The high-level results of our cross-validation experiment are shown in Figure 2. As before, the solid black curves depict IMPUTE2 results with our suggested strategy of using a cosmopolitan reference panel, and different points on the x-axis correspond to different values of khap. Here, the multicolored curves from Figure 1 (which represent imputation from subsets of the HapMap 3 haplotypes) are replaced with orange curves. The identities of the orange curves are omitted for plotting clarity, but full details are provided in File S1. We imputed and evaluated 1,523-2,364 low-frequency SNPs per HapMap 3 panel, with the exact numbers provided in Table S1. The black dashed lines in Figure 2 show the results of using Beagle with the full HapMap 3 reference panel; these lines are flat because Beagle does not have an analog of the khap parameter.
