To control the false discovery rate (FDR) of SNPs and indels at <5%, a variant quality score threshold was defined using high depth (>30×) PCR-free sequence data generated for one individual per population. For structural variants, additional orthogonal methods were used for confirmation, including microarrays and long-read sequencing, resulting in FDR < 5% for deletions, duplications, multi-allelic copy-number variants, Alu and L1 insertions, and <20% for inversions, SVA (SINE/VNTR/Alu) composite retrotransposon insertions and NUMTs8 (nuclear mitochondrial DNA variants). To evaluate variant discovery power and genotyping accuracy, we also generated deep Complete Genomics data (mean depth = 47×) for 427 individuals (129 mother–father–child trios, 12 parent–child duos, and 16 unrelateds). We estimate the power to detect SNPs and indels to be >95% and >80%, respectively, for variants with sample frequency of at least 0.5%, rising to >99% and >85% for frequencies >1% (Extended Data Fig. 2). At lower frequencies, comparison with >60,000 European haplotypes from the Haplotype Reference Consortium9 suggests 75% power to detect SNPs with frequency of 0.1%. Furthermore, we estimate heterozygous genotype accuracy at 99.4% for SNPs and 99.0%
