Fig. 2

Aggregate quality control analysis of the GSA data. A Principal Component Analysis (PCA) plots of 1KG data and GSA genotype data. red: African (AFR), yellow-green: Admixed Americans (AMR), dark-green: East Asian (EAS), blue: European (EUR), purple: South Asian (SAS). B Heatmaps of BeadChip array quality control analysis of call-rate (left), p10GC (middle), and estimated DNA contamination (right). Color gradient scales for the three panels are as follows: call-rate (orange < 0.94–blue > 0.99), p10GC (yellow < 0.50–blue > 0.60) and estimated DNA contamination (rainbow gradient: purple ~ 1%, blue ~ 2%, green ~ 3%, orange/red ~ >4%). C Heatmaps of reproducibility quality control analysis using replicate data as measured by call rate, estimated DNA contamination, number of assays with no genotype calls, and heterozygote to homozygote ratio. Color gradient scales for these four heatmaps are as follows: No genotype calls (blue < 166,000–orange > 400,000), and rainbow gradient for call rate (purple > 0.99–red < 0.94), estimated DNA contamination (purple < 1%–red > 4%), and heterozygote/homozygote ratio (purple > 2.25–red < 1.25), respectively