Fig. 6

Scatterplots of principal components axis of PC1 and PC2. (a) CEU, CHB and YRI populations: the two-dimensional PCA plot reveals distinct separation of CEU, CHB and YRI racial ancestry populations. The first PC contributes 73.5% of the total variation, which clearly distinguishes between Africans from Yoruba and non-Africans samples from Han Chinese. The second PC, contributing 6.8% of the total variation, distinguishes between Europeans and Han Chinese; (b) ASW, CEU and YRI populations: CEU and YRI samples form relatively dense clusters, whereas ASW has a lower density and the sample variance is large. Most of the ASW samples are much closer to YRI than CEU and CEU is separated from the other two populations along the PC1 axis. The first PC explains 64.5% of the total variance and the second PC explains 6.4% of the total variance