The results of this comparison are shown in Figure 4. Results based on the GMB panel are shown in blue, while results based on the GMB+GHN+HM3.afr panel are shown in gray. Accuracy curves for IMPUTE2 and Beagle are drawn with solid and dashed lines, respectively. In concurrence with our previous results on African populations, we found that Beagle was much less accurate than IMPUTE2 when provided with the same reference panel: for each color, the solid line in Figure 4 is consistently above the dashed line. In fact, IMPUTE2 achieved higher accuracy when imputing from 200 GMB haplotypes (solid blue line) than Beagle did when imputing from 1222 African haplotypes (dashed gray line), of which the 200 GMB were a subset. The difference between methods was largest at low-frequency SNPs, but there was a substantial gap across the entire frequency spectrum.
