Crop SNPdb Data Download

Download genotype matrices for all canola and wheat samples in the database by chromosome.

Wheat Barley 40K genotypes for all 32,656 Australian Grains Genebank wheat accessions (VCF, IWGSC RefSeq v2.1) are available from AGG Wheat – Release 260619; all of these accessions can be searched in CropSNPdb.

Wheat 90K: the Ref_SNP column gives the IWGSC RefSeq v1.0 reference/alternate alleles on the forward strand, and Strand gives the orientation of the genotype calls relative to RefSeq v1.0 (+ = calls read directly on the forward strand; − = complement the calls; ambiguous = A/T or C/G SNP). Orientation was inferred by matching probe flanks to RefSeq v1.0; SNPs without a confident match are NA. Full table: Wheat90k_RefSeq_v1_reference_alleles.tsv.

IWGSC RefSeq v2.1 positions for 70,353 wheat 90K SNPs (probe flanks aligned from RefSeq v1.0), with reference/alternate alleles and call strand on v2.1 and the Wheat Barley 40K marker at the same position where there is one (2,050 SNPs): Wheat90k_RefSeq_v2.1_positions.tsv. Of the ~72,600 SNPs on the 90K array, 15,279 have genotypes in CropSNPdb (TCAP SWW2013 panel, 309 lines); the others were not released for this panel.

Brassica chromosome size and maximum SNP count shown for B. napus (A and C genomes) and B. juncea (B genome). Available SNPs will generally be lower than the maximum count from the SNP chip.