484 chr6B 179360033 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_c23224_1425 chr6B 181101696 T/C - A G AG + Excalibur_c63178_243 chr6B 182583134 T/C - A G CT - BS00067644_51 chr6B 185004617 T/C - A G AG + TA002706-2669 chr6B 185674431 T/C - A G AG + Excalibur_c44109_144 chr6B 186595506 A/G + G A CT - Kukri_c49233_594 chr6B 188189508 A/G - T C AG - IACX8906 chr6B 188189576 T/C + T C AG - Excalibur_c16961_85 chr6B 188189690 T/C - G A CT - BobWhite_c47055_231 chr6B 190072975 T/G - C A GT - BS00021705_51 chr6B 191527596 A/C + C A GT - BS00074947_51 chr6B 191538419 T/C - G A CT - Jagger_c555_287 chr6B 191991853 T/C + T C CT + BS00044237_51 chr6B 192349705 T/C - G A CT - Kukri_c36620_1336 chr6B 193892500 T/C - G A CT - Kukri_c28823_142 chr6B 195177697 A/G - T C CT + Kukri_c10641_584 chr6B 195464155 A/C - T G GT + Excalibur_c14257_489 chr6B 198917587 T/C + C T CT + RAC875_c43581_280 chr6B 199014751 A/G + A G AG + RAC875_c77_1176 chr6B 199080103 A/G + G A CT - BS00025302_51 chr6B 199718577 A/G + A G AG + BS00022370_51 chr6B 201200973 A/G - T C AG - Excalibur_c18182_464 chr6B 201222727 T/C + T C CT + Excalibur_c18182_760 chr6B 201223023 A/C + A C AC + BS00058305_51 chr6B 201790467 T/C + T C CT + Ra_c17795_425 chr6B 201792049 A/G + G A AG + RAC875_rep_c110970_173 chr6B 204922809 T/C - G A AG + Excalibur_rep_c111646_110 chr6B 205261090 A/G - C T CT + BobWhite_c17750_568 chr6B 206843435 A/G - C T CT + Kukri_c66290_127 chr6B 207110152 T/C + T C AG - Excalibur_c3810_186 chr6B 207163218 A/G - T C AG - RAC875_c10122_113 chr6B 207928962 A/G - T C CT + IACX9104 chr6B 207929264 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Ra_c3381_1027 chr6B 211215120 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_rep_c54531_95 chr6B 214027825 T/G - A C GT - Excalibur_rep_c103447_433 chr6B 214028702 A/C + C A GT - Ra_c77985_260 chr6B 214089373 A/G + G A AG + RAC875_c7781_531 chr6B 216508178 A/G + G A CT - RAC875_c70_598 chr6B 219096216 T/C - G A CT - BS00041505_51 chr6B 219214809 A/G + G A AG + Kukri_rep_c94998_153 chr6B 219575491 A/G + A G AG + BS00063174_51 chr6B 223259510 T/G + G T AC - BS00060838_51 chr6B 224257152 T/G - A C GT - IAAV4883 chr6B 225868318 T/G - C A AC + CAP8_c4223_13 chr6B 226186880 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c16448_488 chr6B 226362905 A/G - C T AG - BS00045761_51 chr6B 227070547 A/G + A G AG + BS00040868_51 chr6B 228977167 T/G - C A AC + RAC875_c24962_1326 chr6B 229280173 T/C - A G CT - BobWhite_c9563_377 chr6B 231348477 A/G + G A AG + RFL_Contig311_951 chr6B 231354317 A/G - T C CT + Kukri_c20529_1006 chr6B 231476013 T/C - G A CT - Excalibur_c5136_2314 chr6B 231677537 A/C - T G AC - Excalibur_c79066_165 chr6B 232168465 A/G + A G AG + CAP8_c1851_62 chr6B 233694795 A/G - T C AG - RAC875_c5041_328 chr6B 236571171 A/G + G A AG + BobWhite_c16301_60 chr6B 236571842 A/G + A G CT - BS00022772_51 chr6B 240543614 T/C + C T AG - Tdurum_contig15235_951 chr6B 245977486 T/C + T C AG - Kukri_c41694_285 chr6B 247009251 A/C - G T GT + BobWhite_c34920_228 chr6B 249498169 T/G - A C GT - Kukri_c26988_93 chr6B 252388190 A/C - T G GT + Excalibur_c37474_868 chr6B 254357284 T/C - A G CT - BobWhite_c32911_243 chr6B 255268901 A/G + A G CT - Ku_c13514_146 chr6B 256176942 T/C + C T AG - Excalibur_c83451_218 chr6B 257241457 A/G - C T AG - Excalibur_c20503_382 chr6B 257568556 T/C - A G CT - Excalibur_c53834_416 chr6B 257993802 T/C - G A AG + Kukri_c3983_670 chr6B 258012490 T/C + T C AG - Kukri_c52515_442 chr6B 259877872 T/C - G A CT - BS00003955_51 chr6B 260548319 A/G - C T CT + Ex_c49055_617 chr6B 260548488 A/G - C T CT + BobWhite_c17876_192 chr6B 261532048 T/C - A G CT - BS00067871_51 chr6B 261585651 A/G - C T AG - BS00067873_51 chr6B 261585682 T/C - G A CT - Tdurum_contig31043_89 chr6B 262466649 A/G + G A CT - Kukri_c24590_532 chr6B 274209684 T/C - A G AG + Ku_c8353_937 chr6B 279048386 A/G + A G AG + IAAV4514 chr6B 279082433 A/G + G A AG + RAC875_c7110_2706 chr6B 282987590 T/C + T C AG - Ra_c26497_381 chr6B 288418637 T/C - A G CT - Excalibur_rep_c68310_560 chr6B 288649385 A/G + G A CT - Kukri_c26279_503 chr6B 288785983 T/C + T C AG - BS00062970_51 chr6B 289686156 A/G + G A CT - BS00063631_51 chr6B 289686156 T/C - G A CT - BS00026203_51 chr6B 297302255 T/C - G A CT - RAC875_c41604_1001 chr6B 309775111 T/C - A G CT - BS00078932_51 chr6B 320567911 A/G - C T CT + Tdurum_contig15361_1035 chr6B 325029243 A/G - T C CT + Tdurum_contig15361_1009 chr6B 325029269 T/C - A G CT - Jagger_c556_473 chr6B 332413118 T/C - G A AG + Excalibur_c7823_397 chr6B 333506490 A/G + G A AG + Excalibur_c26143_832 chr6B 335170823 T/G - C A GT - Ku_c1044_1007 chr6B 340304228 T/G + G T GT + Ku_c1044_2005 chr6B 340305227 A/G + G A CT - Kukri_c39767_204 chr6B 345228948 T/C - A G CT - RAC875_rep_c86601_164 chr6B 348095132 A/G + G A AG + RAC875_rep_c70007_1483 chr6B 348856399 A/G + G A AG + CAP8_c1801_231 chr6B 353872242 A/G - T C AG - BobWhite_c23946_75 chr6B 356817688 T/C - G A AG + Ku_c32537_247 chr6B 357049465 T/C - G A AG + Ku_c32537_241 chr6B 357049471 T/C - G A CT - Kukri_c14472_859 chr6B 360412852 T/C - A G AG + Kukri_c66050_273 chr6B 361582035 A/G - T C CT + BobWhite_c2053_182 chr6B 366733563 T/C + T C AG - BS00065476_51 chr6B 387093130 A/G - C T AG - RAC875_c32137_751 chr6B 393755081 T/C + T C CT + BS00082760_51 chr6B 394650564 A/G + A G AG + BS00068182_51 chr6B 403727676 A/G - T C CT + IAAV2161 chr6B 408241179 T/G - C A AC + Ku_c12681_198 chr6B 408241179 A/C + C A AC + IAAV8065 chr6B 411097879 A/G - T C CT + Excalibur_c15870_1331 chr6B 413953629 T/C + T C CT + Excalibur_rep_c84475_162 chr6B 415867918 T/C - G A AG + Ku_c35629_568 chr6B 415900218 T/G - A C GT - RAC875_c90029_92 chr6B 418319972 T/C + C T AG - Kukri_c55096_140 chr6B 419771816 A/C - G T GT + IAAV3811 chr6B 419774652 T/G - A C GT - Excalibur_c38128_422 chr6B 422702991 T/C + T C AG - IACX5778 chr6B 422702991 A/G - T C CT + Ku_c1189_1439 chr6B 423087629 T/C + C T CT + CAP7_c2536_65 chr6B 433681681 T/G - C A AC + IACX778 chr6B 437483973 A/G - T C CT + BS00095516_51 chr6B 438628876 A/C - T G AC - RAC875_c63209_154 chr6B 439351481 T/C + C T AG - Excalibur_c58260_332 chr6B 440760923 T/C - G A CT - BobWhite_c36415_378 chr6B 446054795 A/G + A G CT - Excalibur_c6416_1712 chr6B 446837457 A/G + A G CT - BobWhite_c27318_380 chr6B 449446970 T/C - A G CT - CAP7_rep_c8937_117 chr6B 449770773 A/G + A G AG + BobWhite_rep_c63804_353 chr6B 451926960 A/C + A C AC + BS00049942_51 chr6B 455448950 A/G - C T CT + BS00049941_51 chr6B 455449027 T/C - A G AG + Kukri_c50603_164 chr6B 456769523 A/G + G A AG + GENE-4048_299 chr6B 457170366 A/G + G A AG + RAC875_rep_c71393_159 chr6B 457170969 A/G + A G AG + GENE-3990_27 chr6B 459056538 A/C - T G GT + TA005016-0827 chr6B 460087895 T/C NA NA NA AG NA flanks do not match reference at this position Tdurum_contig29294_171 chr6B 461265970 T/C + C T CT + BS00091262_51 chr6B 462132071 T/C + T C CT + BS00054287_51 chr6B 462149542 A/G + A G CT - BobWhite_c42745_221 chr6B 462165710 A/G + G A CT - BS00067836_51 chr6B 462169882 A/C - G T GT + BobWhite_c11301_226 chr6B 462175056 T/C + C T CT + Kukri_c54_306 chr6B 462636823 T/C - A G AG + Tdurum_contig4592_327 chr6B 462636823 A/G + A G AG + RFL_Contig3609_1678 chr6B 465676057 A/G - T C AG - IAAV1460 chr6B 465683331 T/C - A G CT - RAC875_c47035_70 chr6B 465683481 A/G - C T AG - TA006014-0838 chr6B 468735947 T/C NA NA NA CT NA flanks do not match reference at this position BS00094322_51 chr6B 468736046 A/G + A G CT - RAC875_c25154_17 chr6B 468736265 A/G - T C CT + RAC875_c51385_376 chr6B 469061806 T/C - G A CT - IACX13323 chr6B 469073433 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_rep_c81781_202 chr6B 469075402 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig77234_467 chr6B 469285493 T/G + G T AC - Kukri_c7539_1065 chr6B 469291566 A/C + A C GT - Excalibur_c15335_197 chr6B 470114228 T/C + T C AG - Excalibur_rep_c92855_977 chr6B 470118374 A/G + A G AG + RAC875_c26487_145 chr6B 470133011 A/G + A G CT - BS00090277_51 chr6B 470800944 T/C - A G CT - GENE-0363_168 chr6B 470830331 T/C - A G CT - BS00106588_51 chr6B 470913605 A/G - T C CT + Excalibur_c26172_359 chr6B 470914665 T/G NA NA NA AC NA flanks do not match reference at this position RAC875_c27431_212 chr6B 470920654 T/C - A G AG + BobWhite_c13977_91 chr6B 470997172 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c22998_621 chr6B 471158474 A/G - T C CT + Ex_c1145_552 chr6B 471167653 A/G + A G AG + Kukri_c377_2208 chr6B 471168147 T/C - G A CT - Kukri_c377_2164 chr6B 471168191 T/C - G A CT - RFL_Contig3644_757 chr6B 471181428 T/C + C T AG - BS00008727_51 chr6B 471233399 A/C NA NA NA GT NA flanks do not match reference at this position BS00097866_51 chr6B 471233878 A/G - C T AG - GENE-4181_430 chr6B 471234836 T/C - A G AG + RFL_Contig2391_831 chr6B 471307737 A/C - T G GT + BobWhite_c8673_302 chr6B 472610001 A/G - T C CT + BS00022192_51 chr6B 472610525 T/C - A G CT - RAC875_c13325_109 chr6B 474177903 A/G - T C AG - IACX6349 chr6B 474269866 A/G + A G AG + Ku_c106365_329 chr6B 475272891 T/C - G A AG + Tdurum_contig13698_141 chr6B 475725896 A/G + G A CT - Excalibur_c22075_166 chr6B 476123178 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c53506_1141 chr6B 477789205 A/G - C T CT + BobWhite_c6927_691 chr6B 481403386 T/C + T C CT + RFL_Contig6050_941 chr6B 481471050 A/C - T G AC - Excalibur_rep_c69660_398 chr6B 481862135 T/C + C T CT + Ex_c20946_574 chr6B 481863585 T/C - A G CT - tplb0023n15_310 chr6B 484533496 T/C - A G CT - TA003405-0474 chr6B 484986356 A/C - T G GT + Ex_c28261_372 chr6B 484986423 T/C + C T AG - IAAV109 chr6B 492023835 A/G - T C AG - BobWhite_c22638_135 chr6B 496988214 A/G - T C CT + IAAV8279 chr6B 513982106 T/G - A C AC + JD_c17027_460 chr6B 513982106 A/C + A C AC + BS00048191_51 chr6B 515184931 A/G - T C CT + RAC875_c67326_214 chr6B 518391255 A/G + G A AG + RAC875_c4420_1155 chr6B 519139597 A/G - T C AG - RAC875_c4420_371 chr6B 519151099 T/C - G A CT - Ku_c19477_1206 chr6B 519151405 T/C + C T CT + TA003776-0764 chr6B 519404291 T/C - A G AG + Kukri_c16568_287 chr6B 522487423 A/C + C A AC + Excalibur_c21568_1462 chr6B 523051021 A/C + A C GT - Excalibur_c7785_123 chr6B 526481172 T/C - G A CT - RAC875_c18821_137 chr6B 526848818 T/C - G A AG + Excalibur_rep_c67196_143 chr6B 528284143 T/C + C T CT + IAAV7892 chr6B 528284143 A/G - C T CT + Ra_c23874_338 chr6B 528622269 T/C + C T CT + IAAV4147 chr6B 528915436 A/G - T C CT + Excalibur_c11245_880 chr6B 530569370 A/G + G A AG + IAAV2149 chr6B 531008912 T/C - A G CT - Ex_c44510_2109 chr6B 531523500 T/G - A C GT - IAAV7878 chr6B 531524981 T/C - G A AG + RAC875_c34089_249 chr6B 531524981 A/G + G A AG + Kukri_c25725_1921 chr6B 531527658 T/C + T C CT + Excalibur_c20083_433 chr6B 537464236 A/C - G T GT + Excalibur_rep_c94584_98 chr6B 539539615 T/C + C T AG - RAC875_c6417_793 chr6B 540591176 T/C - A G CT - BS00003616_51 chr6B 540593799 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_rep_c72029_380 chr6B 541946250 A/G + A G AG + GENE-4200_87 chr6B 543226436 A/G - T C AG - Excalibur_c24932_199 chr6B 546659724 T/G - A C GT - Kukri_c67741_1361 chr6B 546993887 A/G + A G AG + Ra_c24622_352 chr6B 549030857 A/G + G A AG + Excalibur_c3336_1007 chr6B 551032027 T/C - A G CT - Tdurum_contig5968_1095 chr6B 551926284 T/G + G T AC - Kukri_rep_c102659_221 chr6B 552239489 A/G - C T CT + Tdurum_contig15762_139 chr6B 552406018 A/G + A G CT - Tdurum_contig62005_185 chr6B 554793908 T/C - G A CT - Tdurum_contig60536_304 chr6B 555956011 T/C + C T AG - RAC875_c4198_1065 chr6B 556487920 T/C + C T AG - Excalibur_s113695_111 chr6B 556491270 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig77500_369 chr6B 556757572 T/C - A G CT - IAAV1816 chr6B 557458204 T/C + T C CT + Ku_c2173_206 chr6B 557459063 A/G + G A AG + Kukri_c47551_513 chr6B 558513443 A/G - T C AG - RFL_Contig5080_766 chr6B 558824364 A/C + A C AC + Tdurum_contig30863_137 chr6B 558926640 T/C - G A CT - BobWhite_c47347_420 chr6B 558926756 A/G - C T AG - RFL_Contig4801_686 chr6B 559341747 T/C + T C AG - CAP8_c6370_254 chr6B 559356967 A/G - C T AG - Tdurum_contig62155_325 chr6B 559356967 T/C + C T AG - Tdurum_contig62155_472 chr6B 559357114 A/G + A G CT - RAC875_c432_237 chr6B 561276351 T/C - A G AG + Kukri_rep_c72677_1571 chr6B 561287374 T/C - A G AG + Excalibur_rep_c114175_83 chr6B 561289378 T/C + C T AG - Ra_c15317_1538 chr6B 561292654 A/G + A G AG + RAC875_rep_c70998_974 chr6B 561702860 A/G + A G AG + BobWhite_c13091_385 chr6B 562563663 A/G + G A AG + Ex_c100170_579 chr6B 562563898 T/C + C T CT + Ku_c22709_313 chr6B 562591972 T/G - C A GT - Excalibur_rep_c70364_129 chr6B 562595453 T/C - G A CT - Kukri_c4834_1883 chr6B 562598032 A/C + C A GT - Kukri_rep_c104075_178 chr6B 563132593 A/G - T C AG - CAP8_c7260_77 chr6B 563487567 T/C + C T AG - Excalibur_c28014_99 chr6B 563487827 T/C - G A CT - Kukri_rep_c104217_79 chr6B 564058701 T/G + T G GT + Excalibur_c22563_69 chr6B 564060005 T/G - C A GT - Ra_c68165_926 chr6B 567600482 A/G + A G AG + RAC875_rep_c108200_137 chr6B 569045283 T/C + C T AG - BobWhite_c36416_56 chr6B 573689465 A/G + A G CT - Kukri_rep_c108067_229 chr6B 574027602 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c22106_190 chr6B 574662771 T/G - C A GT - BobWhite_c22075_85 chr6B 575638302 T/C + T C CT + Tdurum_contig44173_572 chr6B 576040835 T/C + T C CT + tplb0061f12_679 chr6B 576041030 A/G + G A AG + Tdurum_contig44173_792 chr6B 576041147 A/G + A G AG + Tdurum_contig7981_70 chr6B 576206096 T/C + C T CT + Excalibur_c10568_826 chr6B 576222175 A/G + G A AG + RAC875_rep_c85751_268 chr6B 576813121 A/C - T G AC - RAC875_rep_c85751_123 chr6B 576813266 A/G - C T CT + RAC875_rep_c85751_72 chr6B 576813317 A/G - C T AG - tplb0036j13_718 chr6B 576826272 A/G - C T CT + RFL_Contig1015_620 chr6B 576850542 T/C - A G AG + RFL_Contig1015_580 chr6B 576850582 T/C - G A AG + Tdurum_contig81414_256 chr6B 576850582 A/G + G A AG + Tdurum_contig63468_1413 chr6B 577174946 T/C + C T CT + GENE-4249_885 chr6B 577185756 T/C - G A CT - Excalibur_c34134_280 chr6B 577357633 A/G - C T AG - BobWhite_c14948_295 chr6B 577359629 A/G - T C AG - BS00066605_51 chr6B 577363546 T/C - A G CT - Ex_c3990_102 chr6B 577478679 A/G + A G CT - Ku_c2212_411 chr6B 577479921 T/C + T C CT + Excalibur_c43557_540 chr6B 578100560 A/G + G A AG + Tdurum_contig51613_821 chr6B 581868833 A/G + G A CT - Tdurum_contig46925_285 chr6B 582340984 A/G - C T CT + RAC875_rep_c112296_198 chr6B 582823107 A/G + A G AG + Tdurum_contig55473_1193 chr6B 582823503 T/C - G A AG + Tdurum_contig55473_989 chr6B 582823808 A/G - C T CT + Tdurum_contig55473_437 chr6B 582824913 T/C - G A CT - Tdurum_contig55473_381 chr6B 582824969 A/G - C T CT + Kukri_c65766_78 chr6B 582825129 T/G + T G GT + Tdurum_contig55473_221 chr6B 582825129 A/C - T G GT + Tdurum_contig54437_476 chr6B 584582036 A/G - C T AG - Kukri_rep_c107419_372 chr6B 587386004 A/G + A G AG + IACX1527 chr6B 591508657 T/C - A G AG + Tdurum_contig47269_904 chr6B 593263246 T/C - G A CT - BobWhite_c27253_91 chr6B 593714280 T/C + C T AG - Ku_c68657_464 chr6B 594657504 A/G + A G CT - Kukri_rep_c105784_515 chr6B 594857725 T/C - A G CT - IACX1162 chr6B 595208438 A/G + A G AG + IAAV6593 chr6B 595212109 T/C - G A CT - JD_c12038_736 chr6B 595288810 T/C - A G CT - JD_c12038_696 chr6B 595288850 A/G - C T AG - Ex_c11348_1256 chr6B 595290002 A/C - T G GT + Kukri_c10369_588 chr6B 595291243 A/G - T C CT + Kukri_rep_c101899_542 chr6B 595952036 T/C + C T AG - Excalibur_c23716_442 chr6B 595954082 T/G - C A GT - IAAV4577 chr6B 595954141 T/G - C A AC + Ku_c23011_3613 chr6B 595954893 A/G + G A AG + Kukri_c23011_4381 chr6B 595955661 T/C + T C CT + Ku_c12345_328 chr6B 598010909 T/C + T C CT + Tdurum_contig26016_243 chr6B 598014593 T/C - G A CT - Ku_c68707_802 chr6B 599066661 T/C - A G AG + IAAV169 chr6B 599070277 A/G - C T AG - Excalibur_c53914_131 chr6B 599071176 A/G - C T CT + Tdurum_contig51741_345 chr6B 599693700 A/G + A G CT - RFL_Contig897_207 chr6B 599696332 T/C - G A CT - Tdurum_contig42414_1071 chr6B 599803440 A/G + A G CT - BobWhite_c45091_53 chr6B 601345823 T/G - C A AC + RAC875_c2370_250 chr6B 603356064 A/G + A G CT - RAC875_c38373_1042 chr6B 604217102 A/G - C T AG - Tdurum_contig50382_639 chr6B 604217130 T/C - A G CT - RAC875_c19357_122 chr6B 605795265 T/G + T G GT + Tdurum_contig81006_704 chr6B 605795508 T/C - G A AG + Ra_c26319_331 chr6B 605799759 T/G + T G GT + Tdurum_contig64065_185 chr6B 606285588 T/C - G A AG + RAC875_c96675_51 chr6B 606299027 A/G - C T AG - Ra_c18593_802 chr6B 606427659 A/C - T G AC - RAC875_rep_c75899_926 chr6B 606430786 T/G + T G GT + GENE-4183_1109 chr6B 606431458 T/C - A G CT - RAC875_c57261_265 chr6B 609380727 A/G + G A CT - Tdurum_contig44825_307 chr6B 612199296 A/G - C T AG - GENE-4114_61 chr6B 613610528 A/C + C A AC + RFL_Contig4251_851 chr6B 616325597 A/G + G A AG + Tdurum_contig66984_143 chr6B 618137739 T/C - A G AG + Kukri_c29122_984 chr6B 618332254 T/C NA NA NA AG NA flanks do not match reference at this position IAAV951 chr6B 618668841 T/C NA NA NA CT NA flanks do not match reference at this position Ku_c10647_585 chr6B 618668841 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_rep_c69710_86 chr6B 618944195 A/G - T C AG - Excalibur_c89155_115 chr6B 619483986 A/G + A G AG + Excalibur_rep_c104544_445 chr6B 623728900 A/C - T G GT + Excalibur_rep_c104544_249 chr6B 623729095 A/G - C T CT + BS00012025_51 chr6B 625379823 T/C + C T AG - Kukri_c44167_272 chr6B 630617289 A/G - C T AG - BobWhite_c22827_193 chr6B 631740499 T/G + G T GT + Excalibur_c6086_771 chr6B 631951388 T/C - A G CT - IAAV3183 chr6B 631960628 T/C - G A CT - GENE-3807_45 chr6B 634331938 A/G - C T CT + Kukri_rep_c104521_601 chr6B 634332420 T/C - G A CT - Kukri_rep_c104521_117 chr6B 634333465 T/C - A G AG + RAC875_c1349_270 chr6B 634334367 T/C - G A CT - Kukri_c25082_328 chr6B 635172419 T/C + C T AG - BobWhite_c28409_462 chr6B 635175381 A/G - T C AG - BobWhite_c3194_125 chr6B 637024384 A/G + A G CT - Kukri_c55163_274 chr6B 639156094 A/C - G T GT + GENE-4086_876 chr6B 641286705 A/G - C T AG - Excalibur_rep_c87878_287 chr6B 641289283 A/G + A G AG + Kukri_c59960_211 chr6B 641291932 T/C - G A CT - RAC875_c58472_109 chr6B 641396996 A/G + A G AG + Tdurum_contig46828_730 chr6B 643165785 T/C - A G AG + CAP7_c7065_166 chr6B 643899226 T/C - G A CT - Ra_c9698_1606 chr6B 644478936 T/C - A G AG + Kukri_c30390_1731 chr6B 644481621 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c6649_642 chr6B 645353503 A/G + A G AG + RAC875_c13216_111 chr6B 645353741 A/G + G A AG + Tdurum_contig76997_244 chr6B 645659540 A/G + G A CT - Tdurum_contig76997_462 chr6B 645659758 A/G + G A CT - BS00104265_51 chr6B 645659866 T/C - G A AG + Tdurum_contig76997_664 chr6B 645659960 A/G + G A CT - BS00023061_51 chr6B 646261585 T/C + T C CT + Kukri_c20412_212 chr6B 646637373 A/G - T C AG - BS00022599_51 chr6B 646707165 A/G - C T CT + RAC875_c14309_317 chr6B 651002685 A/G + G A AG + Kukri_rep_c68504_1403 chr6B 651007806 A/G - C T AG - Kukri_c3292_670 chr6B 651418737 A/G + A G CT - Kukri_c25034_2042 chr6B 651430601 T/C - G A CT - Excalibur_c23296_820 chr6B 652003196 T/C + C T CT + Kukri_c56955_282 chr6B 652639910 T/C - A G CT - Excalibur_c31379_71 chr6B 653212354 T/C - G A CT - BS00065152_51 chr6B 656997397 A/G - T C AG - BS00074024_51 chr6B 664197696 T/C + T C AG - TA004523-0997 chr6B 664218558 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_c49331_77 chr6B 664266096 A/G - C T AG - Ku_c3481_732 chr6B 664393898 A/G + A G CT - BS00062712_51 chr6B 664407511 T/C - A G AG + Tdurum_contig41142_267 chr6B 664460405 T/G + G T GT + Tdurum_contig45559_403 chr6B 664461709 T/C - A G AG + BS00037464_51 chr6B 665512218 A/G - C T AG - BS00037462_51 chr6B 665512303 T/C - A G CT - CAP7_rep_c12929_224 chr6B 665715689 T/C - A G CT - CAP7_rep_c12929_169 chr6B 665715744 T/G - A C AC + Kukri_c73868_961 chr6B 665716080 A/G + A G AG + GENE-3758_627 chr6B 665739612 A/G - C T CT + Tdurum_contig53779_1074 chr6B 667071173 A/G - C T AG - Kukri_c4780_395 chr6B 667071383 A/G NA NA NA AG NA flanks do not match reference at this position BS00063217_51 chr6B 667778550 A/G - C T CT + BS00068504_51 chr6B 667884671 T/C + T C AG - BS00068506_51 chr6B 667884690 T/C + C T AG - Tdurum_contig46808_4106 chr6B 667952961 A/G - C T CT + RAC875_c23461_428 chr6B 667955657 T/C - A G CT - RAC875_c4891_99 chr6B 667956739 A/G - C T CT + Excalibur_c92249_102 chr6B 667963183 T/C + C T CT + BobWhite_c1633_643 chr6B 668773535 T/C - A G CT - BS00037933_51 chr6B 668774009 A/G + A G CT - Excalibur_c2737_197 chr6B 668776650 T/G + NA NA AC NA reference base C not among SNP alleles Ku_c5191_340 chr6B 668776747 A/G + A G AG + RAC875_rep_c69963_514 chr6B 668776747 T/C - A G AG + Ra_c18658_1048 chr6B 673765663 A/G + G A AG + Excalibur_c12464_390 chr6B 673765863 A/G - C T AG - Tdurum_contig51640_847 chr6B 674103610 A/G + A G CT - CAP7_c3697_87 chr6B 674946601 T/C + C T CT + Tdurum_contig68217_361 chr6B 674946601 A/G - C T CT + BS00073898_51 chr6B 676152286 A/G + G A CT - Tdurum_contig29013_239 chr6B 676492639 A/G + G A CT - tplb0021a17_853 chr6B 678175525 A/C + C A AC + Jagger_c3235_381 chr6B 678630224 T/C NA NA NA CT NA flanks do not match reference at this position CAP11_c204_238 chr6B 678665917 A/G - T C AG - Tdurum_contig32579_121 chr6B 680084744 A/G - T C AG - RFL_Contig5037_1482 chr6B 680310576 T/C + C T AG - Kukri_c20060_350 chr6B 680474103 T/C - G A AG + BS00022832_51 chr6B 680862733 T/G + T G AC - Kukri_c75359_152 chr6B 681317026 A/G - C T AG - Excalibur_c29639_65 chr6B 681921038 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c76628_251 chr6B 681924056 T/C - G A AG + RAC875_c12907_515 chr6B 682550764 T/C + C T CT + BS00067983_51 chr6B 682719743 A/C + A C AC + BS00067161_51 chr6B 683213880 T/C + C T CT + BS00067388_51 chr6B 683650041 A/G + G A CT - RAC875_c82640_416 chr6B 686368291 T/C - G A CT - RFL_Contig799_2152 chr6B 686416383 T/C - G A AG + Tdurum_contig17421_310 chr6B 686687772 T/C + T C AG - BS00036830_51 chr6B 686688263 T/C + T C AG - Excalibur_rep_c110824_66 chr6B 686688829 A/G NA NA NA AG NA flanks do not match reference at this position BS00023080_51 chr6B 686799031 A/G - C T CT + BS00109717_51 chr6B 686801972 A/C - G T AC - Kukri_c16404_100 chr6B 687554758 A/G - T C CT + BS00069116_51 chr6B 687969212 T/C - G A AG + BS00034554_51 chr6B 688302706 T/C + T C CT + RFL_Contig2206_1694 chr6B 690730128 T/C + T C CT + BS00022081_51 chr6B 690967366 T/C - G A CT - BS00027770_51 chr6B 690969607 A/G + A G CT - BS00012510_51 chr6B 690978377 T/C + T C CT + Kukri_c609_328 chr6B 691828129 A/G - C T CT + Tdurum_contig67581_1163 chr6B 692778445 T/C + T C AG - Ex_c17379_1431 chr6B 692782106 A/G + A G AG + GENE-4178_327 chr6B 692783029 A/C - G T GT + IAAV1128 chr6B 693097443 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Ex_c4966_2130 chr6B 693938900 A/G + G A CT - RAC875_c17347_341 chr6B 694165841 T/C NA NA NA AG NA flanks do not match reference at this position IACX2322 chr6B 694168405 T/C + C T AG - RAC875_c3455_171 chr6B 694403005 T/C + C T AG - RFL_Contig1075_947 chr6B 694404622 T/G + T G GT + Ku_c24158_1468 chr6B 696150409 T/C - G A AG + Ra_c2557_2531 chr6B 696151765 A/G + G A CT - BS00067417_51 chr6B 696468301 T/C - G A CT - Excalibur_c276_1585 chr6B 696639392 A/C + C A GT - Kukri_rep_c112678_555 chr6B 696639644 A/G + A G CT - GENE-3863_132 chr6B 696640282 A/G + A G AG + BobWhite_c30742_51 chr6B 697462965 T/C - G A CT - RAC875_c6813_168 chr6B 697535103 A/G + A G CT - RAC875_rep_c113188_81 chr6B 697754702 A/G + A G AG + RAC875_rep_c71463_98 chr6B 699006494 T/C - G A CT - Kukri_c85856_60 chr6B 699202202 A/G - C T AG - BS00068166_51 chr6B 699203558 T/C + T C CT + BobWhite_c35035_317 chr6B 701387320 A/G - C T AG - GENE-3871_109 chr6B 701873544 A/G + A G CT - GENE-3876_34 chr6B 702565215 T/C + C T AG - RAC875_c38615_1540 chr6B 702828243 T/C + T C AG - Kukri_c20590_210 chr6B 703285862 A/G + A G AG + Ra_c7673_1773 chr6B 703287322 A/C + C A AC + Ra_c7673_1788 chr6B 703287337 A/C + C A AC + Tdurum_contig76116_469 chr6B 704038849 A/C + C A GT - Ra_c44434_409 chr6B 704040319 A/G - T C CT + RAC875_c17224_741 chr6B 704187606 A/G + G A AG + Kukri_c1145_989 chr6B 704187734 T/C - A G CT - Kukri_c1145_832 chr6B 704187891 A/G - T C AG - Kukri_rep_c106092_300 chr6B 704372658 T/C + T C CT + IAAV3009 chr6B 704947363 T/C + T C AG - Ex_c8134_363 chr6B 705285734 T/C - A G AG + RAC875_c31299_1302 chr6B 705379908 A/G - T C AG - GENE-4307_115 chr6B 705383576 T/C NA NA NA CT NA flanks do not match reference at this position BobWhite_c3506_1151 chr6B 705383961 T/C + T C CT + Excalibur_rep_c69054_960 chr6B 705384310 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_c17847_123 chr6B 705384576 T/G + G T GT + BS00085589_51 chr6B 705385051 A/G + G A AG + RAC875_rep_c106238_237 chr6B 705756974 A/G + A G AG + TA003403-0617 chr6B 705836766 A/C + A C AC + BS00064967_51 chr6B 706332786 A/C + C A GT - Kukri_c22391_192 chr6B 706348520 A/C - T G AC - RAC875_rep_c112646_106 chr6B 706442660 A/C + A C AC + IACX11598 chr6B 706625968 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c23654_214 chr6B 706626081 T/C - G A CT - BobWhite_c6546_423 chr6B 706627368 T/G - C A GT - RFL_Contig2877_804 chr6B 707027206 A/G + A G CT - RFL_Contig2877_936 chr6B 707027338 T/C + T C CT + Kukri_c32985_120 chr6B 707114332 A/G - T C AG - Kukri_c26944_389 chr6B 707181153 A/C + C A GT - Jagger_c1231_85 chr6B 708019344 T/C + T C AG - tplb0046e21_1294 chr6B 708024244 A/G - C T AG - Tdurum_contig7986_704 chr6B 708026998 T/C + T C AG - tplb0046e21_221 chr6B 708027319 T/C - A G AG + CAP12_c67_128 chr6B 708047311 T/C + T C AG - CAP12_c67_212 chr6B 708047395 T/C + C T CT + Kukri_c338_330 chr6B 708660622 T/C - G A CT - Kukri_c338_109 chr6B 708660843 A/G - C T CT + Kukri_c25454_496 chr6B 708939957 A/G - T C AG - CAP7_rep_c12573_189 chr6B 709218289 T/C - A G CT - Kukri_c40038_299 chr6B 709994764 T/C + C T CT + Tdurum_contig12123_197 chr6B 710003281 A/C + A C GT - BobWhite_c23771_525 chr6B 710102554 A/G - T C CT + Tdurum_contig92981_1091 chr6B 710103411 A/G + A G CT - RAC875_c41444_82 chr6B 711236177 A/G + G A AG + RAC875_c41444_939 chr6B 711237586 A/C + A C AC + RAC875_c56205_127 chr6B 712235814 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c45987_132 chr6B 712243672 T/G - A C AC + RAC875_c45987_106 chr6B 712243698 T/C - A G AG + BobWhite_c27364_124 chr6B 713971321 A/C + A C AC + BS00003958_51 chr6B 714635058 A/G - C T CT + Tdurum_contig8030_335 chr6B 715600432 T/C - G A AG + BS00022240_51 chr6B 715724272 T/C - A G CT - Excalibur_rep_c69865_157 chr6B 715750385 A/G - T C AG - BS00012034_51 chr6B 715751072 T/C + T C CT + Tdurum_contig59339_540 chr6B 715751072 A/G - T C CT + BS00073958_51 chr6B 715977827 T/C - G A CT - BS00074289_51 chr6B 715977923 A/G + G A AG + BS00109878_51 chr6B 715977945 T/C + C T CT + Excalibur_rep_c66254_109 chr6B 716010179 T/C + C T AG - Kukri_c38002_757 chr6B 716010203 A/G - T C CT + Kukri_c45876_157 chr6B 716258329 A/G + G A CT - RAC875_c24832_252 chr6B 716258438 A/C + A C AC + Excalibur_c28759_914 chr6B 716259097 A/G + G A AG + IACX7844 chr6B 716622758 T/G + T G AC - Tdurum_contig28247_226 chr6B 717861750 T/C + C T CT + Kukri_c11397_2523 chr6B 717865374 T/C - A G AG + Excalibur_rep_c111903_259 chr6B 717871814 T/G + T G GT + Kukri_c25930_1245 chr6B 717873278 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c78493_305 chr6B 717893266 A/G + A G CT - Excalibur_c2049_2593 chr6B 717916385 T/C - G A CT - BS00023021_51 chr6B 717961307 T/C - G A CT - Tdurum_contig65998_182 chr6B 717967277 A/G + G A AG + Tdurum_contig65998_258 chr6B 717967353 A/G + G A CT - BS00069822_51 chr6B 718231365 T/C - A G CT - Excalibur_c21199_377 chr6B 718327641 A/G - T C CT + Tdurum_contig67619_532 chr6B 718376201 A/G - C T CT + Kukri_c19426_489 chr6B 718639464 T/C + C T AG - Excalibur_c6108_541 chr6B 718773144 A/G - T C CT + BS00022828_51 chr6B 718775217 T/G + G T GT + BS00094584_51 chr6B 718775237 A/C + A C GT - BobWhite_c43263_180 chr6B 718920760 T/G + T G AC - BobWhite_c47040_185 chr6B 719509188 T/C + C T CT + BobWhite_c47040_305 chr6B 719509309 T/C + C T CT + Kukri_c60966_261 chr6B 719509476 A/G - C T AG - Kukri_c60966_205 chr6B 719509532 A/G - C T CT + Kukri_c79048_87 chr6B 719711480 A/G - C T AG - Excalibur_c29748_596 chr6B 719717050 T/C - G A CT - RAC875_c74902_153 chr6B 719719346 T/C - A G CT - RAC875_c74902_63 chr6B 719719436 T/C - A G AG + Excalibur_c30571_346 chr6B 720423128 A/C + C A AC + Excalibur_c73970_243 chr6B 720455500 T/C + T C AG - Excalibur_c40917_325 chr6B 720498052 T/C - A G AG + BobWhite_c13202_462 chr6B 720507067 A/G + A G AG + Excalibur_c55484_272 chr6B 720529223 T/C - G A AG + BS00011795_51 chr6B 720560867 T/G - A C GT - BS00083918_51 chr6B 720952180 T/C - A G CT - RAC875_c49751_54 chr6B 720985855 T/C + C T AG - RAC875_c49751_75 chr6B 720985876 T/C + T C CT + Excalibur_c4789_2748 chr6D 1413279 A/G - C T CT + Excalibur_c10358_1800 chr6D 1773398 A/G + G A CT - GENE-3775_326 chr6D 1781101 T/C + T C AG - Excalibur_c52276_176 chr6D 2167095 T/C - G A CT - CAP7_c1208_150 chr6D 2269185 T/C + T C AG - CAP11_c1087_327 chr6D 2271897 A/G - T C AG - Ex_c477_1253 chr6D 2321052 T/C - G A AG + RAC875_c2102_3487 chr6D 2321460 T/C - A G CT - TA002853-0110-w chr6D 2409066 A/G - C T CT + Kukri_c55362_75 chr6D 2488914 A/C - T G GT + IAAV8808 chr6D 2891087 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c7731_2743 chr6D 3119456 A/G - T C CT + Kukri_c17961_350 chr6D 3727655 A/G - C T CT + Kukri_c89555_57 chr6D 3917522 A/G + A G CT - RAC875_c98242_422 chr6D 3942572 A/G + G A CT - Jagger_c3907_55 chr6D 3992800 A/G - C T AG - BS00065960_51 chr6D 4061583 T/C + C T AG - Excalibur_c53680_124 chr6D 4280608 T/C - G A AG + BS00011821_51 chr6D 4519526 T/C - NA NA AG NA reference base C not among SNP alleles Excalibur_c31801_752 chr6D 4630640 T/C - A G AG + RAC875_c57371_238 chr6D 4635464 T/C + C T CT + BobWhite_rep_c52808_186 chr6D 4775138 T/C - A G CT - BobWhite_c7090_123 chr6D 5065205 A/G - C T CT + Excalibur_c1991_1504 chr6D 5152726 A/G + A G AG + BobWhite_c7090_778 chr6D 5178749 T/C + T C CT + RAC875_c68978_126 chr6D 5987081 T/C + T C CT + RAC875_c68978_220 chr6D 5987175 T/C + C T AG - BobWhite_c3073_1156 chr6D 5987292 A/G - C T AG - IACX9471 chr6D 6342756 T/C - G A AG + BobWhite_c11808_975 chr6D 7098529 A/C + C A AC + IAAV661 chr6D 7106504 T/C - G A CT - RFL_Contig5885_435 chr6D 7397167 A/G + A G AG + Ra_c6065_1145 chr6D 8662159 T/C + C T CT + Excalibur_c13115_348 chr6D 9247472 A/G + A G AG + IAAV2577 chr6D 9470596 T/C + C T AG - Kukri_c6364_578 chr6D 9472053 T/C - A G CT - Excalibur_c24288_548 chr6D 9588401 T/C + C T CT + Excalibur_c64989_556 chr6D 10912459 T/C + T C CT + Kukri_c45843_230 chr6D 13070413 T/G - C A GT - Kukri_c18874_1414 chr6D 14655290 A/G - C T AG - Tdurum_contig44092_939 chr6D 16287585 A/G - T C CT + Kukri_c10377_112 chr6D 16295376 T/C - A G AG + Kukri_c10377_88 chr6D 16295400 A/G - C T AG - RAC875_c41786_417 chr6D 17054603 A/C + A C GT - RAC875_c41786_587 chr6D 17055489 T/C + T C AG - RAC875_c99174_63 chr6D 17055757 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c55270_272 chr6D 17056076 T/C - A G AG + Excalibur_rep_c102994_1689 chr6D 17298001 T/C - G A CT - RAC875_c20222_875 chr6D 18014573 T/G - A C AC + Jagger_c3477_441 chr6D 20852789 A/G + A G AG + BobWhite_c30583_75 chr6D 20932812 T/C - G A AG + Kukri_c1192_825 chr6D 21982117 T/C + T C CT + BS00009331_51 chr6D 21982688 T/G + G T AC - BS00011436_51 chr6D 21983232 T/C NA NA NA AG NA flanks do not match reference at this position Tdurum_contig75595_1072 chr6D 21983232 A/G NA NA NA AG NA flanks do not match reference at this position BobWhite_c4014_508 chr6D 23075899 T/C + T C CT + BS00021970_51 chr6D 24003386 A/G - C T AG - BS00009584_51 chr6D 24230783 A/G - T C CT + IACX7895 chr6D 24262075 T/C + T C CT + CAP12_c2800_262 chr6D 25760345 T/G - A C AC + D_GB5Y7FA02FHK0M_407 chr6D 26242782 T/C - G A CT - RAC875_c26177_632 chr6D 26245055 T/C + C T AG - RAC875_rep_c108445_772 chr6D 27523357 A/G + A G CT - RAC875_c21204_224 chr6D 38887604 T/C + C T CT + RAC875_c47717_388 chr6D 47637555 A/G - T C AG - IAAV8886 chr6D 52868060 T/C - A G CT - GENE-3854_620 chr6D 53665767 T/C + C T CT + JD_c8888_741 chr6D 54265965 A/G - T C CT + RAC875_c13949_923 chr6D 55926655 A/C + A C GT - Tdurum_contig62040_1247 chr6D 56911961 T/C + T C CT + Tdurum_contig62040_1487 chr6D 56912452 T/C + T C CT + Tdurum_contig62040_1494 chr6D 56912459 A/C + A C GT - BobWhite_c15977_107 chr6D 57113773 T/C - G A CT - BS00010441_51 chr6D 60137034 A/G + G A CT - RAC875_c25672_473 chr6D 68103903 T/C - G A CT - RFL_Contig4441_505 chr6D 71521126 T/C + C T AG - JD_c15431_399 chr6D 73063082 A/G + G A CT - Kukri_c30417_305 chr6D 73498772 T/C + T C AG - Excalibur_c44771_588 chr6D 75375711 T/C + T C AG - RAC875_c4254_364 chr6D 75748855 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c52566_447 chr6D 79066266 A/G + G A CT - RAC875_c52566_644 chr6D 79067461 T/C + T C CT + BS00064893_51 chr6D 79091070 T/C - G A CT - GENE-4142_88 chr6D 80523698 A/C - G T GT + RAC875_c14408_783 chr6D 86761555 T/C + C T AG - RFL_Contig4626_873 chr6D 91819972 A/G - C T CT + IAAV2240 chr6D 97713611 A/C + C A AC + BS00010093_51 chr6D 115088410 A/G + G A AG + IAAV9195 chr6D 123056726 A/C + C A GT - RAC875_c24962_294 chr6D 131706636 T/C - A G AG + D_GBB4FNX01BO9N8_336 chr6D 159349643 T/C + T C CT + D_contig09096_210 chr6D 163835346 A/G + A G AG + RAC875_c41613_124 chr6D 163836060 A/C - T G AC - IAAV1488 chr6D 163837466 T/C + T C CT + IACX8190 chr6D 181730826 A/C - G T GT + BS00065309_51 chr6D 202263694 A/G + A G CT - RAC875_c33060_790 chr6D 227388861 T/C + C T CT + IACX8469 chr6D 229397468 A/C + A C AC + IAAV3994 chr6D 271295210 T/G + T G AC - BS00036211_51 chr6D 275163801 A/C - G T GT + Kukri_c34967_226 chr6D 275666554 A/C - T G GT + RAC875_c26887_562 chr6D 278639613 T/C + T C CT + BS00064203_51 chr6D 288554045 T/C - G A CT - Excalibur_c30793_77 chr6D 291928022 T/C + T C CT + RAC875_c25839_225 chr6D 292066763 T/C + C T AG - BS00066209_51 chr6D 294095156 T/C + T C AG - BS00022155_51 chr6D 304116703 A/G - T C AG - Excalibur_c2328_1207 chr6D 304739346 A/G + A G CT - GENE-4153_101 chr6D 306711417 T/C - G A AG + Kukri_c2842_248 chr6D 309581372 T/C + T C AG - D_GDS7LZN01BGS3L_281 chr6D 310486034 A/G - C T AG - IACX10982 chr6D 315597451 T/C + T C CT + GENE-4081_72 chr6D 343946989 A/G - C T CT + GENE-4063_410 chr6D 357587246 T/C + C T AG - Kukri_c10661_480 chr6D 374107225 A/G NA NA NA CT NA flanks do not match reference at this position Kukri_c39369_307 chr6D 374119734 A/G - T C CT + BS00012028_51 chr6D 388120427 T/C - A G CT - IAAV8527 chr6D 389607042 A/G - C T AG - Excalibur_rep_c105491_144 chr6D 389983467 A/G + A G AG + IAAV6297 chr6D 399034658 A/C - G T AC - Kukri_c31995_1948 chr6D 402127283 A/G + G A CT - BS00021881_51 chr6D 422204407 T/C - G A AG + GENE-4005_179 chr6D 424637433 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_rep_c107624_603 chr6D 425895244 T/C - A G AG + Kukri_c15096_4206 chr6D 425901457 T/C + T C AG - GENE-4086_659 chr6D 426061310 A/C + C A AC + Excalibur_c17348_264 chr6D 447907654 T/C + T C CT + Tdurum_contig32258_314 chr6D 448695579 T/C - G A AG + BS00063625_51 chr6D 448960252 T/C - A G CT - Tdurum_contig46670_1680 chr6D 453012539 T/C - A G CT - Excalibur_c827_666 chr6D 453013276 T/C + C T AG - Tdurum_contig46670_1132 chr6D 453013380 T/C - A G AG + RAC875_c79894_52 chr6D 454232795 A/G + A G AG + IACX11357 chr6D 454587848 T/C + T C CT + IACX7618 chr6D 454588778 T/C + C T CT + BS00059791_51 chr6D 454635202 A/C - G T GT + RAC875_c9618_334 chr6D 455134830 T/C + T C CT + BobWhite_c22280_104 chr6D 455135535 T/G + G T GT + BS00003697_51 chr6D 455251659 T/C - G A AG + IACX5833 chr6D 455251659 A/G + G A CT - IAAV7971 chr6D 455735559 A/G + A G AG + BS00011061_51 chr6D 455886663 T/C - G A AG + RAC875_c25738_168 chr6D 455890225 A/C - G T AC - BobWhite_c5872_65 chr6D 455891268 A/C - G T GT + BS00036102_51 chr6D 456456585 A/G + G A CT - BobWhite_c5255_429 chr6D 456555973 T/C + T C CT + Excalibur_c63713_892 chr6D 456558606 T/C + C T CT + IAAV6895 chr6D 456664316 T/C NA NA NA CT NA flanks do not match reference at this position BS00004374_51 chr6D 457471735 A/G - NA NA AG NA reference base G not among SNP alleles BS00068245_51 chr6D 458362043 T/C + C T CT + Ex_c25390_395 chr6D 458365112 A/G - T C AG - Excalibur_c53816_233 chr6D 458506976 T/C - G A AG + CAP7_rep_c12716_77 chr6D 458758827 T/C - G A AG + IAAV1495 chr6D 458764213 T/G NA NA NA GT NA flanks do not match reference at this position tplb0045d23_567 chr6D 459170655 A/G + A G AG + Excalibur_c30035_368 chr6D 459237640 T/C + T C AG - tplb0025h02_630 chr6D 459699046 T/C NA NA NA CT NA flanks do not match reference at this position GENE-3988_79 chr6D 460568443 T/C + T C CT + RAC875_c48570_361 chr6D 460573055 T/C - G A CT - BobWhite_c13504_378 chr6D 460573364 A/G + G A AG + BobWhite_c34996_280 chr6D 460698907 T/C + C T AG - GENE-3871_337 chr6D 460700332 A/G + A G AG + GENE-3852_1100 chr6D 460734413 A/C + A C GT - Excalibur_c24688_407 chr6D 460735016 A/C + A C GT - GENE-3862_178 chr6D 460743340 A/C - T G GT + GENE-3862_349 chr6D 460743425 A/G - C T AG - Kukri_c15205_882 chr6D 460746205 T/C + T C AG - tplb0046a04_774 chr6D 461010134 T/C NA NA NA CT NA flanks do not match reference at this position BobWhite_c24258_496 chr6D 461010355 T/C NA NA NA AG NA flanks do not match reference at this position tplb0046a04_902 chr6D 461010449 A/G + G A CT - Excalibur_c32242_137 chr6D 461316094 A/G - T C AG - Kukri_c35931_565 chr6D 461316254 A/G + G A AG + Excalibur_c83056_83 chr6D 461316610 A/G - C T AG - Excalibur_c50656_660 chr6D 461355105 A/G - C T CT + RAC875_c38615_143 chr6D 461355869 A/G + A G AG + GENE-3864_207 chr6D 461363658 A/G + G A AG + Ex_c7086_154 chr6D 461388460 A/G - C T AG - IAAV3944 chr6D 461393773 T/C + C T CT + RAC875_c13595_669 chr6D 461393867 A/G - C T CT + RAC875_c63262_67 chr6D 461394178 A/G - T C CT + D_GA8KES401DISTP_65 chr6D 461395097 A/G + A G AG + Excalibur_c4261_1098 chr6D 461453163 T/C + C T AG - CAP8_c2210_103 chr6D 461455446 A/C - G T AC - BobWhite_rep_c50999_270 chr6D 461712324 A/G + A G AG + Ex_c5168_849 chr6D 461925117 T/G - C A GT - Kukri_rep_c68091_1144 chr6D 462013599 T/C - A G CT - Kukri_rep_c68091_971 chr6D 462013772 T/C - A G CT - RAC875_c2338_53 chr6D 462013938 T/C + C T AG - Excalibur_c64024_119 chr6D 462198638 A/G - T C AG - BobWhite_c34798_184 chr6D 462201732 T/C + T C AG - Tdurum_contig569_263 chr6D 462321946 A/G - T C CT + RAC875_c24285_1049 chr6D 462466575 T/C + C T AG - Tdurum_contig413_220 chr6D 462537926 A/G - T C AG - Excalibur_c8134_1319 chr6D 462604657 T/G - A C GT - RAC875_c3156_630 chr6D 462604776 T/C + T C CT + RAC875_rep_c103556_427 chr6D 462604912 A/C NA NA NA AC NA flanks do not match reference at this position Kukri_rep_c107975_95 chr6D 462605093 A/G - C T CT + Ex_c31468_763 chr6D 462613428 A/G - T C AG - RAC875_c31299_1215 chr6D 462626707 T/C - A G AG + Excalibur_rep_c67100_1541 chr6D 462630061 A/G - T C CT + BobWhite_rep_c64646_431 chr6D 462630227 A/G + G A AG + Ex_c67100_1172 chr6D 462630768 A/G - T C AG - BobWhite_c3506_1559 chr6D 462631543 T/C + T C CT + IAAV6637 chr6D 462632013 A/C - T G AC - CAP8_c6799_93 chr6D 462632139 T/C - A G AG + Kukri_rep_c101126_881 chr6D 463073396 A/C + A C GT - Ex_c12134_939 chr6D 463224151 T/G + T G GT + Ex_c12134_1160 chr6D 463224372 T/G + T G GT + Excalibur_c46335_97 chr6D 463447067 A/G - C T CT + Kukri_c16065_309 chr6D 463447228 A/G - T C CT + Tdurum_contig10288_317 chr6D 463549538 T/C - G A CT - RAC875_c14354_934 chr6D 463715400 T/C + T C CT + D_contig10996_530 chr6D 463743339 A/G NA NA NA AG NA flanks do not match reference at this position IAAV2130 chr6D 464345143 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_rep_c105937_467 chr6D 464947009 T/C - A G CT - BobWhite_c18136_441 chr6D 464985654 T/C + T C AG - BobWhite_c5847_919 chr6D 465209086 A/C - T G GT + BS00087334_51 chr6D 465209224 A/C + C A AC + Kukri_rep_c103186_134 chr6D 465209608 A/G - C T CT + BS00087343_51 chr6D 465210239 A/G + G A AG + Excalibur_rep_c109065_562 chr6D 465743964 T/C + T C CT + Excalibur_c32219_491 chr6D 466330017 A/C - NA NA AC NA reference base C not among SNP alleles BS00087997_51 chr6D 466908148 A/C + A C GT - BS00003568_51 chr6D 466944457 T/C + C T CT + IACX11026 chr6D 466944713 T/C - A G AG + BS00022787_51 chr6D 467188054 A/G + A G CT - Kukri_c90942_274 chr6D 467317144 T/C + T C CT + RAC875_c57692_88 chr6D 467317165 T/C NA NA NA CT NA flanks do not match reference at this position BS00091909_51 chr6D 467778023 T/C + T C AG - Excalibur_c22876_1040 chr6D 467916732 T/C + T C AG - IACX5858 chr6D 469249663 A/C - G T GT + GENE-3689_680 chr6D 469249733 T/G NA NA NA GT NA flanks do not match reference at this position RAC875_c28319_522 chr6D 469395520 A/G + A G AG + RAC875_c86296_278 chr6D 469576213 A/G + A G AG + BS00077044_51 chr6D 469617774 T/C + C T CT + BS00059046_51 chr6D 469619382 T/C + C T AG - RAC875_c484_1063 chr6D 469829863 A/G - T C AG - Excalibur_c2991_320 chr6D 469919720 T/C - A G CT - BS00043489_51 chr6D 469963038 A/G - C T CT + BobWhite_c13202_399 chr6D 470629062 T/C - A G AG + RAC875_c17011_717 chr6D 470636827 A/G - C T CT + BobWhite_c13435_700 chr6D 471008558 T/C + C T CT + RAC875_c27997_250 chr6D 471013262 A/G - T C AG - IAAV2636 chr6D 471070332 T/C - A G AG + Kukri_c44291_138 chr6D 471070785 A/G + A G AG + Kukri_c44291_223 chr6D 471070870 A/G + G A AG + Kukri_c373_1588 chr6D 471919706 A/G - T C CT + BobWhite_c19298_97 chr6D 471924301 A/G - T C CT + Kukri_c48283_78 chr6D 472720429 T/C NA NA NA AG NA flanks do not match reference at this position Excalibur_c13714_925 chr6D 472720664 T/C - G A AG + Excalibur_c13714_490 chr6D 472721495 A/G - C T CT + RAC875_rep_c104893_620 chr6D 472721837 T/C - G A CT - BS00109902_51 chr6D 472732172 A/G + A G AG + BS00065202_51 chr6D 472751306 T/C + T C AG - BS00070856_51 chr6D 472789865 T/G + T G GT + Excalibur_rep_c87351_347 chr6D 472801768 T/C - A G CT - RFL_Contig2615_982 chr6D 472890095 T/C - A G CT - Excalibur_c21199_533 chr6D 472962073 T/C - A G AG + BobWhite_c5324_168 chr6D 473082864 T/C + T C CT + Kukri_c38459_501 chr6D 473083552 T/C NA NA NA AG NA flanks do not match reference at this position BS00010129_51 chr6D 473418687 T/G - A C GT - Excalibur_c17447_635 chr7A 534562 T/G - A C AC + BS00109912_51 chr7A 653949 T/C + T C CT + tplb0057f21_146 chr7A 1320170 A/C + A C AC + Kukri_c22602_819 chr7A 1320622 A/G - T C CT + Kukri_c22602_791 chr7A 1320650 T/C - A G CT - Excalibur_c20311_240 chr7A 1371439 A/G + G A CT - IAAV822 chr7A 1409599 A/G - T C AG - RAC875_c1553_667 chr7A 1704477 A/G - T C AG - BS00035083_51 chr7A 1714169 T/C NA NA NA CT NA flanks do not match reference at this position Tdurum_contig5646_929 chr7A 1739213 T/C - A G AG + Kukri_c11260_559 chr7A 1739446 T/C - A G AG + BS00037421_51 chr7A 1739673 A/G - C T AG - Excalibur_c21666_712 chr7A 1847103 A/G + G A AG + Excalibur_c2319_1675 chr7A 1977962 T/C - A G CT - Ex_c2767_429 chr7A 1980173 A/G - T C AG - Ex_c2767_419 chr7A 1980183 T/C - A G CT - BS00033782_51 chr7A 2695710 A/G - T C AG - RAC875_c5163_1199 chr7A 2697104 T/C - G A CT - BS00106749_51 chr7A 2716515 T/C + T C AG - Excalibur_c662_229 chr7A 2719173 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c7828_598 chr7A 2827826 A/G + A G AG + RAC875_c42866_1323 chr7A 2829287 T/C - A G AG + Kukri_c9479_2054 chr7A 3413968 A/G - T C AG - BS00063002_51 chr7A 3415104 T/G - C A GT - BS00061123_51 chr7A 3415818 A/G + G A AG + Kukri_c58589_402 chr7A 3843915 T/C + C T AG - Tdurum_contig52015_1320 chr7A 3907296 T/C - A G AG + Tdurum_contig52015_1090 chr7A 3907799 A/G - T C CT + RFL_Contig1460_1426 chr7A 3907802 A/G - T C CT + RFL_Contig1460_693 chr7A 3909962 T/C - G A AG + RFL_Contig1460_645 chr7A 3910107 T/C - G A CT - Tdurum_contig81608_63 chr7A 3983017 A/C + C A AC + RAC875_c14173_207 chr7A 4429978 T/C - A G CT - RAC875_c8714_653 chr7A 4892826 T/C + T C AG - BobWhite_c18267_473 chr7A 4898385 T/C - A G AG + Excalibur_c24750_504 chr7A 6315065 T/C + C T AG - BobWhite_c21647_287 chr7A 6315399 T/C + T C CT + Excalibur_rep_c69170_425 chr7A 6495726 T/G + G T GT + Excalibur_rep_c69170_438 chr7A 6495739 T/C + T C CT + GENE-4923_84 chr7A 6497359 T/G + T G GT + GENE-4923_506 chr7A 6497517 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c55774_126 chr7A 6499010 A/C + C A AC + IAAV136 chr7A 6845762 T/C - G A CT - BS00108549_51 chr7A 6845838 T/C - G A AG + BobWhite_c17467_129 chr7A 6845878 A/G - C T AG - RFL_Contig3483_411 chr7A 7066180 T/C + C T CT + RFL_Contig3483_512 chr7A 7066281 T/C + T C AG - RFL_Contig3483_628 chr7A 7066397 T/C + T C AG - RAC875_c56907_274 chr7A 7586807 T/C - G A CT - Excalibur_rep_c66939_849 chr7A 7587839 T/C - A G AG + Excalibur_rep_c66939_124 chr7A 7588559 A/G - T C AG - BS00004971_51 chr7A 7597288 T/C + C T CT + BobWhite_rep_c64534_141 chr7A 7727496 T/C + T C CT + BS00087471_51 chr7A 8254888 A/G - C T CT + BobWhite_c21200_281 chr7A 8263550 A/C - G T AC - BS00019238_51 chr7A 8263862 T/C - A G CT - TA003860-0675 chr7A 8374756 A/C NA NA NA GT NA flanks do not match reference at this position BS00039766_51 chr7A 8690908 A/C - G T AC - BS00091701_51 chr7A 8895413 A/C + A C AC + RAC875_c44881_150 chr7A 9382858 A/G + A G CT - RAC875_c41169_68 chr7A 10194087 T/C - A G AG + RAC875_c22210_191 chr7A 10357658 T/C - G A CT - RAC875_c346_1226 chr7A 10901927 T/C - A G CT - Tdurum_contig74815_685 chr7A 11099182 A/G + A G AG + Tdurum_contig74815_1413 chr7A 11099910 T/C + T C CT + Tdurum_contig74972_652 chr7A 11102598 T/C + T C AG - RAC875_c48202_231 chr7A 12177366 T/C + T C AG - IAAV2596 chr7A 12177815 A/C - G T AC - Tdurum_contig69003_459 chr7A 12415375 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c21165_1058 chr7A 13100987 A/G - T C AG - BobWhite_c14495_230 chr7A 14189450 T/C + T C AG - Excalibur_c23921_738 chr7A 14734007 A/G - T C AG - GENE-4440_118 chr7A 14734223 T/C + C T AG - RAC875_c55351_223 chr7A 14812491 T/C - A G AG + Kukri_c36885_58 chr7A 15086960 A/G - C T CT + BS00082268_51 chr7A 15689345 T/C - G A CT - BobWhite_c33300_159 chr7A 17331519 A/G - C T AG - BS00081098_51 chr7A 17467571 A/C + C A AC + Tdurum_contig15285_588 chr7A 18874278 A/G + A G CT - BS00084039_51 chr7A 18877090 T/C - G A AG + RAC875_c28585_156 chr7A 18877192 T/C + C T CT + RAC875_c16644_491 chr7A 18887907 A/G + A G AG + Excalibur_c33542_113 chr7A 18890924 A/G + A G AG + Kukri_c1831_56 chr7A 19005061 T/C + C T AG - RAC875_rep_c114991_493 chr7A 19006634 T/C + T C AG - BobWhite_c33103_476 chr7A 19318752 T/G - A C GT - IAAV912 chr7A 19420600 T/G + T G GT + Tdurum_contig13048_89 chr7A 19420674 A/G + G A CT - BS00009543_51 chr7A 19420736 A/G - C T AG - Tdurum_contig92906_272 chr7A 19816950 A/G - T C AG - Excalibur_c43859_166 chr7A 19934783 T/C + C T CT + Kukri_c28866_183 chr7A 19934872 T/C + T C AG - BS00099611_51 chr7A 19969587 T/C - G A AG + BS00099610_51 chr7A 19969617 T/G - C A AC + Tdurum_contig54860_525 chr7A 20171191 A/G + A G AG + Tdurum_contig54860_1393 chr7A 20172969 A/G + G A CT - Tdurum_contig75819_3136 chr7A 20180581 A/G + G A CT - Excalibur_c1310_414 chr7A 20555259 T/G + T G AC - Excalibur_c46018_271 chr7A 21263034 T/C + C T AG - RAC875_c13722_326 chr7A 22896113 T/C + C T CT + RAC875_c18446_506 chr7A 22918708 A/G + A G CT - Excalibur_c46601_212 chr7A 22935536 A/C - G T AC - Excalibur_c46601_57 chr7A 22935807 A/G - C T CT + Tdurum_contig47309_600 chr7A 22935893 T/C - A G CT - Kukri_c75729_221 chr7A 22936140 T/C + C T AG - Tdurum_contig16896_287 chr7A 22937645 T/G + T G GT + CAP11_c3214_133 chr7A 23328793 T/C - A G AG + RAC875_c6736_336 chr7A 24428700 T/C - A G CT - Ex_c10105_526 chr7A 24468115 T/G + T G GT + BS00022978_51 chr7A 25471995 A/C + C A GT - Kukri_c19436_405 chr7A 25922716 T/C - G A CT - RAC875_c63822_185 chr7A 26418365 A/G - T C AG - Excalibur_c60134_182 chr7A 26424142 A/G - T C AG - IAAV6131 chr7A 27288370 A/G + A G CT - Excalibur_c7897_600 chr7A 27462801 T/G - A C AC + BS00032623_51 chr7A 28042564 T/C + T C AG - BS00108523_51 chr7A 29829532 T/C - A G AG + BS00023172_51 chr7A 29829922 A/G - C T AG - Kukri_c1507_69 chr7A 29830481 A/G - T C CT + Excalibur_c37505_88 chr7A 29838861 T/C - A G CT - Tdurum_contig77759_52 chr7A 30029978 A/C - T G GT + BS00022442_51 chr7A 30061907 A/G + A G AG + RAC875_c80504_487 chr7A 30094381 A/G + G A AG + Kukri_c41603_111 chr7A 30134424 T/C - A G CT - Tdurum_contig17050_547 chr7A 30140478 A/G + G A CT - Tdurum_contig85217_286 chr7A 30816851 T/C - G A AG + Excalibur_c31383_82 chr7A 31879084 A/G + G A CT - BS00078359_51 chr7A 34045591 T/C + T C CT + Excalibur_c25471_225 chr7A 34539197 T/C - A G AG + BS00022970_51 chr7A 34539374 T/C - G A CT - Excalibur_c7538_2718 chr7A 35602223 T/C + C T AG - BobWhite_c40535_218 chr7A 35770406 A/G + A G AG + BS00074110_51 chr7A 37706308 A/C - G T GT + BS00065648_51 chr7A 37724730 T/G - C A GT - BS00023055_51 chr7A 41959666 A/G + A G CT - BobWhite_c24803_563 chr7A 42304242 A/G + G A CT - IAAV5448 chr7A 42500549 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00066885_51 chr7A 47283220 A/G + A G AG + Excalibur_c14189_156 chr7A 47444490 A/G + A G AG + RAC875_c50665_202 chr7A 47445872 T/C + C T CT + RAC875_c52560_123 chr7A 47516020 T/C - A G CT - Ku_c12886_1250 chr7A 49178408 A/G - T C AG - RFL_Contig854_2253 chr7A 50019876 A/G + G A AG + RAC875_c220_1354 chr7A 51373661 T/C NA NA NA AG NA flanks do not match reference at this position CAP11_c1473_320 chr7A 52393017 A/G + G A CT - Ku_c71719_137 chr7A 52950873 T/C - G A CT - Ex_c9615_1202 chr7A 52950949 A/G - C T CT + Excalibur_rep_c68004_182 chr7A 52967202 T/C + C T CT + IAAV5150 chr7A 52967281 T/G + T G AC - BS00078460_51 chr7A 52972191 A/G - C T AG - tplb0059b17_358 chr7A 53910983 T/C - A G CT - Tdurum_contig9584_624 chr7A 53916371 T/C - G A AG + Tdurum_contig9584_463 chr7A 53916532 T/C - A G AG + Tdurum_contig9584_455 chr7A 53916540 A/G - C T AG - CAP12_c2951_105 chr7A 53954505 A/G - T C AG - Tdurum_contig75475_454 chr7A 53954505 T/C + T C AG - BobWhite_rep_c58252_112 chr7A 54990997 A/C - G T AC - Tdurum_contig82438_136 chr7A 54997190 A/G - C T AG - Tdurum_contig82438_73 chr7A 54997253 A/G - C T AG - RAC875_c63889_486 chr7A 55881575 A/G - T C AG - Excalibur_c62100_325 chr7A 56153583 A/G - C T CT + Kukri_rep_c110670_553 chr7A 57214263 T/C - A G AG + BS00106074_51 chr7A 57873144 T/C + C T AG - IACX17522 chr7A 57873470 T/C + T C AG - Tdurum_contig20214_279 chr7A 61816447 T/G + G T GT + Tdurum_contig14075_328 chr7A 61816860 T/C - A G AG + Kukri_c106476_709 chr7A 62528294 A/G - T C AG - BS00007429_51 chr7A 62528356 T/C - A G AG + RFL_Contig3271_810 chr7A 62528917 A/G + A G AG + Kukri_c106476_87 chr7A 62529500 A/G - T C CT + BS00010559_51 chr7A 63111864 T/C + T C CT + BS00044694_51 chr7A 64841086 A/G - C T AG - Tdurum_contig85377_141 chr7A 65007461 T/C - A G CT - BS00098026_51 chr7A 65153682 A/G - C T CT + BS00102772_51 chr7A 65328312 T/C + C T CT + Tdurum_contig16445_218 chr7A 65476388 T/C + T C CT + Excalibur_c22196_483 chr7A 66227886 T/C - G A CT - BS00108784_51 chr7A 66227953 T/G - C A AC + BS00111112_51 chr7A 67671413 T/C - A G AG + Kukri_rep_c109098_132 chr7A 67671836 A/G - T C CT + Excalibur_c11579_250 chr7A 67672019 T/C - G A AG + Kukri_c11325_337 chr7A 67676153 A/G + A G AG + Kukri_c27306_162 chr7A 68029509 A/G - T C AG - Ra_c54443_444 chr7A 68043011 T/G - A C AC + RAC875_c3123_1213 chr7A 68087323 T/C - A G CT - RAC875_rep_c112782_91 chr7A 68087529 T/C + T C AG - GENE-4632_471 chr7A 68088520 T/G - A C GT - Excalibur_c1634_333 chr7A 68090124 T/C - A G CT - Excalibur_c37897_473 chr7A 68190703 A/C + A C GT - Tdurum_contig51645_738 chr7A 68190793 T/C - G A AG + Tdurum_contig51645_137 chr7A 68191391 T/C NA NA NA CT NA flanks do not match reference at this position GENE-4660_123 chr7A 68848325 T/G + G T AC - Kukri_c39994_227 chr7A 68882817 T/G + G T GT + RAC875_c35270_234 chr7A 68888247 A/G - T C AG - BobWhite_c8076_154 chr7A 68889553 A/G - C T AG - IAAV2086 chr7A 69220896 T/G + T G GT + RAC875_c57541_193 chr7A 69220896 A/C - T G GT + RAC875_c57541_120 chr7A 69220969 A/C - G T AC - BS00023225_51 chr7A 76124550 A/C - T G AC - Ku_c5938_4221 chr7A 76498040 T/C - A G CT - GENE-4833_102 chr7A 76500623 A/G - C T AG - BS00091891_51 chr7A 77435003 A/G - T C AG - Ra_c9427_300 chr7A 78434199 T/C + T C CT + RAC875_c28842_99 chr7A 78665750 A/C - T G GT + BS00024786_51 chr7A 79542803 T/C + C T CT + RAC875_c75528_355 chr7A 79648907 A/G - C T AG - BS00047811_51 chr7A 79652377 T/C + T C AG - GENE-4375_382 chr7A 79781013 A/G + A G AG + Kukri_c33711_462 chr7A 80016570 T/C - A G AG + BS00110952_51 chr7A 80067052 A/C + C A AC + IAAV7916 chr7A 80852011 T/C - A G AG + BS00110010_51 chr7A 80861432 T/C + C T CT + Excalibur_s114755_67 chr7A 81104242 T/C - G A CT - RAC875_c12961_1029 chr7A 81104472 T/C - G A AG + BS00097659_51 chr7A 81104885 A/G + G A AG + Kukri_c57674_324 chr7A 81133922 T/C - A G AG + Ku_c554_1239 chr7A 81135546 A/G - T C CT + Ra_c8937_191 chr7A 81498352 A/G + G A AG + RFL_Contig3447_1177 chr7A 81498528 T/C - G A AG + BS00074230_51 chr7A 82936652 A/C - G T GT + BS00022145_51 chr7A 83286879 T/G + T G AC - BS00086101_51 chr7A 83287514 A/G + G A AG + Tdurum_contig8441_602 chr7A 83287514 T/C - G A AG + Ra_c17341_2122 chr7A 83541267 A/G - C T AG - Excalibur_rep_c101407_222 chr7A 83544492 T/C - A G CT - BS00062425_51 chr7A 83784491 T/G + G T GT + Excalibur_c60598_158 chr7A 83936809 T/C + T C CT + BS00040929_51 chr7A 83936852 T/C + C T AG - IAAV1971 chr7A 84702233 T/C - A G AG + Kukri_rep_c101532_104 chr7A 84765828 A/G + A G AG + Excalibur_c9488_702 chr7A 84768097 T/C - A G AG + Excalibur_rep_c72139_187 chr7A 84782922 T/C - A G AG + Tdurum_contig99143_205 chr7A 85205128 A/G - T C AG - Excalibur_c42993_561 chr7A 85215972 T/C - G A CT - BS00035033_51 chr7A 85345350 T/G - A C AC + BS00035032_51 chr7A 85345352 T/C - G A CT - IACX9283 chr7A 85414786 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Kukri_c96054_123 chr7A 85609494 T/C + T C CT + GENE-1245_664 chr7A 85616826 T/G NA NA NA GT NA flanks do not match reference at this position JD_c19177_1462 chr7A 87307542 T/G - A C AC + JD_c19177_1284 chr7A 87307849 T/C - G A CT - GENE-3018_145 chr7A 87308253 T/C - A G CT - BS00046976_51 chr7A 88987024 A/C - G T AC - BS00065866_51 chr7A 89042301 T/C - A G AG + CAP11_c3138_241 chr7A 89827879 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c5757_530 chr7A 90652757 A/G + A G AG + BobWhite_c24295_777 chr7A 92420774 A/G - C T AG - RAC875_rep_c105041_121 chr7A 92892087 T/C + T C CT + Ex_c6196_971 chr7A 92892096 A/G - C T AG - Excalibur_c6196_668 chr7A 92892399 A/G - T C AG - RFL_Contig2200_1024 chr7A 93036212 A/G - T C CT + RAC875_c50689_142 chr7A 93077291 A/G + G A AG + RAC875_c7988_1588 chr7A 97575130 T/C - G A CT - Kukri_c15594_386 chr7A 100763259 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c48684_527 chr7A 102534189 T/C + T C CT + GENE-4329_154 chr7A 105141903 T/G + T G AC - Kukri_c26605_854 chr7A 105361567 T/C + T C CT + GENE-4598_467 chr7A 106200263 A/G + A G AG + TA004831-0260 chr7A 106245418 T/C - A G AG + Tdurum_contig10932_375 chr7A 107848461 T/C + C T AG - CAP8_c702_377 chr7A 108807857 T/C - G A CT - BS00011072_51 chr7A 108816503 T/C + T C CT + Ku_c11827_464 chr7A 108816571 A/G - T C CT + RAC875_c34650_378 chr7A 109354385 T/C - A G CT - Tdurum_contig69247_268 chr7A 109843023 T/C - G A CT - RAC875_c14386_822 chr7A 110252630 A/G - T C CT + RAC875_c67063_703 chr7A 112265416 T/C + T C CT + BS00003726_51 chr7A 112265505 T/C + C T CT + RAC875_c67063_984 chr7A 112265789 A/G + G A CT - BS00038787_51 chr7A 115812802 T/C - A G AG + RAC875_rep_c76772_850 chr7A 116875800 A/G + A G AG + Tdurum_contig61653_948 chr7A 117346294 T/C - A G CT - BS00111120_51 chr7A 117346845 A/G - C T CT + Tdurum_contig61653_358 chr7A 117347783 T/C - A G AG + RAC875_rep_c72596_466 chr7A 117347991 A/G + G A CT - BS00021997_51 chr7A 118328500 A/G + G A AG + RAC875_c100339_541 chr7A 118448261 A/G - T C CT + Tdurum_contig47443_361 chr7A 118448261 T/C + T C CT + Tdurum_contig12084_1122 chr7A 118461639 A/G + G A AG + BS00082180_51 chr7A 120176466 T/G + G T AC - GENE-4750_46 chr7A 122184833 A/G + G A CT - Kukri_c484_1704 chr7A 122494703 T/C + T C AG - RAC875_rep_c69766_246 chr7A 124791956 T/C + T C CT + BobWhite_c40583_146 chr7A 124793329 A/G + G A CT - BS00022435_51 chr7A 127572885 A/G - T C AG - Ku_c12139_1714 chr7A 127834151 T/C - A G CT - BobWhite_c24760_142 chr7A 128510291 T/C - G A CT - JD_c42022_319 chr7A 128756250 T/C - G A AG + BS00067399_51 chr7A 128918181 T/C - A G CT - BS00067398_51 chr7A 128918186 T/G - C A GT - BS00039561_51 chr7A 129871521 T/C - G A CT - RAC875_c13221_1017 chr7A 131815953 A/G + A G AG + Kukri_c47852_121 chr7A 134476712 A/G - C T AG - Tdurum_contig13431_127 chr7A 138163046 T/C + T C CT + Kukri_rep_c105330_552 chr7A 140994052 A/G + G A AG + Kukri_rep_c75743_357 chr7A 141857695 A/G - C T AG - BS00022751_51 chr7A 159557314 A/G - T C CT + BS00055445_51 chr7A 174199635 A/G - T C AG - BS00061151_51 chr7A 174696522 A/C + C A GT - JD_c11426_334 chr7A 175691947 T/C + T C CT + BS00084370_51 chr7A 187431401 A/G - C T CT + Ra_c56305_654 chr7A 205170316 A/G + A G AG + BobWhite_rep_c66957_84 chr7A 213097835 T/C + C T AG - Ra_c32003_420 chr7A 218244507 T/C + C T CT + Kukri_c36213_211 chr7A 221680793 A/G - T C CT + CAP8_c4926_348 chr7A 225358183 A/G + A G AG + IACX1831 chr7A 226720217 T/C - A G AG + Kukri_c717_98 chr7A 227090795 T/C NA NA NA AG NA flanks do not match reference at this position BS00052668_51 chr7A 227092362 T/C - A G CT - RAC875_rep_c117475_289 chr7A 230300157 T/C - G A CT - BS00066651_51 chr7A 232382784 A/G + G A CT - Kukri_rep_c70389_57 chr7A 232588721 T/C + C T AG - Kukri_c39894_178 chr7A 232593112 A/G - C T AG - BobWhite_c24063_231 chr7A 232746015 T/C - A G CT - Kukri_c36710_1007 chr7A 232757583 T/C + T C CT + RAC875_c32895_304 chr7A 233335147 T/C - A G CT - RAC875_c32895_211 chr7A 233335240 T/C - G A CT - BS00030911_51 chr7A 233336447 A/G + G A AG + TA002579-1137 chr7A 235461719 T/C + T C CT + IAAV5328 chr7A 236620390 T/C + T C AG - CAP7_rep_c8696_241 chr7A 237389296 T/C + C T AG - GENE-4654_196 chr7A 237518954 T/C - A G AG + RAC875_c66369_296 chr7A 251804492 T/C - G A CT - Tdurum_contig25631_143 chr7A 261584096 A/G - T C AG - BobWhite_rep_c49997_147 chr7A 263730272 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c67076_479 chr7A 264847399 A/G + A G AG + Ex_c6870_1704 chr7A 266640793 T/C + C T AG - Ku_c12129_1036 chr7A 266641260 T/C - G A CT - CAP11_c4929_307 chr7A 266977091 T/C - A G CT - BobWhite_c14471_411 chr7A 267569474 T/C - G A CT - IAAV3946 chr7A 268179145 A/G + G A CT - BS00064336_51 chr7A 268183539 A/G - C T CT + Kukri_c19025_244 chr7A 270889203 A/G + G A CT - RAC875_c64241_470 chr7A 277731133 A/C + A C GT - Excalibur_c34091_311 chr7A 281374161 A/G - T C AG - RFL_Contig428_290 chr7A 284526902 A/G + A G CT - BobWhite_c20374_162 chr7A 284528237 A/G + A G AG + Kukri_c55196_445 chr7A 284730570 T/C + C T AG - Excalibur_c1625_1215 chr7A 308303784 T/C + C T AG - Excalibur_c94951_349 chr7A 343365306 T/C + T C CT + Tdurum_contig8849_343 chr7A 405803537 T/C + T C CT + CAP8_c3451_65 chr7A 410730699 T/C + T C AG - Excalibur_c42978_149 chr7A 464237714 T/C + C T AG - RFL_Contig4956_2526 chr7A 481587624 T/G + T G AC - BS00022049_51 chr7A 484083044 A/C + A C GT - BS00023673_51 chr7A 484221355 T/C + C T AG - Kukri_c45412_177 chr7A 485194556 T/C + T C AG - Kukri_c14516_224 chr7A 486154673 T/C + C T AG - BS00108184_51 chr7A 487249122 A/C - T G AC - Tdurum_contig10002_533 chr7A 487635090 T/C - G A CT - GENE-4914_349 chr7A 487709715 A/G NA NA NA CT NA flanks do not match reference at this position BS00054183_51 chr7A 495539751 T/C - A G CT - Kukri_c5101_2636 chr7A 498939023 A/G - C T AG - RAC875_c32212_84 chr7A 501069535 T/C - G A AG + CAP7_c3756_190 chr7A 501588135 T/C - G A AG + CAP7_c3756_77 chr7A 501588246 T/C - A G AG + BS00054416_51 chr7A 501647802 A/C - T G GT + RAC875_c57962_101 chr7A 502756648 A/G - C T CT + RAC875_c11662_470 chr7A 503856211 A/G - C T AG - RAC875_c11662_401 chr7A 503856359 T/C NA NA NA CT NA flanks do not match reference at this position BS00023755_51 chr7A 504207488 T/C + C T CT + Excalibur_rep_c68850_592 chr7A 504210469 T/C NA NA NA CT NA flanks do not match reference at this position CAP11_rep_c6423_103 chr7A 506490295 T/G + T G GT + BS00097987_51 chr7A 506819093 A/G - T C AG - RFL_Contig2920_563 chr7A 509220720 T/C NA NA NA AG NA flanks do not match reference at this position BS00006674_51 chr7A 511497144 T/C + C T AG - BS00092197_51 chr7A 511498863 T/C + C T AG - tplb0024l08_1395 chr7A 511499659 T/C + T C CT + BS00040590_51 chr7A 511931149 A/G - C T AG - BS00100351_51 chr7A 512339058 T/C - G A AG + IACX11096 chr7A 512339091 T/C - A G CT - Jagger_c319_99 chr7A 512344076 A/G - C T CT + BS00099881_51 chr7A 512760201 A/G - C T CT + IACX3013 chr7A 512760263 A/G - T C AG - Ex_c9556_2547 chr7A 514822445 T/C - A G AG + Kukri_rep_c97425_164 chr7A 515003255 T/C + T C CT + BS00093016_51 chr7A 515199491 A/C + C A AC + CAP8_c8768_51 chr7A 519133955 T/C - A G CT - RAC875_c5549_149 chr7A 519172788 T/C - A G AG + RFL_Contig3590_811 chr7A 520334649 T/C - A G AG + RAC875_c9168_633 chr7A 520905350 T/C - G A CT - BS00091168_51 chr7A 521952054 T/C - A G AG + CAP7_c11350_73 chr7A 522326130 A/G - C T CT + RAC875_c18798_103 chr7A 531188810 A/G + G A CT - BobWhite_c13098_526 chr7A 534446396 T/C - A G AG + BS00080365_51 chr7A 537058999 T/G - C A AC + Kukri_c64283_212 chr7A 538693397 T/C + C T CT + Tdurum_contig42093_1170 chr7A 538783850 A/G - T C AG - IAAV6170 chr7A 538784357 T/C - A G AG + BS00046930_51 chr7A 539310696 T/C + C T CT + Kukri_c26517_691 chr7A 539325587 T/C - A G CT - BS00026056_51 chr7A 539408615 A/C + C A AC + BobWhite_c5506_1551 chr7A 539449409 A/G + A G AG + BS00043869_51 chr7A 539544151 T/C - A G CT - BS00043866_51 chr7A 539544264 A/G - C T CT + Ra_c18741_604 chr7A 539852330 A/G - T C CT + BS00049871_51 chr7A 539856482 T/C + T C CT + BS00064351_51 chr7A 540287138 A/G + G A AG + BobWhite_c66165_77 chr7A 540879860 T/C + T C AG - BS00022959_51 chr7A 544261588 T/C - A G AG + Kukri_c66328_222 chr7A 544263610 T/G - C A AC + BS00065250_51 chr7A 545543410 A/G - C T CT + Kukri_c1406_275 chr7A 546041513 A/G + A G CT - Kukri_c1406_490 chr7A 546041728 T/C + T C AG - Excalibur_c52798_196 chr7A 546043241 A/G - C T AG - RAC875_c14195_758 chr7A 553993418 A/G + A G CT - RAC875_c14195_1155 chr7A 553993815 T/C + T C CT + Kukri_c42742_319 chr7A 559388890 T/C - A G CT - CAP7_c12333_392 chr7A 561800218 T/C - G A CT - BS00041244_51 chr7A 562001673 T/C - A G CT - BS00024619_51 chr7A 562096445 A/G - T C AG - BS00082412_51 chr7A 562215833 T/C + T C CT + Ku_c62201_992 chr7A 562275477 A/G - T C AG - Excalibur_c51942_75 chr7A 564078312 T/C + C T AG - BS00040992_51 chr7A 566774093 T/C + T C CT + GENE-4616_496 chr7A 567005753 T/C + C T AG - RAC875_c114809_130 chr7A 569390805 A/G + A G AG + CAP7_c10038_214 chr7A 570123805 A/G - T C CT + IAAV942 chr7A 570182618 A/G - C T AG - Excalibur_c53632_204 chr7A 573677207 A/G + A G AG + RAC875_c52318_188 chr7A 574116386 T/C - A G AG + RAC875_c36250_185 chr7A 574127566 T/C - G A CT - Tdurum_contig56144_369 chr7A 575268716 T/C - G A AG + Tdurum_contig56144_277 chr7A 575268808 A/C - G T AC - BS00021668_51 chr7A 575273017 T/C + T C AG - Tdurum_contig46611_1061 chr7A 575436676 A/G + A G CT - Excalibur_c2359_1511 chr7A 576454314 T/G + T G AC - RAC875_c5330_1016 chr7A 577228381 A/G - T C AG - Ra_c4601_2417 chr7A 577778163 T/C + T C AG - BobWhite_c26529_106 chr7A 581375928 T/C + C T CT + Ra_c1227_2718 chr7A 582634378 A/C - G T AC - RAC875_rep_c105182_460 chr7A 585066092 A/C + C A AC + Kukri_c48125_714 chr7A 589755086 T/C + C T AG - Excalibur_c33866_120 chr7A 589755939 T/C + T C CT + Excalibur_c33866_404 chr7A 589756223 T/G + T G GT + IAAV1915 chr7A 589760730 T/C - A G CT - Ku_c28853_1518 chr7A 589760730 A/G + A G CT - Kukri_rep_c102463_862 chr7A 594459133 A/G - T C AG - BobWhite_c12343_253 chr7A 594554916 T/C - A G AG + Excalibur_c2736_159 chr7A 594557566 T/G - A C AC + Ex_c7397_545 chr7A 596039243 T/C - G A CT - Ex_c7397_535 chr7A 596039253 T/G - C A GT - Excalibur_rep_c79404_164 chr7A 596039713 T/C + T C CT + BS00002491_51 chr7A 596723091 T/C - A G AG + IAAV2329 chr7A 596744532 T/G - A C AC + Excalibur_c9617_292 chr7A 601518393 T/C - A G AG + BS00035807_51 chr7A 602233090 T/C + T C AG - BS00059928_51 chr7A 603091602 A/G + G A AG + BS00075525_51 chr7A 603568401 A/G + G A CT - RAC875_c44025_160 chr7A 604386521 T/C + C T CT + Kukri_c24646_396 chr7A 604388849 T/C + C T AG - tplb0057h24_734 chr7A 605163367 T/G + T G AC - BobWhite_c11374_530 chr7A 605774600 T/C + C T CT + IACX2907 chr7A 606322712 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles IAAV491 chr7A 607553665 A/G - C T AG - Kukri_rep_c101625_94 chr7A 607553665 T/C + C T AG - Ra_c72413_1987 chr7A 607556213 T/C + T C AG - IAAV6597 chr7A 608205374 A/G - C T CT + RAC875_rep_c104959_434 chr7A 608205859 A/C - G T AC - Ra_c104959_422 chr7A 608205871 T/C - A G CT - Excalibur_rep_c103301_387 chr7A 608398580 T/C - A G AG + Ku_c5901_1487 chr7A 609386068 A/G + A G CT - Excalibur_c96483_520 chr7A 610205741 A/C - G T GT + Excalibur_c96483_102 chr7A 610209084 T/C - A G AG + BS00003494_51 chr7A 610498048 T/C + T C CT + BS00092631_51 chr7A 610929541 T/C + C T AG - BS00022747_51 chr7A 610929716 T/C + C T CT + IAAV3025 chr7A 610930285 T/G + T G AC - IAAV6180 chr7A 610930285 A/C - T G AC - Kukri_c6676_172 chr7A 610934198 A/G - T C AG - Kukri_c8006_347 chr7A 611333850 A/C + C A AC + Kukri_rep_c105999_572 chr7A 611493830 T/C + C T CT + Tdurum_contig62357_527 chr7A 611493830 A/G - C T CT + IAAV3315 chr7A 611494033 T/G + G T AC - BS00065822_51 chr7A 611554042 A/G - T C CT + Ra_c8985_557 chr7A 611804514 T/C - G A CT - BS00027448_51 chr7A 612381112 T/C - A G CT - BS00027447_51 chr7A 612381130 T/C - G A CT - Jagger_c8331_69 chr7A 612381140 T/C - G A CT - GENE-4536_186 chr7A 612413175 A/G - T C AG - Kukri_c16922_106 chr7A 612767637 A/G + A G AG + tplb0045b22_854 chr7A 612769801 A/G - C T CT + BobWhite_c17095_237 chr7A 613728677 A/G - C T AG - Ku_c29856_132 chr7A 616431875 T/C + T C CT + Ku_c29856_174 chr7A 616431917 T/C + T C AG - BS00070857_51 chr7A 617578383 A/G + A G CT - BS00078324_51 chr7A 617687633 T/G - A C GT - BS00109319_51 chr7A 617690375 A/G + G A AG + BS00092381_51 chr7A 617855085 A/C + C A GT - CAP7_c1522_255 chr7A 617855304 T/G + T G AC - Tdurum_contig45680_434 chr7A 618083702 A/G - C T AG - RAC875_c57656_170 chr7A 619150795 T/C - G A AG + IACX5974 chr7A 620534090 A/T - A T AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RFL_Contig3669_1048 chr7A 620749310 T/C - G A AG + Excalibur_c20486_268 chr7A 621028419 T/C - G A AG + Excalibur_c20307_654 chr7A 621320529 A/G - C T AG - Ku_c2990_604 chr7A 621320909 T/G + G T GT + Ku_c2990_1939 chr7A 621322244 A/G + G A AG + Ku_c2990_1997 chr7A 621322302 A/C + A C GT - RAC875_c60161_145 chr7A 621583833 T/G NA NA NA GT NA flanks do not match reference at this position RAC875_c23935_84 chr7A 621584189 A/G - C T AG - RAC875_c60161_1223 chr7A 621585176 T/C + T C CT + RAC875_c22201_461 chr7A 623451405 A/G + A G AG + CAP11_c3781_95 chr7A 623456939 A/C + C A GT - Kukri_c22645_255 chr7A 624641321 T/C - A G CT - CAP12_c1717_222 chr7A 624687253 A/G - T C CT + BS00074166_51 chr7A 625629537 T/C + C T AG - RAC875_c10878_1223 chr7A 625639774 A/C - T G AC - Kukri_rep_c114803_98 chr7A 625738176 T/C - A G AG + Excalibur_c63900_724 chr7A 625739072 T/C - A G CT - Excalibur_c63900_433 chr7A 625739363 A/G - T C CT + Excalibur_c63900_370 chr7A 625739426 A/G - T C CT + BobWhite_c7082_184 chr7A 625742882 A/G + A G CT - RAC875_c7104_929 chr7A 625743294 A/G NA NA NA AG NA flanks do not match reference at this position BS00031887_51 chr7A 628236259 A/G - C T CT + RFL_Contig3869_808 chr7A 628866638 A/G - C T CT + Kukri_c46218_66 chr7A 629195392 T/C - A G AG + RAC875_c23665_68 chr7A 629801566 A/G + G A AG + Tdurum_contig32378_366 chr7A 630870568 T/G + T G AC - BS00048007_51 chr7A 631971993 T/C - A G CT - BobWhite_c1441_1123 chr7A 632587705 A/G - C T AG - IAAV4510 chr7A 634387268 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Excalibur_c46518_120 chr7A 634877221 T/C + T C CT + RAC875_c4501_2088 chr7A 634959322 T/C - A G AG + JD_c4813_987 chr7A 634961279 T/C - A G CT - BS00093156_51 chr7A 635035682 T/G + T G AC - BobWhite_c15497_609 chr7A 635493799 T/C - A G CT - BS00087413_51 chr7A 635495647 A/G - C T AG - BS00087411_51 chr7A 635495782 A/G - C T CT + BobWhite_c15497_199 chr7A 635495885 T/G - C A GT - Kukri_c4143_1055 chr7A 635500635 A/C - T G GT + BS00044234_51 chr7A 636890035 A/G - C T CT + Excalibur_rep_c108075_472 chr7A 638865768 T/C + C T CT + Kukri_c33363_393 chr7A 638866411 A/C + A C AC + BobWhite_rep_c49790_351 chr7A 641012381 T/C + T C CT + Ex_c40921_242 chr7A 641317410 A/G - T C AG - CAP7_c7296_88 chr7A 642736799 A/G + G A CT - BS00063458_51 chr7A 642737028 A/G - T C CT + Excalibur_c31216_744 chr7A 642946864 A/G - T C CT + GENE-4746_72 chr7A 642947116 A/G + G A AG + BobWhite_rep_c49367_405 chr7A 643422765 A/C - T G AC - Ra_c29886_494 chr7A 643423118 T/C + T C CT + BobWhite_c5235_710 chr7A 644117800 A/G - T C CT + Excalibur_c3298_533 chr7A 644343644 A/G + A G CT - RAC875_c27696_2299 chr7A 644612962 T/C + C T AG - Kukri_c53682_85 chr7A 644619148 T/C - A G AG + BobWhite_c46534_74 chr7A 645035537 T/C + C T AG - Ra_c8394_1381 chr7A 645092162 A/G + A G CT - IAAV6287 chr7A 645093960 A/C - G T GT + Kukri_c1552_1059 chr7A 645943943 A/G + A G AG + BS00103846_51 chr7A 646956140 T/C - G A CT - BS00022202_51 chr7A 646956290 A/G - T C AG - BobWhite_c53517_181 chr7A 647305950 T/G - A C AC + Tdurum_contig83837_251 chr7A 647305950 A/C + A C AC + BS00034085_51 chr7A 647307746 A/C + C A AC + BS00077891_51 chr7A 647308626 T/G - C A GT - BobWhite_c30461_131 chr7A 647933727 T/C - A G CT - Tdurum_contig8615_683 chr7A 657020668 T/C - G A AG + Tdurum_contig8615_370 chr7A 657020981 A/G - C T CT + Tdurum_contig8615_230 chr7A 657021122 A/C - T G GT + BS00066295_51 chr7A 657375437 A/G - T C AG - RAC875_c35723_106 chr7A 657716753 A/G NA NA NA CT NA flanks do not match reference at this position BS00093512_51 chr7A 659371015 T/C + T C AG - Tdurum_contig61966_1069 chr7A 659371015 A/G - T C AG - Excalibur_c22219_254 chr7A 659374297 T/C - G A AG + BS00089939_51 chr7A 659553622 T/C - A G CT - Tdurum_contig14265_509 chr7A 659553622 A/G + A G CT - Tdurum_contig14265_689 chr7A 659553802 A/G + A G AG + Kukri_rep_c74538_62 chr7A 660550514 A/C + A C GT - Excalibur_c60995_109 chr7A 660554443 T/C + C T CT + Tdurum_contig41918_2140 chr7A 661164590 A/G NA NA NA CT NA flanks do not match reference at this position RAC875_c5019_804 chr7A 663540674 T/C - A G CT - D_contig26521_701 chr7A 663603629 A/G - T C AG - Kukri_c24366_104 chr7A 663957979 A/C + A C GT - Ex_c24988_401 chr7A 667222267 T/C + T C CT + IACX2471 chr7A 669728991 A/G + A G CT - BS00094965_51 chr7A 669729091 A/C + C A AC + RAC875_c37085_317 chr7A 670245171 A/G - C T AG - BobWhite_c149_3064 chr7A 670767495 T/C - A G CT - BobWhite_c5602_291 chr7A 670818920 T/G + T G AC - Kukri_c25451_119 chr7A 670959758 A/G - C T AG - RAC875_c65908_1080 chr7A 670960481 A/G + A G CT - BS00023128_51 chr7A 671218901 A/G - T C CT + Ku_c11884_1220 chr7A 671466914 A/G - T C AG - BS00021657_51 chr7A 672032033 T/C + T C CT + Excalibur_c95707_285 chr7A 672042243 T/C - A G CT - BS00026622_51 chr7A 674272225 T/G + G T GT + RAC875_c19111_628 chr7A 674277105 T/C - G A AG + BS00004257_51 chr7A 674801909 T/G + T G AC - IACX4216 chr7A 674801909 A/C - T G AC - tplb0045p11_893 chr7A 675235632 T/C - G A CT - Excalibur_c14451_1313 chr7A 675268151 A/G - C T AG - Excalibur_c14451_389 chr7A 675269395 T/C NA NA NA AG NA flanks do not match reference at this position BS00066468_51 chr7A 675388797 T/C - G A CT - RAC875_c46980_148 chr7A 675396203 A/C + A C AC + Ra_c1834_2501 chr7A 675506390 T/C - A G CT - RAC875_c1834_2299 chr7A 675506592 T/C - G A CT - RAC875_c13093_86 chr7A 675508361 A/G + A G CT - RAC875_c63057_601 chr7A 675587626 T/G + G T AC - IACX7848 chr7A 677822559 A/C - G T AC - BS00023027_51 chr7A 678145123 T/C - G A CT - Kukri_c16852_96 chr7A 678581867 A/G + G A AG + Kukri_c16852_314 chr7A 678582085 A/G + A G AG + IAAV8644 chr7A 679757313 A/G + A G AG + Ra_c70829_369 chr7A 679840299 T/C NA NA NA CT NA flanks do not match reference at this position Ra_c70829_1329 chr7A 679841800 A/G + G A AG + Ra_c70829_1425 chr7A 679841896 T/G + G T AC - IAAV5578 chr7A 679877165 A/G + G A AG + IAAV9161 chr7A 679896464 T/C - A G CT - RAC875_c105310_155 chr7A 679896953 A/G - T C AG - Tdurum_contig29834_165 chr7A 679898217 A/G + G A AG + Excalibur_c17899_352 chr7A 680341686 T/C + T C CT + Kukri_c40735_318 chr7A 683486210 T/G - C A AC + Excalibur_c60238_251 chr7A 686108809 T/C - A G CT - RAC875_rep_c119304_226 chr7A 688688301 T/C - A G CT - RAC875_rep_c105769_150 chr7A 688967223 T/G + T G AC - Excalibur_c113078_320 chr7A 688967553 T/C + T C CT + BS00065529_51 chr7A 689260146 A/G + A G AG + Kukri_c45749_158 chr7A 691130767 A/C - T G GT + RFL_Contig6074_1058 chr7A 691535765 A/G - C T CT + GENE-4672_55 chr7A 691603442 A/G + A G CT - Excalibur_c1791_819 chr7A 692128497 T/C - A G CT - RAC875_c80253_153 chr7A 692521641 A/G - C T AG - BobWhite_c21838_152 chr7A 692784727 T/C - A G AG + Excalibur_c3188_1352 chr7A 692879432 T/G + G T AC - Kukri_c31449_620 chr7A 692880892 A/G + G A CT - BS00053365_51 chr7A 692907393 T/C - G A AG + Excalibur_rep_c102881_88 chr7A 694545845 A/G + G A AG + GENE-4579_458 chr7A 696030930 T/C - A G CT - IACX6080 chr7A 696802587 A/C - G T AC - Ku_c30941_113 chr7A 696805689 A/C + C A GT - Kukri_c31824_636 chr7A 696977689 T/C + T C CT + Tdurum_contig31699_276 chr7A 696977689 A/G - T C AG - BobWhite_c41378_234 chr7A 699293413 T/C + C T CT + Tdurum_contig83498_219 chr7A 699296193 T/G - A C AC + Kukri_c26118_583 chr7A 699299876 T/C - A G AG + Tdurum_contig54832_139 chr7A 700677576 T/C - A G CT - Ra_c74686_615 chr7A 700702237 A/G + A G CT - Kukri_c9683_150 chr7A 700705060 A/G - T C CT + Excalibur_c61603_1209 chr7A 700705343 T/C - A G AG + Excalibur_c61603_1138 chr7A 700705414 A/G - T C AG - Excalibur_c61603_1052 chr7A 700705500 A/G - C T CT + RAC875_c59682_222 chr7A 700706505 T/C + C T CT + Tdurum_contig61864_1352 chr7A 700706991 A/G + G A CT - Tdurum_contig16065_567 chr7A 700708397 A/G + A G CT - RAC875_c4682_646 chr7A 700708427 A/G - C T AG - Excalibur_c50408_663 chr7A 700710154 A/G + G A AG + IAAV2580 chr7A 701531501 T/C NA NA NA CT NA flanks do not match reference at this position Ku_c68368_1724 chr7A 701638033 T/C - A G CT - Kukri_rep_c98227_230 chr7A 701638186 A/G + G A AG + Ku_c68368_1447 chr7A 701638310 T/C - A G AG + Kukri_rep_c98227_390 chr7A 701638346 A/G + G A AG + Excalibur_rep_c66918_307 chr7A 701638770 A/G - T C CT + tplb0032g12_1241 chr7A 701683510 T/C + T C CT + GENE-4717_796 chr7A 701769865 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c42185_156 chr7A 701878090 T/C - A G CT - Excalibur_c20018_214 chr7A 703561929 T/C - A G AG + BobWhite_c13400_608 chr7A 705125287 A/G - C T CT + BobWhite_c13400_229 chr7A 705127000 A/G - C T CT + Kukri_c24148_254 chr7A 705270901 A/G + A G CT - Kukri_c24148_1414 chr7A 705272973 T/C + T C AG - Excalibur_c10388_1379 chr7A 705688328 T/C - A G CT - Kukri_rep_c82239_85 chr7A 706907036 A/G + A G CT - Kukri_c855_2107 chr7A 708138675 A/G - T C CT + IAAV6058 chr7A 708138732 A/C + C A GT - Kukri_c855_1907 chr7A 708138875 T/C - A G AG + RAC875_rep_c115178_103 chr7A 708138973 A/G + A G AG + IAAV6961 chr7A 708139014 T/C + C T CT + BS00111016_51 chr7A 708139129 T/C + T C CT + BS00110681_51 chr7A 708139206 T/C + C T AG - TA002896-0591 chr7A 708143204 T/C NA NA NA CT NA flanks do not match reference at this position BobWhite_c32347_219 chr7A 708145187 A/G - C T AG - Excalibur_c24486_947 chr7A 708145659 A/G + G A AG + CAP11_c3666_426 chr7A 708624800 T/G - A C GT - BS00023207_51 chr7A 708625039 A/G - T C CT + BS00003730_51 chr7A 708625171 A/C - T G AC - IAAV6807 chr7A 708665352 T/C + NA NA AG NA reference base A not among SNP alleles IAAV3676 chr7A 709118648 T/C - A G CT - CAP7_rep_c5949_55 chr7A 709122554 A/C - G T GT + CAP7_c950_137 chr7A 709122729 A/G - T C CT + BS00060187_51 chr7A 709142543 A/C - G T AC - IAAV6119 chr7A 709405453 A/C - NA NA AC NA reference base C not among SNP alleles BobWhite_c46250_98 chr7A 709405507 A/C - G T GT + RAC875_rep_c85189_127 chr7A 709407032 T/C - G A CT - Kukri_rep_c70199_638 chr7A 709407065 A/C - G T AC - RAC875_c76318_145 chr7A 709407376 A/G - T C CT + GENE-4528_1252 chr7A 709407732 A/G + G A AG + BobWhite_rep_c54108_202 chr7A 709409121 T/C - A G CT - BobWhite_c25105_507 chr7A 709639574 T/C - A G CT - BS00022811_51 chr7A 709639589 T/C + T C CT + Kukri_c43981_300 chr7A 709639640 T/C + T C AG - Tdurum_contig27856_230 chr7A 711607683 A/G + G A AG + Ex_c24796_2499 chr7A 712056803 T/C - G A CT - Ku_c19745_892 chr7A 712058609 A/G - T C CT + Ku_c19745_833 chr7A 712058668 T/C - A G CT - Ra_c65729_683 chr7A 712058776 T/C - A G AG + Excalibur_rep_c105674_99 chr7A 712307115 T/C + T C AG - Excalibur_rep_c105674_315 chr7A 712307419 T/C + T C CT + BS00011622_51 chr7A 712309034 T/G - A C GT - IACX13137 chr7A 712309297 T/C - G A CT - Tdurum_contig59836_250 chr7A 712417005 T/C + C T CT + RAC875_rep_c83934_91 chr7A 712417095 A/G - T C AG - RFL_Contig4417_602 chr7A 712771148 A/G + A G CT - BS00104760_51 chr7A 712771172 T/C + C T CT + IAAV416 chr7A 713743180 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Ex_c56664_126 chr7A 713743447 A/G + A G AG + Excalibur_c3286_103 chr7A 715224656 A/C + A C AC + Tdurum_contig59467_433 chr7A 715692093 A/C + C A AC + RAC875_rep_c70399_328 chr7A 715692976 T/C - A G AG + RAC875_c2532_64 chr7A 715700809 T/C - A G AG + IAAV5550 chr7A 716246600 A/C + A C GT - BS00084193_51 chr7A 716247644 T/C + C T CT + Kukri_c28968_130 chr7A 716404423 A/G + G A AG + BS00105531_51 chr7A 717036848 T/C - G A CT - RAC875_c7112_816 chr7A 717041121 T/C + T C CT + BobWhite_c25527_133 chr7A 717090190 A/G + A G AG + Tdurum_contig97505_172 chr7A 717090199 A/C - G T AC - BobWhite_c12355_1548 chr7A 717090250 A/G - T C AG - GENE-4715_311 chr7A 717091031 A/G + A G AG + Excalibur_c53387_637 chr7A 717091550 A/G - T C CT + BS00080311_51 chr7A 717092367 A/G + G A AG + BS00076120_51 chr7A 717823226 T/C - G A CT - Ex_c499_767 chr7A 717833540 A/G + G A AG + Tdurum_contig12454_585 chr7A 719562881 A/C NA NA NA AC NA flanks do not match reference at this position Kukri_c64163_128 chr7A 719562899 T/G + G T AC - Kukri_c9728_1171 chr7A 719567282 A/G - T C CT + Excalibur_c46453_216 chr7A 719568260 T/C - A G CT - Excalibur_c46453_144 chr7A 719568332 A/G - C T AG - IAAV2968 chr7A 719577254 A/G - C T AG - Tdurum_contig93328_869 chr7A 719577263 A/G - T C AG - BS00002510_51 chr7A 721000076 T/C - G A AG + Excalibur_c6101_608 chr7A 721174928 T/C - A G CT - BS00067682_51 chr7A 721223744 T/C + C T CT + RAC875_c90330_82 chr7A 721224063 A/C - T G AC - BS00068033_51 chr7A 721417500 A/C - G T GT + BS00068032_51 chr7A 721417546 A/G - C T AG - Kukri_c51453_406 chr7A 721707504 T/C + C T CT + BobWhite_rep_c50003_377 chr7A 721915729 A/G + A G CT - BS00061911_51 chr7A 722573912 A/C - G T AC - Kukri_rep_c68371_1242 chr7A 723260844 A/G NA NA NA CT NA flanks do not match reference at this position TA001664-1167 chr7A 723263688 A/G NA NA NA AG NA flanks do not match reference at this position tplb0031i24_1212 chr7A 723296553 T/G - A C AC + Kukri_c18148_1288 chr7A 724128123 T/C - A G AG + Kukri_c18148_913 chr7A 724128642 T/C - A G AG + Kukri_rep_c69223_241 chr7A 725928143 T/C - G A AG + RAC875_c50676_588 chr7A 725934179 T/G - A C GT - BS00022137_51 chr7A 729397498 A/G - T C AG - BS00020236_51 chr7A 730426156 T/C + T C AG - RAC875_c6562_745 chr7A 730431483 T/C - G A CT - IACX5996 chr7A 730431559 T/C - G A CT - Kukri_c5265_693 chr7A 730432928 T/C + T C AG - Tdurum_contig46717_2021 chr7A 731267923 T/C - G A CT - Kukri_c2348_2340 chr7A 731268586 A/G + A G AG + Kukri_c11530_92 chr7A 731270573 T/C - A G CT - Kukri_c11530_60 chr7A 731270605 T/C - A G AG + RFL_Contig2814_604 chr7A 731272684 T/C - G A CT - Kukri_c2022_784 chr7A 731981776 A/G + A G CT - Kukri_c92030_109 chr7A 731987449 T/C + C T AG - Tdurum_contig10827_492 chr7A 732089301 T/C + C T CT + RAC875_c525_106 chr7A 733333995 A/G - T C AG - Ra_c956_2318 chr7A 733362422 T/C - A G CT - BS00023200_51 chr7A 733362700 A/G - T C CT + BS00071736_51 chr7A 733367384 T/G - C A GT - Kukri_rep_c109206_383 chr7A 735841520 T/G - A C GT - BobWhite_c35334_247 chr7A 736432211 A/C NA NA NA GT NA flanks do not match reference at this position Tdurum_contig50628_448 chr7A 736520902 A/C - T G GT + RAC875_c18550_65 chr7A 736688998 T/C + C T AG - BS00025580_51 chr7B 426504 T/G + G T GT + BS00085194_51 chr7B 426894 A/G - C T CT + Kukri_c542_1538 chr7B 429714 T/C NA NA NA CT NA flanks do not match reference at this position BS00022562_51 chr7B 430216 A/G - C T AG - RFL_Contig6075_618 chr7B 605173 T/C + T C CT + RFL_Contig6075_1128 chr7B 605975 A/G + A G AG + Tdurum_contig57324_104 chr7B 606356 T/C - A G AG + RAC875_c17182_600 chr7B 1254575 A/G - T C CT + Kukri_rep_c71778_644 chr7B 1254684 T/C - A G AG + Kukri_c46310_84 chr7B 1255171 A/G - T C AG - Kukri_c3734_400 chr7B 1255728 A/G + G A CT - Kukri_c3734_438 chr7B 1255766 A/G + A G AG + Kukri_c3734_892 chr7B 1256220 A/G + A G CT - RAC875_rep_c105927_650 chr7B 1256449 A/G - T C AG - Excalibur_c53111_215 chr7B 1258238 A/G - T C CT + Kukri_c21384_1475 chr7B 1280338 T/C - A G AG + Jagger_c3075_99 chr7B 3336832 T/G + G T GT + Excalibur_c8486_419 chr7B 3338714 T/C + C T AG - BS00022127_51 chr7B 3541590 A/G + G A AG + BS00076402_51 chr7B 3794576 T/C + C T CT + Tdurum_contig25857_274 chr7B 3795334 T/C - G A CT - Kukri_c41117_824 chr7B 3848336 A/C - T G GT + Tdurum_contig10861_942 chr7B 3848751 A/G + A G CT - RFL_Contig801_2124 chr7B 3848966 T/C + C T CT + Tdurum_contig98005_345 chr7B 4908005 A/G - T C CT + Tdurum_contig98005_272 chr7B 4908078 A/G - T C AG - Tdurum_contig61255_86 chr7B 4909060 A/G - T C AG - RAC875_c23816_266 chr7B 4910198 T/C - A G AG + Jagger_c5275_99 chr7B 5515190 T/C - A G AG + Tdurum_contig85266_280 chr7B 6153898 T/C - G A CT - Excalibur_c50044_749 chr7B 6179392 A/G + A G AG + Excalibur_c3423_1170 chr7B 6372285 A/G + A G CT - IAAV6833 chr7B 6372540 A/C - T G GT + Tdurum_contig30677_66 chr7B 6393757 T/C + T C AG - IACX198 chr7B 9755243 T/G + T G GT + BS00081132_51 chr7B 11962600 A/G + G A AG + BobWhite_c4253_568 chr7B 14063847 A/G + G A AG + IAAV5530 chr7B 15304729 T/C - A G AG + BobWhite_c44404_312 chr7B 17656905 A/G + A G CT - CAP12_c1816_325 chr7B 21668998 T/C + T C AG - Ex_c101666_634 chr7B 24060529 T/G - C A AC + Tdurum_contig10108_246 chr7B 27063831 A/C + A C GT - Excalibur_c14925_444 chr7B 28314340 A/G + A G AG + RAC875_c32923_95 chr7B 28315537 T/C + T C AG - TA002655-1964 chr7B 28501207 T/G NA NA NA AC NA flanks do not match reference at this position BobWhite_c36693_210 chr7B 33598532 T/C + C T CT + Tdurum_contig27634_93 chr7B 35082196 A/G + A G CT - Excalibur_c25991_184 chr7B 35669809 T/C + C T AG - RAC875_c26328_75 chr7B 36456046 A/G - T C AG - RAC875_c46751_112 chr7B 36490121 T/C + C T CT + BS00083806_51 chr7B 37361211 T/C + C T AG - IACX3991 chr7B 37854718 T/C - G A CT - BS00022056_51 chr7B 37854795 A/G - C T AG - RAC875_c10672_440 chr7B 40354210 A/G - C T CT + Ra_c71101_755 chr7B 42030233 T/C + C T CT + GENE-4376_439 chr7B 42030958 T/C + C T AG - GENE-4376_518 chr7B 42031033 T/C + T C AG - Excalibur_rep_c67369_364 chr7B 42031196 T/C + C T AG - Kukri_c24895_558 chr7B 42077344 A/G - C T AG - Kukri_c24895_402 chr7B 42077500 A/G - C T CT + IAAV3215 chr7B 43192176 A/G + A G AG + Kukri_c31419_399 chr7B 43545375 A/G - C T CT + Excalibur_c20062_195 chr7B 43877858 T/C + T C CT + BS00031746_51 chr7B 43882175 A/G + A G AG + BS00054881_51 chr7B 44623104 T/C - G A AG + BS00064344_51 chr7B 44878503 T/C - G A AG + Kukri_c35354_321 chr7B 44941961 T/C - G A AG + BS00069075_51 chr7B 45175588 A/C - G T AC - Kukri_rep_c72909_657 chr7B 46351517 A/G + G A AG + Tdurum_contig57370_82 chr7B 46886985 T/C + T C CT + Tdurum_contig57370_318 chr7B 46887221 T/C + T C CT + Tdurum_contig46877_488 chr7B 46999521 T/C - G A CT - Excalibur_c25545_249 chr7B 46999659 A/G + G A CT - Jagger_c9314_100 chr7B 46999836 T/C + C T CT + Tdurum_contig46877_173 chr7B 46999836 A/G - C T AG - Tdurum_contig46877_84 chr7B 46999925 A/G - C T CT + Tdurum_contig46877_76 chr7B 46999933 A/G - C T AG - Kukri_c36225_133 chr7B 48769162 A/G + A G AG + Tdurum_contig81683_217 chr7B 51068018 T/C + T C CT + Tdurum_contig11028_236 chr7B 52565461 A/G - T C AG - RAC875_c33934_341 chr7B 52910515 T/C - G A CT - Tdurum_contig49572_643 chr7B 53646858 T/C + C T CT + Tdurum_contig51024_1234 chr7B 53647651 T/C NA NA NA AG NA flanks do not match reference at this position Kukri_c15310_755 chr7B 53648240 A/G + A G AG + Excalibur_c54242_704 chr7B 54787902 A/G - C T CT + BobWhite_c39364_231 chr7B 54788606 A/G - T C AG - BobWhite_c4481_96 chr7B 58249132 T/C + C T AG - Kukri_c19823_491 chr7B 58539901 A/G + G A AG + Kukri_c22450_963 chr7B 58542061 A/G + A G AG + Ku_c665_985 chr7B 58727993 A/G - T C AG - BS00021683_51 chr7B 59179319 A/G - T C AG - RAC875_c77603_334 chr7B 59607406 T/C - A G CT - Jagger_c2161_211 chr7B 59607669 A/C - T G AC - Excalibur_c22903_710 chr7B 59607928 A/C + A C GT - BS00021695_51 chr7B 59632081 A/C + A C AC + GENE-4862_901 chr7B 59647615 A/G + G A AG + GENE-4862_1014 chr7B 59647704 A/G + G A CT - GENE-4862_1104 chr7B 59647790 T/C + C T CT + GENE-4826_641 chr7B 61557781 A/G + A G AG + GENE-4337_558 chr7B 61627599 A/C - T G AC - BS00074083_51 chr7B 62687199 A/G + A G AG + BS00011186_51 chr7B 63568829 A/G + A G CT - BS00010616_51 chr7B 63569874 T/C - A G CT - BobWhite_c10448_80 chr7B 66979341 A/C - G T AC - RAC875_rep_c105494_293 chr7B 68344983 A/G + G A AG + Tdurum_contig20094_458 chr7B 72288283 A/G - T C AG - RAC875_c92464_53 chr7B 72452016 A/G + G A CT - Tdurum_contig44261_127 chr7B 72996414 T/G + G T AC - Tdurum_contig44261_795 chr7B 72997198 A/G + G A AG + Tdurum_contig32954_195 chr7B 73134221 T/C + T C CT + RAC875_c30123_913 chr7B 78246850 A/C + C A AC + BS00084788_51 chr7B 81423572 A/C - T G AC - BS00022550_51 chr7B 81423597 A/G - C T AG - GENE-4273_67 chr7B 81685349 A/G + A G CT - BS00024215_51 chr7B 83030077 T/C - G A AG + CAP7_c10566_170 chr7B 83912264 A/G + A G CT - BobWhite_rep_c64768_264 chr7B 84183792 T/C + T C CT + BS00079019_51 chr7B 84184072 A/G + A G CT - Tdurum_contig84962_266 chr7B 84186271 T/C - G A AG + BS00022841_51 chr7B 84186281 A/G + G A AG + Tdurum_contig84962_256 chr7B 84186281 T/C - G A CT - IAAV7544 chr7B 84215316 A/G - C T AG - IAAV3391 chr7B 84215789 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c14215_217 chr7B 87403120 T/G - A C GT - Excalibur_c54967_930 chr7B 88636265 A/G - T C AG - BobWhite_c41441_185 chr7B 90194603 T/G + G T AC - RAC875_c53709_351 chr7B 94271868 A/G + G A AG + CAP8_c195_441 chr7B 94629947 T/C - G A CT - BS00064483_51 chr7B 94994743 T/C + C T CT + BobWhite_c11119_83 chr7B 100027265 A/G + G A CT - CAP12_rep_c4520_207 chr7B 100409898 A/G + G A CT - IACX2382 chr7B 103883379 A/C - G T GT + GENE-1477_748 chr7B 104301384 T/G + T G GT + RAC875_c54366_845 chr7B 105836470 A/G + A G AG + Kukri_c29304_447 chr7B 105836528 T/G + T G GT + BobWhite_c14812_828 chr7B 106339881 A/G - C T AG - CAP11_c106_97 chr7B 109041633 T/G + G T GT + Ex_c39052_1533 chr7B 109181974 T/G - C A GT - Kukri_c14596_265 chr7B 109679726 A/G + G A AG + Tdurum_contig68347_605 chr7B 111904029 A/G - T C CT + BS00067599_51 chr7B 115244466 A/G - C T CT + BS00062967_51 chr7B 115404535 T/G - C A AC + RAC875_c26464_514 chr7B 115811431 A/G + A G CT - BobWhite_c8294_482 chr7B 115813971 A/G + A G AG + Tdurum_contig51087_573 chr7B 120169954 T/C - G A CT - RFL_Contig124_558 chr7B 121054037 T/C + T C AG - RAC875_rep_c74622_456 chr7B 125134245 A/G - C T AG - RAC875_c3492_2195 chr7B 125135889 T/C - G A CT - Excalibur_c11146_1322 chr7B 126556506 T/C - G A CT - RAC875_rep_c116436_106 chr7B 126557665 A/G - T C AG - RAC875_rep_c72877_159 chr7B 126559179 A/G + G A CT - GENE-4867_119 chr7B 127022824 T/C + C T CT + GENE-4507_56 chr7B 129535415 A/G + G A AG + GENE-4507_113 chr7B 129535468 A/G + A G CT - Kukri_rep_c115333_249 chr7B 131742575 A/G + G A CT - Kukri_c53648_585 chr7B 136314011 T/G - C A GT - RAC875_c19552_137 chr7B 137788615 A/G + G A AG + Ex_c2857_1303 chr7B 137799098 T/C - A G AG + Ku_c1839_202 chr7B 141072320 T/C + T C CT + RAC875_c3876_1123 chr7B 141074931 A/G + G A AG + BobWhite_c20290_226 chr7B 141963816 A/G - T C AG - Ra_c11468_305 chr7B 143325450 T/C - G A CT - Ex_c68356_765 chr7B 143325519 T/C - G A CT - Ra_c38371_1171 chr7B 143328388 T/G + G T GT + IAAV3646 chr7B 144662206 A/G + G A AG + RAC875_rep_c73990_174 chr7B 144662206 T/C - G A AG + RFL_Contig5734_2039 chr7B 146058387 A/C - G T GT + Tdurum_contig15991_260 chr7B 146058387 T/G + G T GT + RAC875_rep_c107786_171 chr7B 146816934 A/G + G A CT - RAC875_rep_c107786_249 chr7B 146817012 A/G + A G CT - Tdurum_contig9619_123 chr7B 146818530 T/G - A C GT - Tdurum_contig9619_68 chr7B 146818585 A/G - T C CT + Tdurum_contig19526_331 chr7B 147162823 T/C - G A CT - Tdurum_contig4901_527 chr7B 148226166 A/G - T C CT + Excalibur_c50328_368 chr7B 148951398 A/G - C T CT + Kukri_c99538_516 chr7B 152075227 A/C - G T GT + BS00073602_51 chr7B 153178076 T/C + C T AG - Excalibur_c21854_1154 chr7B 154771470 A/G + G A AG + Kukri_c57677_355 chr7B 155727232 A/G - T C AG - Kukri_c61972_419 chr7B 156431764 A/G + G A AG + RFL_Contig5098_1248 chr7B 156707664 T/C + C T CT + BS00088495_51 chr7B 157216718 A/G - T C AG - Kukri_c56220_199 chr7B 158939593 A/G + G A AG + Kukri_c56220_237 chr7B 158939631 T/C + C T AG - IAAV503 chr7B 160484676 T/C - A G CT - Tdurum_contig51313_408 chr7B 162779227 A/C + C A GT - BS00031611_51 chr7B 162780891 T/C + C T CT + Tdurum_contig47854_182 chr7B 162780891 A/G - C T CT + BS00031612_51 chr7B 162780931 A/G + G A AG + Tdurum_contig47854_142 chr7B 162780931 T/C - G A CT - GENE-4790_279 chr7B 164100944 A/C - T G GT + RFL_Contig1599_906 chr7B 167686707 T/C - A G CT - IAAV5646 chr7B 171995856 A/C - T G GT + RAC875_c99084_580 chr7B 172572323 A/G - C T AG - IAAV4869 chr7B 178424751 A/G - T C CT + IAAV285 chr7B 179251876 C/G - C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles RAC875_c11731_112 chr7B 179255425 T/G - C A GT - BS00072941_51 chr7B 182142503 A/G + G A AG + BS00028793_51 chr7B 184983945 T/C + C T AG - Kukri_c78330_327 chr7B 185624086 A/G + A G AG + Tdurum_contig57220_173 chr7B 190260450 T/G - A C AC + BS00095819_51 chr7B 190800807 T/C - A G CT - Tdurum_contig75931_1967 chr7B 190801341 T/C + T C AG - Excalibur_c27158_671 chr7B 194925725 T/C - G A AG + BS00023763_51 chr7B 195425128 T/G + G T AC - Tdurum_contig42813_935 chr7B 195425308 A/G - C T CT + Tdurum_contig42813_397 chr7B 195427177 A/C - T G AC - BobWhite_c15796_315 chr7B 195427289 T/C + T C CT + Tdurum_contig42813_285 chr7B 195427289 A/G - T C CT + BS00067540_51 chr7B 196380833 A/C + C A AC + BS00015653_51 chr7B 196907979 T/G + G T AC - tplb0037k05_1475 chr7B 198552006 T/C + C T AG - BS00031141_51 chr7B 198610813 T/G - C A GT - BobWhite_c16787_205 chr7B 198614133 T/C - G A CT - RAC875_rep_c70874_1920 chr7B 198938672 T/C - A G AG + RAC875_rep_c70874_1309 chr7B 198939283 T/C - G A CT - RAC875_c23724_118 chr7B 198979978 A/G + G A AG + RAC875_c23724_182 chr7B 198980042 T/C + C T CT + tplb0022m23_742 chr7B 203029266 T/C - G A CT - Kukri_rep_c73612_444 chr7B 203745013 A/G + G A CT - RAC875_c315_1309 chr7B 210331529 A/G + G A CT - RAC875_c102640_92 chr7B 211420153 T/G + G T AC - BobWhite_rep_c63166_725 chr7B 213251467 T/C + T C AG - RAC875_s120306_162 chr7B 215006356 A/G + A G CT - RAC875_c27722_73 chr7B 217799931 T/C + T C AG - RAC875_c19880_1414 chr7B 218561592 A/G - C T CT + RAC875_rep_c106698_86 chr7B 220134471 T/C + T C AG - RAC875_c18513_376 chr7B 222700520 A/G + G A AG + BobWhite_c44558_325 chr7B 223181797 T/C - G A CT - BobWhite_c18672_103 chr7B 223812314 A/G - T C AG - Excalibur_c39238_158 chr7B 225509836 A/C - T G AC - RAC875_c65686_126 chr7B 230344641 A/G + G A CT - RAC875_rep_c71932_86 chr7B 230345016 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_rep_c113231_244 chr7B 231722143 T/C - G A AG + CAP7_c782_374 chr7B 232748664 A/G + G A CT - BS00066613_51 chr7B 234381494 T/G + G T GT + RFL_Contig2648_1070 chr7B 236785293 A/G + G A CT - BobWhite_c12889_390 chr7B 237490093 T/C + T C CT + BobWhite_c29953_89 chr7B 238527329 T/C - A G CT - Excalibur_c41549_276 chr7B 243566481 T/C + C T AG - Excalibur_c29607_442 chr7B 244278190 T/C + C T AG - Excalibur_c21908_97 chr7B 245855407 T/C + T C AG - BS00068508_51 chr7B 265441775 A/G + G A AG + Ra_c9932_515 chr7B 270534866 A/G - T C CT + Excalibur_c45099_1048 chr7B 296356520 A/G + G A AG + IAAV3268 chr7B 325980744 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles TA004043-0135 chr7B 327145520 A/C - T G GT + Ku_c24482_1132 chr7B 328969644 T/C - G A AG + Kukri_c14134_415 chr7B 328973307 T/C - A G AG + TA003034-1922 chr7B 329033870 T/C + T C CT + Excalibur_rep_c72097_583 chr7B 329082296 A/G - T C CT + BS00062785_51 chr7B 331061079 A/G + A G AG + Kukri_rep_c68742_543 chr7B 332807428 T/C NA NA NA CT NA flanks do not match reference at this position BS00040415_51 chr7B 334806240 A/G - T C CT + RAC875_c5965_317 chr7B 337638663 A/G - T C CT + tplb0025i03_2004 chr7B 351577567 A/G + A G CT - Ku_c32389_1009 chr7B 362541622 T/G + G T GT + Tdurum_contig11521_102 chr7B 377158436 T/C + T C AG - BobWhite_rep_c49390_455 chr7B 384373544 T/C - G A AG + Kukri_rep_c109239_223 chr7B 393317429 T/C NA NA NA CT NA flanks do not match reference at this position CAP7_c143_498 chr7B 394399084 T/C - A G AG + RAC875_c9715_679 chr7B 411058977 T/C - G A AG + Kukri_c31305_75 chr7B 426881359 A/C - G T GT + Tdurum_contig50984_553 chr7B 426881589 A/G + A G AG + BobWhite_c17544_571 chr7B 438789407 A/G + A G AG + BobWhite_c17544_776 chr7B 438789930 T/G NA NA NA AC NA flanks do not match reference at this position Kukri_c1853_1975 chr7B 439111222 T/C + T C CT + tplb0031m07_1342 chr7B 440005332 T/C - A G AG + Tdurum_contig43945_501 chr7B 441507001 T/C - G A AG + BobWhite_c45353_232 chr7B 441510009 T/C + T C CT + Tdurum_contig44171_1744 chr7B 441511134 A/C - T G AC - CAP12_c8025_110 chr7B 450280103 T/C + C T CT + IAAV2037 chr7B 450578869 A/G - T C AG - Excalibur_c49622_60 chr7B 450641795 A/G + A G CT - Excalibur_rep_c103688_258 chr7B 450642379 T/G NA NA NA GT NA flanks do not match reference at this position CAP12_rep_c4929_51 chr7B 451078548 A/G + G A CT - Kukri_c4424_1081 chr7B 451080832 T/C - A G CT - JD_c5200_835 chr7B 451935254 T/C - A G AG + TA001679-0356 chr7B 451935254 T/C - A G AG + Tdurum_contig48695_527 chr7B 457384008 T/C - G A CT - RAC875_c7610_81 chr7B 457788083 A/G - C T AG - Tdurum_contig81318_116 chr7B 467423060 T/C + T C CT + Excalibur_c17078_400 chr7B 467974289 A/G NA NA NA AG NA flanks do not match reference at this position BS00062829_51 chr7B 475663888 A/G - T C CT + BobWhite_rep_c49196_319 chr7B 483774369 A/G - T C AG - Kukri_c3997_1400 chr7B 483775580 A/G + A G AG + RFL_Contig3306_194 chr7B 483776058 A/G - T C CT + Excalibur_c16687_476 chr7B 488410704 T/C - A G CT - Excalibur_c16687_380 chr7B 488410800 A/G - C T CT + Kukri_c48870_115 chr7B 488410867 A/G - T C CT + BobWhite_c42974_184 chr7B 488704345 T/G - A C AC + BobWhite_rep_c49587_1290 chr7B 488704491 T/C - G A CT - BS00053287_51 chr7B 491394245 A/G - C T CT + BS00053286_51 chr7B 491394251 A/C - G T GT + BS00068060_51 chr7B 491394496 A/G + A G AG + BS00065626_51 chr7B 491397648 A/G + G A CT - Kukri_c78788_84 chr7B 491398541 T/C + T C CT + Excalibur_c22667_292 chr7B 492740690 A/G NA NA NA AG NA flanks do not match reference at this position Excalibur_c15029_144 chr7B 497883295 A/G - C T AG - BS00044443_51 chr7B 498149722 T/C + C T AG - Excalibur_rep_c102136_270 chr7B 498519645 T/C + T C AG - IAAV1218 chr7B 498888175 T/C - A G CT - BS00048090_51 chr7B 498970838 A/G + G A CT - Tdurum_contig54833_200 chr7B 505570633 A/C + A C GT - Tdurum_contig43589_869 chr7B 505938925 A/G - T C CT + Tdurum_contig43589_825 chr7B 505938969 T/C - A G CT - RAC875_c7474_1661 chr7B 505939784 T/C + C T CT + Tdurum_contig43589_340 chr7B 505939784 A/G - C T CT + BobWhite_rep_c63008_468 chr7B 506561102 A/C + A C AC + RAC875_c45389_425 chr7B 506751666 A/G - T C AG - Excalibur_c36408_381 chr7B 508659851 T/C + C T AG - RAC875_c59860_167 chr7B 516472805 A/G + A G AG + tplb0049c01_710 chr7B 516479436 T/C + T C AG - Kukri_c9921_1554 chr7B 516480338 A/C - G T GT + RFL_Contig1959_244 chr7B 516802754 A/G + G A AG + RAC875_c2887_52 chr7B 518386568 A/G - C T AG - Excalibur_c23789_280 chr7B 518680068 T/C - G A CT - CAP12_c606_221 chr7B 520418470 T/C + C T CT + CAP11_c846_221 chr7B 524613833 A/C - T G AC - Tdurum_contig76683_147 chr7B 527626238 T/C NA NA NA AG NA flanks do not match reference at this position BS00064085_51 chr7B 538056718 A/G + G A AG + Kukri_c39759_102 chr7B 538225523 A/G - T C AG - Tdurum_contig52239_120 chr7B 538869093 T/C + T C AG - Kukri_c34355_722 chr7B 539220074 A/G + A G CT - Tdurum_contig65979_289 chr7B 539220074 T/C - A G CT - BS00024065_51 chr7B 539232208 A/G - C T AG - Tdurum_contig64387_859 chr7B 539232208 T/C + C T AG - Kukri_c12822_132 chr7B 539232675 A/G - T C AG - Tdurum_contig28176_55 chr7B 544138657 A/G + A G CT - BobWhite_c41328_265 chr7B 544138735 T/C + T C CT + Excalibur_rep_c111660_89 chr7B 544139047 A/G + A G AG + BS00059061_51 chr7B 545991555 T/C - G A CT - Tdurum_contig56342_134 chr7B 547342280 T/C + T C CT + GENE-4270_242 chr7B 548380534 A/G + A G AG + Excalibur_c8994_1297 chr7B 551060844 T/C - A G CT - RAC875_c58656_89 chr7B 552122421 T/C + C T CT + RAC875_c30453_292 chr7B 552126806 T/C - A G AG + Kukri_c82220_112 chr7B 552536461 T/C + C T CT + Excalibur_c16661_122 chr7B 552566195 T/C + C T CT + Excalibur_rep_c111629_239 chr7B 553444914 A/G + G A AG + BS00089181_51 chr7B 553628502 A/G - T C AG - GENE-4981_53 chr7B 553631848 A/C + C A AC + BobWhite_c3564_81 chr7B 553632621 A/G - C T AG - BS00022009_51 chr7B 553884310 T/C + C T CT + GENE-4949_336 chr7B 553885717 T/G - A C GT - Kukri_c16907_390 chr7B 554176240 T/C + T C AG - Excalibur_c41452_997 chr7B 559163969 A/G + A G AG + BS00010557_51 chr7B 560531650 T/G - A C AC + RAC875_c27149_1331 chr7B 561748116 A/C + A C AC + Ex_c54863_29 chr7B 561748617 A/G NA NA NA CT NA flanks do not match reference at this position Ra_c9803_939 chr7B 564172965 A/G - C T CT + BobWhite_c13156_773 chr7B 564173059 A/C - G T GT + BS00066128_51 chr7B 564185717 T/G - A C AC + RAC875_c32843_265 chr7B 564186924 T/C - A G CT - Ex_c12057_797 chr7B 565054172 T/C - G A CT - RAC875_c45839_105 chr7B 565578900 T/C - G A CT - Tdurum_contig102328_129 chr7B 565742112 T/G - A C GT - Kukri_c51296_438 chr7B 565911676 A/G - C T AG - Kukri_c99107_143 chr7B 566476765 T/C - A G CT - BobWhite_c3269_141 chr7B 566479879 A/G + G A AG + JD_c3269_342 chr7B 566480080 A/G + A G AG + RAC875_c3229_165 chr7B 566480417 T/C + T C AG - BS00108573_51 chr7B 568497062 T/C - A G AG + Tdurum_contig47605_1362 chr7B 569423722 T/G NA NA NA AC NA flanks do not match reference at this position Kukri_c20611_293 chr7B 569939175 T/C - A G CT - BS00092630_51 chr7B 569952500 A/G + A G CT - BS00022542_51 chr7B 569956310 T/C + T C AG - Excalibur_rep_c69070_180 chr7B 569956310 T/C + T C AG - Excalibur_rep_c66583_1595 chr7B 570457645 T/C - G A AG + BobWhite_c16489_327 chr7B 570905510 A/G - T C AG - RAC875_c8890_148 chr7B 570905634 A/G + A G AG + RAC875_c8890_244 chr7B 570905730 A/G + A G CT - Tdurum_contig22364_580 chr7B 571259368 T/C + T C CT + Excalibur_rep_c106939_325 chr7B 571568170 A/C + A C GT - Kukri_c18296_567 chr7B 572416662 A/G + G A CT - Kukri_c21426_234 chr7B 574477260 A/G + G A AG + RAC875_c60161_243 chr7B 583476662 A/G + A G CT - RAC875_c60161_281 chr7B 583476700 T/C + T C CT + Excalibur_c38547_118 chr7B 583477435 T/C - A G AG + Kukri_c50417_99 chr7B 584035043 A/G + A G AG + Excalibur_rep_c113065_100 chr7B 584307283 T/C + T C CT + Kukri_c7495_824 chr7B 584308749 T/C + C T CT + Jagger_c1882_85 chr7B 584308937 A/G - C T AG - Tdurum_contig15690_413 chr7B 584317212 A/G + A G AG + Kukri_c14804_757 chr7B 584812826 T/C + T C CT + Kukri_c14804_876 chr7B 584812945 T/C + T C CT + Kukri_rep_c109805_195 chr7B 587910575 T/C - A G CT - RAC875_rep_c72524_90 chr7B 587911370 T/C + T C AG - Kukri_c1957_581 chr7B 587911565 A/G + A G AG + RAC875_c7104_160 chr7B 587916736 T/G - A C GT - IAAV7912 chr7B 589710927 A/G + G A AG + RAC875_c478_1364 chr7B 592510123 A/C + A C GT - Excalibur_c2217_731 chr7B 593185134 A/G - C T CT + Tdurum_contig58110_441 chr7B 593411805 A/G + G A CT - RAC875_c5646_774 chr7B 594411334 A/G - C T CT + Tdurum_contig11452_222 chr7B 595790796 A/G - T C AG - RFL_Contig1404_351 chr7B 598180193 A/G - T C CT + RAC875_c1742_2710 chr7B 599423221 T/G - A C AC + Excalibur_c6738_2072 chr7B 599424615 A/G + A G AG + RAC875_c7251_656 chr7B 604035430 T/G - A C GT - RAC875_c64596_302 chr7B 605451012 T/C + T C AG - Jagger_c1294_346 chr7B 607586418 T/C - A G CT - Kukri_c21628_1215 chr7B 608716486 A/G - C T AG - Tdurum_contig9966_724 chr7B 608725083 T/C - A G CT - Tdurum_contig9966_646 chr7B 608725161 T/C - G A AG + Excalibur_c5700_527 chr7B 608907182 T/C - A G CT - Excalibur_c5700_244 chr7B 608907465 A/C - T G GT + Excalibur_c58742_144 chr7B 608914608 T/G - A C AC + BS00075332_51 chr7B 611615637 T/G - C A GT - Tdurum_contig90495_232 chr7B 611719265 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c4834_694 chr7B 613176574 T/C - A G CT - Excalibur_c13444_235 chr7B 613177266 A/G - T C CT + RAC875_c101928_381 chr7B 615180244 A/C + A C GT - Kukri_c19696_60 chr7B 620758899 T/C - A G AG + Ku_c5351_1820 chr7B 622271822 A/G - C T AG - BobWhite_rep_c66630_331 chr7B 624351237 T/C + C T AG - BS00068310_51 chr7B 624784151 A/G - T C AG - BS00022045_51 chr7B 626068707 T/C + T C CT + Kukri_rep_c68107_833 chr7B 626070117 A/G - T C AG - BS00089942_51 chr7B 626239239 A/G - C T CT + RAC875_c27548_234 chr7B 626239307 T/G - C A GT - GENE-4624_79 chr7B 627300171 T/C - A G CT - BS00022106_51 chr7B 628454867 A/G - T C AG - BS00109533_51 chr7B 628454932 T/C - G A CT - BS00058464_51 chr7B 628465224 T/C - A G CT - Ku_c10179_1837 chr7B 629579540 T/C - A G CT - Kukri_c51101_351 chr7B 630107851 T/G - A C GT - GENE-4608_372 chr7B 630109598 A/G + A G AG + Ra_c10804_1595 chr7B 630179391 A/G + A G AG + Kukri_c14766_484 chr7B 633922578 T/G + T G GT + RAC875_c21489_908 chr7B 634387709 T/C + T C CT + IACX486 chr7B 634834856 T/C - A G CT - Kukri_c10078_1683 chr7B 638070726 A/G - C T CT + Kukri_c22652_165 chr7B 638132383 T/C - A G CT - BS00079076_51 chr7B 638510367 A/G - C T AG - GENE-4958_208 chr7B 638884397 T/C + T C AG - Excalibur_c11093_519 chr7B 638924052 A/G NA NA NA CT NA flanks do not match reference at this position BS00066484_51 chr7B 638924737 A/G + A G AG + Kukri_c35918_164 chr7B 639363706 T/C + T C CT + BS00035559_51 chr7B 639794510 A/C + C A AC + BS00029286_51 chr7B 639848288 A/G + A G CT - Kukri_c14891_64 chr7B 640715737 A/G + A G AG + IACX5924 chr7B 640914907 T/G + G T GT + BS00022053_51 chr7B 640915888 A/C + NA NA GT NA reference base G not among SNP alleles Tdurum_contig97814_355 chr7B 641148781 A/G NA NA NA CT NA flanks do not match reference at this position BS00070791_51 chr7B 642475413 T/C + C T CT + Ku_c25310_780 chr7B 642482410 T/C + T C CT + Ku_c25310_843 chr7B 642482473 T/C + T C CT + Tdurum_contig13930_254 chr7B 642758505 T/C - G A AG + RAC875_c3361_180 chr7B 643352902 A/G + G A CT - Excalibur_rep_c68461_1046 chr7B 643353245 T/C - A G CT - TA012914-1198 chr7B 643353545 T/C + T C CT + Excalibur_c57808_355 chr7B 643354493 A/G + A G AG + RAC875_c3361_2093 chr7B 643354814 T/C + T C CT + Tdurum_contig5083_1164 chr7B 644438801 A/G - C T AG - Ku_c16895_793 chr7B 645124763 T/C + T C AG - Ku_c16895_803 chr7B 645124773 A/G + G A CT - BS00028279_51 chr7B 645129700 T/C + C T AG - Ku_c556_1056 chr7B 645249630 T/G - C A AC + Kukri_c12901_706 chr7B 646063954 A/G - T C AG - BS00067530_51 chr7B 648924105 A/G + G A CT - BS00080621_51 chr7B 648926328 T/C + T C CT + IAAV6740 chr7B 648926438 A/G - T C AG - BobWhite_c8890_279 chr7B 650130699 A/C + C A AC + tplb0021f14_984 chr7B 653888638 A/G + A G AG + tplb0021f14_1700 chr7B 653889814 A/G + G A AG + Excalibur_rep_c74234_183 chr7B 654949817 T/C - A G AG + BS00078785_51 chr7B 654951760 T/G - A C AC + BS00064146_51 chr7B 655818427 A/G - T C CT + BS00039118_51 chr7B 656929260 T/G + G T AC - GENE-4996_592 chr7B 657871524 A/G - T C CT + Tdurum_contig10677_529 chr7B 657933319 T/C - A G AG + Tdurum_contig43995_370 chr7B 658219637 T/C + T C CT + Kukri_c31628_571 chr7B 658219727 A/C - T G AC - Tdurum_contig43995_611 chr7B 658219878 A/G + A G AG + Excalibur_c91560_445 chr7B 658220495 T/C + T C AG - BobWhite_c9774_101 chr7B 659010216 A/G - T C CT + RAC875_c400_2722 chr7B 669137788 A/C + A C GT - Kukri_c15912_860 chr7B 673961480 T/C + T C CT + Kukri_c15912_1189 chr7B 673961809 A/G + G A AG + Kukri_c15912_1839 chr7B 673962458 T/C + T C AG - Kukri_c15912_2330 chr7B 673962949 A/G + G A CT - Tdurum_contig47317_100 chr7B 675149692 T/C - G A CT - Kukri_c11141_203 chr7B 675313562 T/G - C A AC + Excalibur_c30730_276 chr7B 675315079 A/G - T C AG - Excalibur_c30730_253 chr7B 675315102 A/G - C T CT + RFL_Contig5701_783 chr7B 675318649 A/G - T C CT + Kukri_c29396_58 chr7B 675318882 A/G + G A AG + RFL_Contig5701_169 chr7B 675319338 A/G - T C CT + BobWhite_c7208_88 chr7B 675723347 T/C + C T CT + BobWhite_rep_c63532_121 chr7B 676412124 A/G - T C CT + Excalibur_rep_c74778_252 chr7B 678635327 T/C - A G CT - BS00085556_51 chr7B 678635351 T/G - A C AC + RAC875_c89312_61 chr7B 678832378 T/C - A G AG + IAAV8521 chr7B 679794155 T/G + G T AC - Kukri_c292_2231 chr7B 679794517 T/C - G A CT - Tdurum_contig5360_182 chr7B 679794580 A/G - T C AG - BobWhite_c1802_456 chr7B 680171220 A/G - T C AG - Tdurum_contig4658_418 chr7B 680171220 T/C + T C CT + Ra_c21094_506 chr7B 680853443 T/G - A C AC + IACX8294 chr7B 681792644 T/C - G A AG + BS00023023_51 chr7B 683445833 T/C - A G CT - Excalibur_c13033_261 chr7B 687323092 A/G + G A AG + BS00057323_51 chr7B 687591700 A/G - C T CT + BS00081841_51 chr7B 687595782 A/G - T C AG - BS00068309_51 chr7B 687659784 A/C - T G GT + RAC875_c40569_716 chr7B 687673127 A/C + C A GT - Kukri_c23722_81 chr7B 687685102 A/G + A G CT - TA002394-1002 chr7B 687686332 T/G NA NA NA AC NA flanks do not match reference at this position Kukri_c87702_530 chr7B 689516419 T/C - A G AG + Tdurum_contig30217_195 chr7B 692605677 T/C + C T AG - Kukri_c26118_1645 chr7B 692607876 T/C - A G CT - RAC875_c43360_456 chr7B 697078030 T/G - A C GT - Kukri_c10430_642 chr7B 698937442 A/G - T C CT + RAC875_c1679_539 chr7B 699374939 T/C - A G AG + BobWhite_c14736_188 chr7B 699375105 A/G + A G AG + Excalibur_c888_1609 chr7B 699376126 A/G - C T AG - BS00010756_51 chr7B 699380597 T/G + T G AC - IAAV1478 chr7B 699380633 A/C + C A AC + Kukri_rep_c101502_613 chr7B 699828639 A/G + A G AG + Kukri_c9683_804 chr7B 699834506 A/G - T C CT + Kukri_c9683_723 chr7B 699834587 A/G - T C CT + Excalibur_c12064_78 chr7B 699837142 T/C + T C AG - IAAV7708 chr7B 699837470 A/T - A T AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Tdurum_contig44948_1809 chr7B 699838468 A/G + A G AG + Tdurum_contig44948_1812 chr7B 699838471 T/C + C T AG - Tdurum_contig44948_2175 chr7B 699838834 T/G + T G GT + Excalibur_c5213_788 chr7B 699842849 T/C + C T CT + IAAV5167 chr7B 699922395 A/G - C T AG - JD_c1565_238 chr7B 699922401 T/C + T C AG - BS00066479_51 chr7B 700388976 A/G - C T CT + IACX7721 chr7B 700393120 C/G + G C CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Kukri_c8405_1394 chr7B 700393938 T/C - A G AG + IACX1897 chr7B 700393958 T/C - A G CT - IACX1735 chr7B 700394086 T/C - A G CT - Kukri_c55731_81 chr7B 700403708 T/G - C A GT - Tdurum_contig55961_526 chr7B 700403728 T/C - G A AG + Tdurum_contig55961_384 chr7B 700403952 A/G - T C CT + Excalibur_c50612_146 chr7B 700551478 T/C + C T AG - IACX11047 chr7B 700572251 T/C + T C CT + IACX9353 chr7B 700573221 C/G + C G CG ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles Excalibur_c1055_565 chr7B 700573264 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c11959_587 chr7B 700818581 T/C + C T CT + Excalibur_c7338_242 chr7B 700830099 T/C + C T CT + Ra_c26852_957 chr7B 700830464 T/C - G A AG + Excalibur_c7338_563 chr7B 700830715 T/C + C T CT + Kukri_c16814_103 chr7B 700831017 T/C + T C AG - Ra_c26852_560 chr7B 700831081 A/G - C T AG - BobWhite_c12048_145 chr7B 701172675 A/C - T G AC - Ku_c203_584 chr7B 701175089 T/C - G A AG + BS00022522_51 chr7B 701188222 T/C - G A AG + BS00083578_51 chr7B 701188341 T/C - A G AG + Kukri_c7036_87 chr7B 701188928 A/C - G T AC - Tdurum_contig43954_2291 chr7B 701188999 A/G + G A AG + BS00108264_51 chr7B 701212530 A/G + G A CT - BS00023166_51 chr7B 701212586 A/C + A C AC + BobWhite_c34068_833 chr7B 701302097 T/C - A G CT - Excalibur_c101292_132 chr7B 701303456 T/C - A G AG + tplb0058p02_2806 chr7B 701304737 T/C + C T AG - RAC875_rep_c78007_349 chr7B 701339756 A/G + G A AG + RAC875_rep_c78007_394 chr7B 701339801 T/C + T C AG - RAC875_rep_c78007_425 chr7B 701339832 A/G + A G CT - RAC875_c41938_471 chr7B 701339905 T/C + C T CT + Ku_c108027_54 chr7B 701871790 A/G - T C CT + RAC875_c57326_85 chr7B 701871855 T/C + T C CT + BobWhite_c28058_232 chr7B 702233767 A/G + A G AG + IAAV9045 chr7B 702233767 T/C - A G AG + CAP11_c8077_69 chr7B 702454984 T/C - G A AG + Ku_c9679_441 chr7B 703166524 T/C + T C CT + Ra_c73114_428 chr7B 703167685 T/C + C T AG - IAAV6137 chr7B 703246274 T/C + C T CT + BS00026694_51 chr7B 703266960 A/G - C T AG - RAC875_rep_c90152_309 chr7B 703299530 A/G + G A AG + Tdurum_contig67161_99 chr7B 703300186 T/C + T C CT + Tdurum_contig52079_1174 chr7B 703302709 A/G - C T CT + IAAV2686 chr7B 704040384 T/G + T G AC - Tdurum_contig28884_460 chr7B 704040384 A/C - T G AC - Tdurum_contig93425_441 chr7B 704247540 T/C + C T AG - TA005284-0990 chr7B 704271881 T/C NA NA NA CT NA flanks do not match reference at this position RFL_Contig2905_503 chr7B 704281215 T/C + C T CT + Tdurum_contig82534_237 chr7B 704281274 T/C - G A AG + BS00031923_51 chr7B 704281884 A/G - T C AG - BobWhite_c12264_248 chr7B 704281965 A/G + A G AG + RFL_Contig2905_931 chr7B 704282245 T/C + C T CT + Excalibur_c642_481 chr7B 706483621 T/C + T C CT + Kukri_c55780_296 chr7B 706485543 T/C + T C CT + Excalibur_c3738_1316 chr7B 706813997 A/G - T C CT + Tdurum_contig76864_755 chr7B 706814650 A/G + G A AG + Ex_c3738_390 chr7B 706814922 T/C - A G CT - Ku_c5969_1667 chr7B 706815067 A/G + G A CT - Kukri_rep_c105704_342 chr7B 708113454 T/C - G A AG + Ku_c22990_969 chr7B 708114221 T/C + T C CT + RAC875_rep_c117259_207 chr7B 708114916 T/C - G A CT - RAC875_c4960_951 chr7B 708477894 T/C + T C CT + tplb0035h03_1251 chr7B 709198270 T/C + C T AG - BS00040283_51 chr7B 709256015 A/G + A G CT - Excalibur_c1205_188 chr7B 709522057 T/G + G T GT + Excalibur_c4948_454 chr7B 709525740 A/G NA NA NA CT NA flanks do not match reference at this position Excalibur_c4948_90 chr7B 709526920 A/G - C T AG - BobWhite_c4729_243 chr7B 709608612 T/C - A G AG + BobWhite_c6690_965 chr7B 709608789 A/G - C T CT + BobWhite_rep_c63346_248 chr7B 709609190 T/C - A G CT - GENE-4528_455 chr7B 709611417 T/C - A G CT - BobWhite_rep_c55035_124 chr7B 709611496 A/G + A G CT - GENE-4528_28 chr7B 709611496 T/C - A G AG + BS00022810_51 chr7B 710991237 A/G + A G AG + Tdurum_contig8402_460 chr7B 711165291 A/C NA NA NA GT NA flanks do not match reference at this position Tdurum_contig8402_638 chr7B 711165469 A/C + A C AC + Kukri_c3148_780 chr7B 711361966 A/C + A C AC + Kukri_c91360_220 chr7B 711539009 A/G - T C CT + CAP12_c1587_70 chr7B 712082714 A/C + C A AC + CAP12_c1587_142 chr7B 712082786 A/C + A C AC + BS00066404_51 chr7B 712736214 A/G - T C CT + Tdurum_contig23273_426 chr7B 713859981 A/C + A C AC + GENE-4943_470 chr7B 715292297 T/G + G T GT + Kukri_c28160_2017 chr7B 716958100 A/G - C T CT + RAC875_rep_c111788_130 chr7B 716961573 A/G NA NA NA AG NA flanks do not match reference at this position IACX9217 chr7B 716963536 A/G - C T CT + BobWhite_c160_276 chr7B 717338843 A/G + A G CT - RAC875_c21760_200 chr7B 717794219 A/G - C T CT + BS00075615_51 chr7B 718136907 T/C + C T AG - BS00075616_51 chr7B 718136980 T/C + C T CT + BS00080759_51 chr7B 718148349 A/G - T C AG - Excalibur_c51720_84 chr7B 718356312 A/C + A C AC + BS00022162_51 chr7B 718359023 T/C - A G CT - Kukri_c46447_1738 chr7B 718359215 T/C + C T AG - RAC875_c30471_670 chr7B 718361415 T/C + T C CT + Kukri_c7284_674 chr7B 718467475 T/G + T G AC - Kukri_c48418_149 chr7B 718471145 A/C - G T AC - BobWhite_c2514_109 chr7B 718471477 A/C - T G AC - Excalibur_c45337_64 chr7B 718850340 T/C - A G AG + Tdurum_contig42586_720 chr7B 718850815 A/G - C T CT + Tdurum_contig42586_290 chr7B 718851515 A/C - G T AC - Tdurum_contig72092_197 chr7B 719081824 A/G + A G AG + Tdurum_contig75127_589 chr7B 719721310 A/G + A G CT - Kukri_c11467_993 chr7B 719721898 T/C + T C CT + Excalibur_c1070_1978 chr7B 720118517 A/G + G A CT - Tdurum_contig28598_245 chr7B 721195484 A/C + C A AC + BobWhite_c2892_167 chr7B 721207702 A/G + G A AG + Tdurum_contig49656_679 chr7B 721207702 T/C - G A AG + BobWhite_c2892_211 chr7B 721207746 T/C + T C AG - Excalibur_c23777_74 chr7B 721816335 A/G - T C CT + Kukri_c45628_892 chr7B 725379025 T/C + T C CT + BS00021666_51 chr7B 725520340 T/C + C T CT + Kukri_c35975_593 chr7B 725965505 T/C + T C AG - BS00101258_51 chr7B 727529962 A/G - T C AG - Excalibur_c4484_985 chr7B 727635103 A/G + G A CT - Excalibur_c49736_1197 chr7B 728691991 A/G + A G AG + BS00010819_51 chr7B 728694736 A/G + G A CT - Kukri_s109646_139 chr7B 728694837 T/G + T G AC - Tdurum_contig52096_330 chr7B 728808770 A/G - C T AG - Tdurum_contig52096_270 chr7B 728808830 T/C - A G CT - Excalibur_rep_c69840_85 chr7B 730152487 T/C + T C CT + Ku_c15539_433 chr7B 730152518 A/C - T G AC - RAC875_rep_c72959_187 chr7B 730152783 T/C + T C CT + CAP7_c3950_160 chr7B 730178654 T/C - A G AG + BS00025724_51 chr7B 730905849 A/G + A G AG + BS00050328_51 chr7B 730908221 A/G - C T AG - BS00058970_51 chr7B 730909354 A/G - T C CT + BS00023884_51 chr7B 732325079 A/G - C T CT + CAP7_c9291_206 chr7B 732650133 T/C + T C CT + IAAV4636 chr7B 732650133 A/G - T C AG - Kukri_rep_c105287_81 chr7B 732650618 A/G - T C CT + Ex_c69252_628 chr7B 732650642 T/C - A G AG + Tdurum_contig45280_451 chr7B 732652220 T/C + C T AG - Ku_c3676_1280 chr7B 732655248 T/C - G A CT - BobWhite_c21129_830 chr7B 732656559 T/C + C T AG - BS00047623_51 chr7B 733376976 T/C + C T AG - BS00004376_51 chr7B 733528562 A/C + A C GT - RAC875_rep_c110526_229 chr7B 733530032 T/G + T G GT + RAC875_rep_c110526_324 chr7B 733530127 T/C + T C CT + BS00042112_51 chr7B 733596122 A/C - G T GT + Excalibur_c3870_288 chr7B 733597291 T/C - G A CT - Excalibur_c3870_89 chr7B 733597490 A/G - T C AG - Excalibur_c1688_491 chr7B 733609762 T/C + C T AG - Excalibur_rep_c66257_477 chr7B 733610000 A/G + G A AG + RAC875_c43579_80 chr7B 733610106 T/C NA NA NA CT NA flanks do not match reference at this position RAC875_rep_c70367_185 chr7B 733610387 A/G - T C AG - RAC875_rep_c70367_158 chr7B 733610414 A/C - T G AC - Kukri_c3524_92 chr7B 734259495 A/G + G A AG + BS00066862_51 chr7B 734684200 A/G - C T AG - Tdurum_contig8448_363 chr7B 739383870 A/C + A C GT - Kukri_c81094_434 chr7B 739392094 A/G - T C CT + BS00003703_51 chr7B 739443040 T/C - G A AG + GENE-4848_95 chr7B 739931213 A/C + A C GT - Excalibur_rep_c110429_536 chr7B 740033618 T/C - G A AG + Excalibur_c5938_1703 chr7B 740038517 T/G - A C GT - Excalibur_c5938_994 chr7B 740039226 A/G - T C CT + Excalibur_c5938_371 chr7B 740039849 A/G - C T CT + Excalibur_c5938_301 chr7B 740039919 A/G - C T AG - Kukri_c65663_642 chr7B 740040411 A/G + G A AG + RAC875_c14064_177 chr7B 740040449 A/G - C T CT + RAC875_c5744_115 chr7B 740055258 T/C + T C AG - RAC875_c5744_412 chr7B 740055567 A/G + G A AG + BS00004403_51 chr7B 741571278 A/C + C A GT - IACX6478 chr7B 741571278 T/G - C A GT - RFL_Contig2647_624 chr7B 741573552 T/C + C T CT + RAC875_c34939_467 chr7B 741576998 A/C - T G GT + BobWhite_c43557_103 chr7B 741577105 A/G + G A CT - RFL_Contig71_386 chr7B 741718465 T/G - C A GT - CAP12_c194_240 chr7B 742463681 A/G - T C CT + tplb0060b03_1008 chr7B 742464077 T/C NA NA NA CT NA flanks do not match reference at this position tplb0060b03_921 chr7B 742464279 T/C - A G CT - tplb0040b02_681 chr7B 743300700 A/G + A G AG + Tdurum_contig30909_76 chr7B 743304167 T/G - A C AC + Excalibur_c8449_280 chr7B 744226043 T/C - A G AG + Kukri_rep_c101620_1848 chr7B 744402154 A/G + A G CT - Tdurum_contig51105_510 chr7B 744402964 T/C + C T CT + BS00004171_51 chr7B 744404071 T/C + C T CT + RAC875_rep_c105012_111 chr7B 744404849 T/C + T C CT + Tdurum_contig51105_1538 chr7B 744405110 T/C + T C CT + Kukri_c30714_633 chr7B 744652231 T/G + G T AC - RAC875_c15215_554 chr7B 745586305 T/C - A G AG + RAC875_c906_657 chr7B 746533988 T/C - G A AG + RAC875_c48671_172 chr7B 749423949 A/G - C T AG - BS00063474_51 chr7B 749526673 T/C + C T CT + Kukri_c80861_118 chr7B 749559318 A/G + A G CT - RAC875_c525_1372 chr7B 750086340 A/G + A G CT - BS00009283_51 chr7B 750087672 T/C + C T AG - RAC875_c525_1885 chr7B 750087678 T/C + T C AG - Tdurum_contig42584_1100 chr7B 750589139 T/C - A G CT - CAP12_c580_309 chr7B 750593641 A/G + A G AG + Excalibur_c34115_226 chr7D 1295915 T/C + C T CT + Tdurum_contig51001_186 chr7D 1962225 T/C + T C AG - Tdurum_contig62445_667 chr7D 1967660 A/G NA NA NA AG NA flanks do not match reference at this position Tdurum_contig59690_2020 chr7D 2327189 T/C - G A CT - GENE-4461_104 chr7D 2351189 T/C + T C AG - Kukri_c24194_536 chr7D 3438527 T/C + T C CT + Tdurum_contig42590_317 chr7D 3782373 T/C - A G CT - BS00065623_51 chr7D 4005296 A/G + G A CT - BS00070821_51 chr7D 4008442 A/G + G A CT - Kukri_c22088_62 chr7D 4015743 T/G - A C AC + RAC875_c11702_658 chr7D 4072393 A/G + A G CT - Excalibur_c1209_935 chr7D 4516010 T/C - G A AG + Excalibur_c1209_755 chr7D 4516190 T/C - A G AG + Excalibur_c22830_2010 chr7D 4633728 T/C - A G CT - BS00079969_51 chr7D 4895049 T/G + G T AC - RAC875_c8714_1139 chr7D 4991518 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c50999_269 chr7D 4994998 T/C + T C AG - Kukri_c37227_579 chr7D 5049527 A/G + G A AG + Kukri_c6091_327 chr7D 5174531 A/G NA NA NA AG NA flanks do not match reference at this position Kukri_c6274_1283 chr7D 5177291 T/G - C A GT - Excalibur_c46904_84 chr7D 5198961 T/C + C T AG - Tdurum_contig10289_1265 chr7D 5331583 A/G - C T AG - BS00009565_51 chr7D 5334772 A/C + C A AC + BS00108793_51 chr7D 5378304 T/G - A C AC + BobWhite_c3351_329 chr7D 5378548 T/C NA NA NA CT NA flanks do not match reference at this position Excalibur_c9687_1021 chr7D 5448579 A/G - T C CT + BS00065628_51 chr7D 5582725 T/G - A C GT - BS00064394_51 chr7D 6012792 A/G + G A AG + Kukri_c8124_237 chr7D 6013690 A/G + A G AG + D_GBUVHFX02IW8MH_278 chr7D 6397903 T/G - C A AC + Excalibur_c46262_263 chr7D 6472082 A/G - T C AG - RAC875_c14501_102 chr7D 6694195 A/G + A G AG + Excalibur_c88899_626 chr7D 7072630 T/C - G A CT - Kukri_c80931_147 chr7D 7073045 A/G + A G CT - BobWhite_c12316_383 chr7D 7297617 A/G - C T CT + IACX7857 chr7D 7297836 T/C - G A CT - BobWhite_c5654_231 chr7D 7446590 A/G - C T CT + IAAV9104 chr7D 9309573 A/C + C A GT - BobWhite_c2260_168 chr7D 9310166 A/G + G A CT - Kukri_rep_c102191_135 chr7D 10047520 T/G + T G AC - Excalibur_c30119_285 chr7D 10506396 T/C - G A AG + D_contig78519_72 chr7D 10724859 A/C - T G AC - RFL_Contig1323_544 chr7D 10835093 A/G - C T AG - IACX11794 chr7D 12470290 T/C + T C CT + D_contig36176_338 chr7D 13001473 A/G - T C CT + Excalibur_c9183_1397 chr7D 13011013 A/G + A G CT - tplb0022c16_494 chr7D 13295291 T/C - A G AG + TA005377-1076 chr7D 13295583 A/G - T C CT + Kukri_c18677_255 chr7D 13477116 A/G + G A CT - Excalibur_c7255_697 chr7D 13602378 A/G - T C CT + Kukri_rep_c103404_314 chr7D 13604901 T/G + T G AC - Ex_c25027_535 chr7D 14426906 T/C - A G AG + Excalibur_c2023_345 chr7D 14883103 A/G - T C CT + Tdurum_contig54973_1510 chr7D 14883103 T/C + T C CT + BS00110642_51 chr7D 15322747 T/C - A G CT - BS00110124_51 chr7D 15322939 A/G - T C AG - GENE-4606_1208 chr7D 15906783 A/G + G A AG + BobWhite_c8454_782 chr7D 16154786 A/G + G A AG + TA004646-0293 chr7D 16710032 T/C - A G AG + RAC875_rep_c114991_394 chr7D 18682868 T/G + G T AC - BobWhite_c11327_185 chr7D 19405530 T/C + C T AG - IAAV2823 chr7D 19718989 A/T - T A AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles GENE-4277_295 chr7D 20064119 T/C + C T CT + Excalibur_c16355_712 chr7D 20328191 T/C + T C AG - RAC875_c6280_292 chr7D 20952806 T/G + T G GT + IACX8322 chr7D 22223161 T/C - A G AG + Excalibur_c30151_528 chr7D 22223512 T/C NA NA NA AG NA flanks do not match reference at this position CAP7_c1706_56 chr7D 22611812 T/C + T C CT + IAAV6615 chr7D 22612066 A/G - C T AG - RAC875_c7670_219 chr7D 23491935 T/C + T C AG - IACX7905 chr7D 27047060 A/C + C A AC + Excalibur_c44485_362 chr7D 28040388 T/C - A G CT - Kukri_c17754_1179 chr7D 31433460 A/G + A G CT - RFL_Contig4686_700 chr7D 31948893 A/G + A G AG + Excalibur_c14217_1260 chr7D 36204766 A/G + A G CT - Excalibur_rep_c68458_1536 chr7D 37285414 T/C - A G CT - Ra_c63534_581 chr7D 40128372 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c29294_1281 chr7D 41838399 T/G NA NA NA GT NA flanks do not match reference at this position D_F5XZDLF02G9H4M_286 chr7D 43037081 A/G + G A AG + BS00064892_51 chr7D 43366397 A/G + G A CT - BS00066391_51 chr7D 46090337 A/G - T C AG - Excalibur_c43044_385 chr7D 53260933 A/G - T C CT + Kukri_rep_c103248_582 chr7D 55002547 T/C - A G CT - D_GCE8AKX02ILA1U_88 chr7D 55073787 T/G - C A GT - IAAV1940 chr7D 56401610 T/C + T C CT + BobWhite_c40479_283 chr7D 58258719 T/C - A G CT - Kukri_c92151_216 chr7D 58485535 T/C + C T CT + D_GDS7LZN02FSYZC_227 chr7D 58491641 A/G - C T AG - Kukri_c32845_116 chr7D 58504355 T/C - G A CT - TA002473-0717 chr7D 58644241 A/G - T C CT + RAC875_c57243_236 chr7D 58740596 A/G + A G AG + BS00022203_51 chr7D 58868443 T/C + T C AG - Excalibur_c22419_460 chr7D 59091519 T/C - A G AG + BS00066549_51 chr7D 62978867 T/C + C T CT + BS00066015_51 chr7D 77175796 A/G - C T AG - Excalibur_c41298_459 chr7D 80974297 T/G + T G GT + Ku_c20410_424 chr7D 86070772 T/C + T C CT + Kukri_rep_c108604_137 chr7D 100276912 T/C + T C CT + D_contig12156_209 chr7D 100751330 A/C - T G GT + RFL_Contig1820_712 chr7D 101558969 A/G + A G CT - RFL_Contig1820_846 chr7D 101559103 T/C + T C CT + IAAV872 chr7D 104524919 A/C - T G AC - RAC875_c4453_2678 chr7D 104524954 A/G - C T CT + Ex_c6280_1262 chr7D 108266797 T/G - A C AC + BobWhite_rep_c49048_493 chr7D 111114972 T/C + T C AG - Kukri_c100613_331 chr7D 112431179 A/G + G A CT - D_contig09229_928 chr7D 119746777 T/C - G A AG + Kukri_c51068_528 chr7D 119894909 A/G + A G CT - RAC875_c21946_234 chr7D 119895240 A/G + A G AG + RAC875_c53629_483 chr7D 142688520 A/G + G A AG + Excalibur_rep_c71057_1199 chr7D 177111151 T/C - A G AG + Excalibur_c6542_1171 chr7D 180668440 A/C + C A GT - Tdurum_contig10833_308 chr7D 183318238 A/G + A G AG + BobWhite_rep_c50229_413 chr7D 185927387 A/G + A G CT - IAAV3448 chr7D 186416150 A/G - C T AG - BS00110409_51 chr7D 206695834 T/C + C T CT + D_GDEEGVY02GHITF_405 chr7D 215154672 T/C - G A AG + GENE-4953_139 chr7D 220286110 A/G - T C AG - GENE-4859_218 chr7D 224472450 T/C - A G AG + Excalibur_c13094_523 chr7D 235982986 T/C - A G AG + Excalibur_rep_c85891_96 chr7D 237549852 A/G + G A AG + GENE-3132_118 chr7D 242007087 A/G - C T CT + RAC875_c21521_345 chr7D 365260875 A/C + C A AC + BS00009457_51 chr7D 386646308 T/G - C A AC + IACX7714 chr7D 386646308 A/C + C A AC + IAAV4133 chr7D 391576285 T/G - A C GT - BobWhite_c8027_421 chr7D 405116132 T/C - A G CT - Excalibur_c72450_483 chr7D 409606566 T/G - A C GT - Excalibur_c15411_643 chr7D 424099360 A/G + A G CT - Kukri_rep_c112161_392 chr7D 424099898 T/G + G T AC - RFL_Contig1686_427 chr7D 426730091 T/C + C T CT + IAAV3414 chr7D 434911310 T/C - A G AG + RAC875_c13060_197 chr7D 459924210 A/G + G A AG + Excalibur_c20931_669 chr7D 468514042 T/C - G A CT - RAC875_c47003_445 chr7D 473620371 T/C - A G AG + IAAV3506 chr7D 476681669 A/T + A T AT ambiguous A/T or C/G SNP: call strand cannot be inferred from alleles BS00020610_51 chr7D 480055333 A/C + C A GT - Kukri_c22996_334 chr7D 489721515 T/G - A C AC + BS00064164_51 chr7D 499622494 A/G - T C AG - RAC875_c13300_139 chr7D 501091432 A/G + A G AG + BobWhite_c18121_478 chr7D 503328463 A/G - C T AG - BS00035732_51 chr7D 516029971 A/G - T C AG - D_GDS7LZN01CWBG5_74 chr7D 517220929 T/C - G A CT - Excalibur_c4508_1959 chr7D 518780205 A/G - T C AG - Excalibur_c4508_1007 chr7D 518781335 A/G - T C CT + Excalibur_c23328_127 chr7D 520402001 T/C + T C AG - BS00051607_51 chr7D 526000766 A/G + G A CT - BS00003830_51 chr7D 526240626 A/C - T G AC - IAAV1468 chr7D 527707315 T/C + C T AG - Excalibur_c39966_367 chr7D 528894757 A/G - T C CT + BS00083421_51 chr7D 529044228 T/G - A C AC + Kukri_c53638_1090 chr7D 530913698 T/C + T C CT + Excalibur_c12996_775 chr7D 535753904 T/C - A G CT - Kukri_c59357_370 chr7D 536972477 T/C - A G AG + D_GDS7LZN02HAZ1Y_333 chr7D 539852735 A/G + A G AG + Kukri_c2796_1436 chr7D 540235681 T/C - G A AG + RAC875_c60770_82 chr7D 540713733 A/G + A G AG + RAC875_c25143_110 chr7D 540848260 A/G + A G AG + Excalibur_c48577_577 chr7D 540848369 T/C - A G CT - Kukri_c39981_381 chr7D 540848393 A/G + G A AG + Tdurum_contig19852_242 chr7D 540854604 A/G + A G AG + CAP7_c4608_228 chr7D 540857168 A/G + A G AG + Tdurum_contig15690_195 chr7D 540858031 T/C + T C AG - Kukri_c41297_284 chr7D 540858087 T/C + C T CT + Kukri_c14804_352 chr7D 541238206 T/C + T C CT + Excalibur_c13912_587 chr7D 541241676 T/C - A G CT - Excalibur_c13912_521 chr7D 541241742 T/C NA NA NA AG NA flanks do not match reference at this position RFL_Contig2864_661 chr7D 543728322 T/C + T C CT + GENE-4924_88 chr7D 544473524 T/C NA NA NA CT NA flanks do not match reference at this position Kukri_c11269_2054 chr7D 546127437 T/C - A G CT - Ku_c32426_324 chr7D 548804453 T/G - C A GT - BS00065210_51 chr7D 549297357 T/C - A G CT - Ku_c47803_245 chr7D 549545901 A/C + C A GT - BobWhite_c15497_788 chr7D 550095478 A/G - T C CT + BS00066148_51 chr7D 550214563 A/G - T C AG - Kukri_c15768_1383 chr7D 550216801 T/C - A G AG + Kukri_c33014_459 chr7D 552950542 A/G - T C AG - BS00063744_51 chr7D 552954217 A/G - C T AG - RAC875_rep_c106588_205 chr7D 553220134 A/G - T C CT + tplb0032a06_1305 chr7D 554594687 T/C - A G CT - BS00077071_51 chr7D 554907786 T/C - A G AG + D_contig26753_367 chr7D 556220380 T/C - G A CT - D_F5MV3MU01DLEVA_384 chr7D 556639996 A/G + A G CT - GENE-4746_1032 chr7D 557406819 T/C - G A AG + IAAV8855 chr7D 559449020 T/C + T C AG - D_contig05962_325 chr7D 559459461 T/G - C A GT - BS00070188_51 chr7D 559460440 T/G + T G AC - Kukri_c30457_342 chr7D 561021948 T/C + T C AG - JD_c19335_229 chr7D 562815158 T/C + T C AG - D_contig10767_771 chr7D 563291885 A/C + A C GT - Kukri_rep_c70697_2196 chr7D 564973023 A/G + A G CT - RFL_Contig2257_810 chr7D 565198540 T/C + T C CT + BobWhite_c15489_142 chr7D 568600746 T/C - A G AG + RAC875_c16367_81 chr7D 568629462 T/G - A C GT - BobWhite_c23455_184 chr7D 568754388 T/C + T C AG - tplb0041e14_1096 chr7D 570648425 T/C - G A CT - Excalibur_c7895_385 chr7D 570665966 A/G - T C CT + Ex_c7895_287 chr7D 570666064 T/C - G A CT - D_GBB4FNX02ILZW2_114 chr7D 570825150 T/C + T C CT + BobWhite_c11549_468 chr7D 571196430 A/G + A G AG + Kukri_c101311_72 chr7D 571255095 A/G - T C CT + D_GB5Y7FA01A62Z6_240 chr7D 571255894 T/C - G A CT - Ra_c10518_735 chr7D 571971890 T/C + C T CT + tplb0057p21_1042 chr7D 573434059 T/C - A G AG + Excalibur_c21739_688 chr7D 573694499 A/G - T C CT + GENE-4796_109 chr7D 575863587 A/G - C T CT + GENE-4796_65 chr7D 575863627 T/C - A G CT - Kukri_c59891_110 chr7D 576303288 A/G + A G AG + BobWhite_c23295_270 chr7D 576748117 A/G + A G AG + Excalibur_c17686_588 chr7D 576750852 T/C + C T CT + D_contig59414_135 chr7D 577259448 T/C + T C AG - D_contig10891_118 chr7D 577594509 A/C + C A AC + Ku_c25310_669 chr7D 578723408 T/C + T C AG - D_GDS7LZN02F6AEK_164 chr7D 579333481 T/C + T C CT + RAC875_c48766_224 chr7D 579826067 T/G - A C GT - CAP8_c3122_210 chr7D 580481710 A/G + G A AG + RAC875_c33564_120 chr7D 580500373 A/G + G A CT - RAC875_c37552_149 chr7D 580501097 A/G + A G CT - Excalibur_c3611_584 chr7D 583478162 A/G - T C CT + D_GB5Y7FA02IX9R3_112 chr7D 585546607 A/C + C A GT - Tdurum_contig28304_335 chr7D 586486153 A/G + A G CT - Kukri_c46303_512 chr7D 586487717 T/C + C T CT + D_GB5Y7FA02GUQ3K_192 chr7D 587926934 T/C - A G CT - D_GA8KES402JKYH8_236 chr7D 592078968 T/C + C T CT + RFL_Contig5387_1497 chr7D 593667802 T/C - G A AG + CAP8_c2948_51 chr7D 594729503 A/G + A G AG + Excalibur_c23280_604 chr7D 596009272 T/C - G A CT - D_GBB4FNX02GLQFH_120 chr7D 596876462 A/G + A G CT - Kukri_c10944_704 chr7D 596898345 A/G + A G AG + BobWhite_c5419_165 chr7D 597026763 A/C + A C AC + RAC875_c89312_129 chr7D 599498953 A/G - T C AG - IAAV6659 chr7D 600451148 A/G + A G CT - Tdurum_contig5360_95 chr7D 600451298 T/G - C A GT - RAC875_c19332_645 chr7D 600455819 A/G + A G CT - GENE-4442_121 chr7D 600456601 T/C - G A CT - Excalibur_c31707_302 chr7D 600883389 T/C + T C CT + Ex_c32065_720 chr7D 601064412 T/C + T C AG - Kukri_c17449_1492 chr7D 602901197 A/G - T C CT + Ku_c17449_1303 chr7D 602901386 T/G - A C AC + RAC875_rep_c107526_171 chr7D 603360603 T/G - A C GT - BS00066389_51 chr7D 603664725 A/G + G A CT - BobWhite_c11902_88 chr7D 608197485 A/G - T C AG - Excalibur_c27057_757 chr7D 608289339 T/C - G A CT - BS00022463_51 chr7D 608810464 T/C + C T AG - IAAV4624 chr7D 608810464 A/G - C T AG - Kukri_rep_c70351_203 chr7D 608812029 A/G - C T AG - RAC875_rep_c106109_130 chr7D 610818589 T/C + T C CT + Tdurum_contig44948_1132 chr7D 610818671 A/G + A G AG + IAAV4818 chr7D 610820846 T/C - A G CT - Excalibur_rep_c75066_126 chr7D 610822149 A/G + A G AG + RAC875_rep_c111159_57 chr7D 610853757 T/C + C T CT + Kukri_s106214_192 chr7D 611233733 T/C - A G CT - D_contig22976_123 chr7D 611761974 A/C + A C AC + GENE-4717_482 chr7D 611820269 T/G + T G GT + tplb0021n05_1349 chr7D 611840323 T/C + T C AG - D_contig46973_461 chr7D 611871194 T/C NA NA NA AG NA flanks do not match reference at this position RAC875_c3826_2443 chr7D 612439607 A/G + A G AG + Kukri_c42052_491 chr7D 612964570 T/C + C T CT + Tdurum_contig28884_379 chr7D 613549389 T/G - C A GT - Tdurum_contig28884_302 chr7D 613549466 T/C - G A AG + D_contig18045_60 chr7D 613638001 A/G - T C AG - RAC875_c31791_400 chr7D 613701864 A/G NA NA NA AG NA flanks do not match reference at this position RAC875_c8221_649 chr7D 613872117 T/C - A G CT - Kukri_c10757_1398 chr7D 614539420 T/C - A G CT - Ex_c24486_503 chr7D 615485453 T/C + C T CT + Ex_c24486_509 chr7D 615485459 A/C + C A AC + Ex_c47822_2353 chr7D 615935560 A/G + A G CT - BS00064783_51 chr7D 616502295 T/C + C T CT + BS00001450_51 chr7D 616505751 A/G - C T CT + IAAV8836 chr7D 616903066 T/C + T C CT + Excalibur_c25798_219 chr7D 616903123 A/G + G A AG + BS00110528_51 chr7D 617932728 A/G - T C CT + Kukri_c21255_1076 chr7D 619878835 T/C - A G AG + RAC875_rep_c118655_110 chr7D 619881590 A/G - C T CT + Kukri_rep_c69740_288 chr7D 619882182 T/C + T C CT + IAAV14 chr7D 619884342 T/G + G T AC - Kukri_c9068_691 chr7D 621264260 A/G - T C AG - Kukri_c7284_1859 chr7D 621482857 T/C - A G CT - IAAV5220 chr7D 623541639 A/G + A G CT - BobWhite_rep_c52163_55 chr7D 627117292 T/C + T C AG - IACX7421 chr7D 627323708 A/C - T G AC - RAC875_c34012_983 chr7D 627325532 A/G + A G CT - RAC875_c40237_269 chr7D 629531162 A/G + G A AG + BS00079734_51 chr7D 629830952 T/C - A G CT - Excalibur_c11062_582 chr7D 630527102 A/C - G T AC - Kukri_rep_c106477_365 chr7D 630527129 A/G - T C AG - RAC875_rep_c110526_154 chr7D 630527506 T/C - A G CT - BS00096025_51 chr7D 630527944 T/C - A G CT - BS00096024_51 chr7D 630527959 T/C - A G CT - Excalibur_c25090_830 chr7D 630528873 A/G + G A CT - RAC875_c20837_654 chr7D 630714772 A/G - T C CT + RAC875_c2713_3350 chr7D 632332978 T/C + T C CT + RAC875_rep_c108382_824 chr7D 633604488 A/G - T C AG - IAAV4542 chr7D 633606191 T/G + T G AC - Excalibur_c18631_810 chr7D 633606756 T/C + T C CT + CAP12_c2044_288 chr7D 633875068 A/G + A G CT - RFL_Contig3607_648 chr7D 634096012 A/C - G T GT + RAC875_rep_c113248_366 chr7D 634694371 T/G - A C GT - Kukri_rep_c105097_275 chr7D 635562952 A/G + A G CT - Kukri_c5265_1144 chr7D 635580855 A/G - T C AG - RAC875_c14064_308 chr7D 635581077 T/C + C T CT + GENE-4848_348 chr7D 635846804 A/G - T C AG - CAP11_c1515_137 chr7D 636769785 T/C + T C AG - BS00084631_51 chr7D 636770931 A/C + C A GT - Kukri_rep_c69829_711 chrUn 2220797 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) RAC875_c63359_192 chrUn 2220839 A/C NA NA NA GT NA not on chr1A-7D (no RefSeq v1 position) Kukri_c8527_53 chrUn 2221016 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Excalibur_rep_c67492_1119 chrUn 2222024 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Kukri_c4204_1673 chrUn 2224677 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) GENE-0543_201 chrUn 2225277 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) GENE-0543_113 chrUn 2225345 A/C NA NA NA AC NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig11349_810 chrUn 2227489 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c12932_2102 chrUn 2230047 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Kukri_c5638_1087 chrUn 2568162 T/G NA NA NA GT NA not on chr1A-7D (no RefSeq v1 position) RAC875_c21801_126 chrUn 2569612 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Kukri_c3754_1260 chrUn 2570517 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) RAC875_c21801_1262 chrUn 2570748 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) RAC875_c21801_1572 chrUn 2571058 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) RAC875_c24429_132 chrUn 5335010 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BS00065108_51 chrUn 8121694 A/C NA NA NA AC NA not on chr1A-7D (no RefSeq v1 position) BS00021667_51 chrUn 8830617 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) IAAV1297 chrUn 11747582 T/G NA NA NA GT NA not on chr1A-7D (no RefSeq v1 position) CAP12_rep_c4748_249 chrUn 12182674 T/G NA NA NA GT NA not on chr1A-7D (no RefSeq v1 position) Kukri_c24446_306 chrUn 12592868 A/C NA NA NA AC NA not on chr1A-7D (no RefSeq v1 position) Ku_c42579_870 chrUn 12632179 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) RAC875_c13918_444 chrUn 15910184 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Kukri_rep_c71976_113 chrUn 17537510 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Kukri_c38519_639 chrUn 22053864 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) CAP11_c3226_221 chrUn 23525332 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) RAC875_c4602_886 chrUn 23679226 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BobWhite_c27251_77 chrUn 24276905 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BobWhite_c30520_323 chrUn 24403614 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BS00067816_51 chrUn 29232846 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) CAP11_c896_88 chrUn 30529794 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig50839_593 chrUn 30831106 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Kukri_c16094_406 chrUn 31112049 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) GENE-0918_159 chrUn 31112211 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Kukri_c18971_279 chrUn 31213138 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Kukri_c21135_1109 chrUn 31215699 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig64286_268 chrUn 31228909 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BS00098312_51 chrUn 31481357 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c15671_87 chrUn 31519973 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Kukri_c35024_116 chrUn 32065959 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c11079_749 chrUn 32201585 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c11079_923 chrUn 32202089 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) RAC875_rep_c69730_522 chrUn 32204566 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BS00003733_51 chrUn 32204692 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BS00009793_51 chrUn 32204725 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BS00010059_51 chrUn 32205933 T/G NA NA NA AC NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c42951_136 chrUn 32206860 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BS00066230_51 chrUn 32325116 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) GENE-1606_307 chrUn 32914299 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BobWhite_rep_c66215_299 chrUn 35317203 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c18645_857 chrUn 35322097 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) RAC875_rep_c69820_103 chrUn 35338578 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Excalibur_rep_c66331_1967 chrUn 35342250 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Ra_c17608_960 chrUn 35424176 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BS00068168_51 chrUn 35634122 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BS00058654_51 chrUn 35634995 T/G NA NA NA AC NA not on chr1A-7D (no RefSeq v1 position) RAC875_c19475_61 chrUn 37811539 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Ku_c1976_1351 chrUn 39187530 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) RFL_Contig1801_429 chrUn 39602098 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) RFL_Contig1801_1436 chrUn 39603282 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) RAC875_c69_392 chrUn 40650890 T/G NA NA NA GT NA not on chr1A-7D (no RefSeq v1 position) RAC875_c69_499 chrUn 40650997 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) RAC875_c69_717 chrUn 40651309 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) GENE-1743_274 chrUn 43325644 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) GENE-1743_224 chrUn 43325670 T/G NA NA NA GT NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c6782_253 chrUn 43327428 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) RAC875_c12996_2320 chrUn 49995227 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) RFL_Contig3424_931 chrUn 50747206 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BS00093255_51 chrUn 50752312 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BS00045454_51 chrUn 50753729 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BS00084042_51 chrUn 50835907 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) RAC875_c82470_174 chrUn 51199268 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig47476_528 chrUn 51199268 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig47476_495 chrUn 51199301 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig47476_441 chrUn 51199355 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BS00063708_51 chrUn 51205558 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Kukri_c1911_120 chrUn 51345318 T/G NA NA NA GT NA not on chr1A-7D (no RefSeq v1 position) Kukri_c8386_767 chrUn 52072742 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) GENE-2993_336 chrUn 52972321 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c4483_1053 chrUn 62649512 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BobWhite_c32973_167 chrUn 62649658 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Ra_c68425_1406 chrUn 65431410 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Ra_c68425_1419 chrUn 65431423 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) IACX7443 chrUn 65436398 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BobWhite_c34750_360 chrUn 65437161 A/C NA NA NA AC NA not on chr1A-7D (no RefSeq v1 position) GENE-1530_263 chrUn 71720235 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c35350_424 chrUn 74816375 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig8608_553 chrUn 74816375 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Kukri_c373_982 chrUn 74818709 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Ku_c5353_293 chrUn 75073182 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig28726_120 chrUn 75177631 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) IACX6086 chrUn 75180108 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BobWhite_c12261_130 chrUn 75205625 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BS00055768_51 chrUn 76052215 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BS00055769_51 chrUn 76052220 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) CAP8_c1361_367 chrUn 77275454 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Ex_c28973_935 chrUn 81298168 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig82510_556 chrUn 82513787 T/G NA NA NA GT NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig82510_574 chrUn 82513805 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c34807_431 chrUn 82529696 T/G NA NA NA GT NA not on chr1A-7D (no RefSeq v1 position) RAC875_c56439_58 chrUn 82530997 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c1402_210 chrUn 82531103 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BS00068351_51 chrUn 82600670 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig93266_145 chrUn 86288103 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BS00022449_51 chrUn 89193215 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Ex_c18266_680 chrUn 89363684 A/C NA NA NA GT NA not on chr1A-7D (no RefSeq v1 position) GENE-4862_674 chrUn 91518700 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Excalibur_rep_c70043_395 chrUn 92720093 A/C NA NA NA AC NA not on chr1A-7D (no RefSeq v1 position) GENE-4895_101 chrUn 92744783 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) RAC875_c5546_2847 chrUn 95975979 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) RAC875_c5546_2773 chrUn 95976053 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Kukri_c18486_347 chrUn 100841693 T/G NA NA NA GT NA not on chr1A-7D (no RefSeq v1 position) IAAV3899 chrUn 108987864 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig17216_310 chrUn 110513739 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BS00100738_51 chrUn 110650962 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig81113_395 chrUn 110650962 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Kukri_c5097_2340 chrUn 110797732 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) IAAV5850 chrUn 110798323 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig47762_975 chrUn 122395828 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig47762_1140 chrUn 122395993 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BobWhite_c12016_88 chrUn 122397766 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) RAC875_c228_481 chrUn 124685009 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) GENE-0221_721 chrUn 143903012 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) RAC875_c28639_621 chrUn 146407029 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BS00033749_51 chrUn 150797615 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BS00033750_51 chrUn 150797643 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) tplb0037h13_1274 chrUn 156529750 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Excalibur_rep_c115261_135 chrUn 194635497 A/C NA NA NA AC NA not on chr1A-7D (no RefSeq v1 position) Kukri_c3948_209 chrUn 194672014 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c1554_465 chrUn 194672478 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BS00022229_51 chrUn 214330352 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Tdurum_contig94629_258 chrUn 244511681 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Ku_c10243_855 chrUn 270903188 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) IAAV2388 chrUn 294782645 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c83177_99 chrUn 308558323 T/G NA NA NA GT NA not on chr1A-7D (no RefSeq v1 position) Ku_c24488_1050 chrUn 311047606 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Ku_c24488_313 chrUn 311048343 T/C NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BS00064905_51 chrUn 314905429 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BS00064028_51 chrUn 321937125 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) Excalibur_c39447_143 chrUn 328055637 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BS00023003_51 chrUn 364242842 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) Ra_c69_1443 chrUn 394401648 A/G NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position) BS00022366_51 chrUn 414701733 A/G NA NA NA AG NA not on chr1A-7D (no RefSeq v1 position) BobWhite_c25234_418 chrUn 424056177 T/C NA NA NA CT NA not on chr1A-7D (no RefSeq v1 position)