Genotype concordance was tested between the sequence-based genotypes and the array-based genotypes obtained by integrating the 660W-Quad and HumanExome arrays, as described in detail in a companion article to this special issue (Vrieze et al., 2014). All 1,325 directly sequenced individuals had array genotype data, and autosomal genotypes showed 99.91% concordance between the sequenced and array-based genetic variants. Array-based genotyping technology is highly accurate, and this result indicates that the sequence genotypes were also highly accurate. We expect accuracy to decline for rarer genotypes, which can be seen in Figure 2, where we display genotype concordance between the sequence genotypes and array genotypes across the minor allele frequency spectrum, from rare variants to common variants.
