Table 2.

Principal components analysis with rare and common WGS variants

			PCA-Seq			EIGENSTRAT
	PCs	MAF	CEU	AMR	YRI	CEU	AMR	YRI
R2 for rare variants	10	<0.01	0.18	0.16	0.33	0.17	0.15	0.33
		<0.05	0.79	0.80	0.55	0.78	0.79	0.54
	20	<0.01	0.42	0.42	0.43	0.42	0.42	0.42
		<0.05	0.83	0.84	0.66	0.82	0.83	0.65
R2 for common variants	10	<0.01	0.95	0.95	0.13	0.95	0.95	0.17
		<0.05	0.95	0.95	0.13	0.95	0.95	0.11
	20	<0.01	0.97	0.97	0.22	0.97	0.97	0.41
		<0.05	0.97	0.97	0.22	0.97	0.97	0.23
R2 for all variants	10	—	0.95	0.96	0.18	0.96	0.96	0.22
	20	—	0.97	0.97	0.41	0.97	0.97	0.49

MAF minor allele frequency, R², the coefficient of determination from a linear regression model with 10 PCs included as predictors and the proportion of CEU, AMR, and YRI ancestry proportions from ADMIXTURE analysis as the response