Calculated confusion matrices for all three analyzed DNA samples are shown in Fig. 4, with metrics values presented in Table 3. These values show high overall concordance in genotyping between both WGS and BeadChip techniques. Detected discordant results may have arisen from ambiguous BeadChip genotyping call within multiallelic sites. Nevertheless, all calculated quality metrics values surpassed the recommended thresholds [6]. Table 3Quality metrics of genotyping comparison between BeadChip and WGS call setsSampleGenotype concordanceNon-reference genotype concordanceNon-reference genotype sensitivitySensitivityPrecisionSpecificityAccuracy0010.997830.996160.996870.997830.997830.999250.999280020.991560.979730.987730.991560.991560.996960.997180030.992530.9850.984020.992530.992530.997420.9975
