26 listed in Table 6 were used for confusion matrices calculation using Sanger-derived calls as a “truth” call set, which resulted in WGS and BeadChip precision of 0.81 and 0.5, respectively, and the accuracy values of 0.87 and 0.61. Results of Sanger validation may possibly be explained by low complexity or repetitive genomic context which surrounds some of the validated variants, hindering accuracy and precision of either genotyping or read alignment. All the listed variants which were discordant between BeadChip and WGS were plotted (Fig. 5) to reveal possible clustering of discordant variants based on the initial BeadChip genotyping metrics. No clustering of the validated variants was observed. Thus, current analysis did not allow to make any definite conclusions about the clustering of discordant and concordant variants based on their genotyping quality metrics. Table 6Sanger validation results for sample_002rsIDChromosomePosition (GRCh38)BeadChip genotypeWGS genotypeSanger genotypers12731384d1109711898TGGGTTrs1633365c1109711919TCTTTCrs58877308a1109712113CGGGGGrs1386876441109759369GGGGG–rs202018423b1109759339CCCCCCrs7572930271109759384CCCCC–rs760279355b1109759346CCCCCCrs7678098121109759359DDIII–rs793943411109759361GGGGG–rs786205634a285663647DIIIIIrs3832043d2233671807IIDIDDrs144484152a6160246683GGAAAArs149262397b6160246574CCCCCCrs316022a6160246568GGAAAArs529525717b6160246473GGGGGGrs537568133a6160246590TTCCCCrs549969754b6160246607CCCCCCrs5550244716160246297GGGGG–rs563560445b6160246467CCCCCCrs5638295926160246443GGGGG–rs5773527956160246460TTTTT–rs757852385b6160246688AAAAAArs7595662846160246458GGGGG–rs20089633510101010536DDIINArs7534209531349792587DDDINArs397515367a2237973817DDIIIIaconcordance between Sanger and WGS genotypesbconcordance between all three genotyping methodscconcordance between Sanger and BeadChip genotypesdabsence of concordance between any of the methods
