After removing the 1,193 expected duplicates, QC procedures for the 43,398 individuals are summarized in Supplementary Note Figure 1. Standard quality control procedures (detailed in the Supplementary Note) were used to exclude underperforming individuals (number of DNAs=1,708) and genotyping assays (judged by success rate, genotype distributions deviated from that expected by Hardy Weinberg equilibrium, number of variants=16,149). After filtering, there were 517,482 SNPs available for analysis.
