From: Estimating relationships between phenotypes and subjects drawn from admixed families
 | 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 |