The list of designed primers with respective amplification parameters can be found in Table 5. The gDNA of sample_002 was used for amplifying regions of interest (ROIs) in Table 4. All ROIs, except those located on chromosomes 10 and 13, were successfully amplified and Sanger sequenced. The comparison of genotypes obtained via microarray genotyping, whole genome sequencing and Sanger sequencing of the amplified ROIs is shown in Table 6. Sanger-derived genotypes containing only one letter were the ones obtained from only one read. Plus signs denote Sanger genotypes concordant with the WGS-derived genotype, while double plus signs denote concordance of all three genotyping methods. Hashtag represents concordance with the BeadChip-derived genotype, and asterisk — an absence of concordance with any of the tested methods. Sixteen Sanger-resolved diploid genotypes (forward and reverse Sanger chromatograms covered the variant location) out of the 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
