To assess population matching, the assigned versus known population and super-population for each 1KGP sample was examined. The average 1KGP cross-population mismatch rate was 0.09 (ranging from 0.03 for AFR to 0.185 for SAS). However, there were no cross super-population mismatches. For S4S, the concordance rate between super-population assignment based on minimum Mahalanobis distance and self-reported census race was greater than 92.4% with 4.6% of the samples within the major census categories changing super-populations. As expected, the census category Asian split into EAS and SAS super-populations. Furthermore, samples in “More than one race” and “Unknown” groups were empirically assigned. Additional details are shown in Table 1 and plots of the first three PCs for the empirically matched S4S super-population assignments are shown in Figure 1c. Although there is high concordance between self-reported census race and empirical genetic population match, there is reduction in variance for most ancestry PCs for the genetic based super population assignments. Specifically, of the 10 PCs constructed variances were smaller for all 10 PCs in the EUR, 8 in the AFR, 8 in EAS, 7 in
