Imputation in admixed populations was examined by comparing reference panels based on either one population, or on mixtures of other populations; one mixture (COSMO1) combined chromosomes from the original three HapMap population panels, whereas the other (COSMO2) included seven populations (CEU, CHB, GIH, JPT, MKK, MXL and YRI, see Methods for details). For ASW, the best reference panel was YRI+CEU, which yielded mean r2 = 0.87 and mean r2 = 0.72 for common and low-frequency SNPs, respectively. For the other admixed populations, the best reference panels were the same-population panel (when available) followed by the diverse reference panel of seven populations (COSMO2) (Supplementary Table 10).
