To specify the coding-region SNPs (cSNPs), perigenic SNPs (pSNPs), and intergenic SNPs (iSNPs) among the SNP markers mapped in the KJ-RIL genetic map, a BLASTX search was performed against the CDS of T. aestivum, using SNP flanking sequences and the corresponding contig sequences as queries. Using SNP flanking sequences as the query, 8.9% (10104 SNPs) were best hits to the CDSs of the T. aestivum, and these were considered to be the cSNPs. When using the contig sequences where the markers were best hits to as the query, approximately 36.8% (41689 SNPs) were best hits for the CDSs of the T. aestivum, indicating that 27.9% (36.8–8.9%) of SNPs were pSNPs. The remaining 63.2% are likely iSNPs (Table S5).