Figure 4 focuses on the estimated r2 between imputed and observed allele counts. In each stripe, accuracy of imputation is assessed using a different reference panel. Superimposed in pink is the coverage that would be provided by single marker tagging approaches. Broadly, it is clear that imputation using an appropriate reference panel will improve coverage. Using an inappropriate reference panel (for example using the HapMap CEU to impute genotypes for one of the African populations), can result in imputed genotypes and allele counts that are not as strongly correlated with the true genotypes as the best available single marker tag but, even then, the loss appears to be small. Importantly—in all cases—combining the three HapMap panels resulted in substantial improvements in coverage over single marker tagging—suggesting that this might be a cautious approach when the choice of reference panel is unclear. Combining the three HapMap panels is also a good choice for genotype imputation in admixed populations [Mathias et al., 2010] where, depending on the ancestry of each stretch of the genome, the best matching haplotype will likely originate from
