The sliding window approach performed on sample_002 resulted in the mapping of 6 regions containing from 1 to 3 variants successfully genotyped on both WGS and BeadChip platforms and exhibiting discordant genotypes between the used platforms. Locations of these regions and encompassed variants are collated in Tables 4 and 5. A total of 12 discordant variants were selected for validation by Sanger sequencing. These variants were accompanied by 14 concordant variants located closely to discordant variants. These 12 discordant variants included 6 SNVs and 6 INDELs, of which 4 SNVs were of AA vs BB type discordancy, 2 — AA vs AB type, 3 INDELs of II vs DD type and the remaining 3 INDELs of DD vs DI (II vs DI) type. The selection was performed based on the following criteria: Selected SNPs were successfully genotyped using both WGS and BeadChip platforms.Selected SNPs are located close to each other within 500 bp window length (reasonable limit of one Sanger read).Specific primers can be selected for these SNPs-containing region (by Primer-BLAST [7]).Table 4The chosen regions for validation by Sanger sequencing
