phase II CEU variation by only 1% using the phase II CEU reference panel. In stark contrast, imputation using MACH increased coverage of phase II YRI variation by 21% (from 55% to 76%) using only the phase II YRI reference panel; coverage was increased by 13% (from 62% to 75%) for the combined phase II CEU+YRI variation based on the unweighted phase II CEU+YRI reference panel. The merged set of separately imputed SNPs achieved the best coverage (78%) of the 40,281 phase II CEU+YRI reference SNPs.
