In this section, we present results for the ASW (African American) and TSI (Italian) panels, which exhibit general trends and unexpected outcomes from our HapMap 3 cross-validations. Figure 1 shows how imputation accuracy depends on reference panel composition and the number of surrogate family haplotypes chosen from each composite panel (khap). We constructed these plots in ways that highlight interesting features, and we restricted the results to SNPs with MAF < 5% in the target panel. We provide analogous plots for all HapMap 3 target panels in File S1.
