Figure S1 Fold coverage of the features on the NimbleGen array for the combined sequences of all eight wheat varieties.

Figure S2 The percentage of the four nucleotides A, C, G and T at the 511 439 putative single-nucleotide polymorphism loci for each of the eight wheat varieties studied.

Figure S3 The bars of the graphs represent the average scores for the 400 contigs contained in each of the three bins.

Table S1 All 59 000 contigs and the 511 439 putative single-nucleotide polymorphisms identified in the eight wheat varieties, Alchemy, Avalon, Cadenza, Hereward, Rialto, Robigus, Savannah and Xi19.

Table S2 The 96 varietal single-nucleotide polymorphisms validated against a panel of 23 wheat varieties.

Table S3 The total number of tri-homoeoallelic loci (row 1) and the number of contigs that contained loci with one (row 2) or more (rows 3 and 4) tri-homoeoallelics single-nucleotide polymorphisms.

Table S4 The loci that were tri-homoeoallelic for all eight varieties.

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