Assemblies for each of the wheat 7A, B and D chromosomes, including the syntenic builds and extra contigs, were generated as described by Berkman et al. and used as references for variety specific read mapping. The latest versions of the syntenic builds are accessible at the wheatgenome.info web site . The assembly for chromosome 4AL was kindly provided by Dr Pilar Hernandez .Whole genome Illumina sequence data was downloaded from the bioplatforms web site