Figure 2 .

Imputation accuracy at low-frequency SNPs in HapMap 3 cross-validations, as a function of target panel, reference panel composition, k_hap value, and imputation method. These plots show the imputation accuracy of IMPUTE2 and Beagle in various cross-validation experiments. The accuracy of each experiment is plotted on the y-axis as the mean R² across all SNPs with MAF < 5% in the cross-validation panel (identified by the gray box in each plot). The x-axis shows the k_hap parameter, which scales linearly with the computational burden of imputation updates in IMPUTE2. The solid black curves show how R² varies with k_hap when using IMPUTE2 with a reference panel containing the full set of 2020 HapMap 3 haplotypes; the dashed black lines show the accuracy of Beagle with this reference panel. IMPUTE2 was also applied to subpanels of the full HapMap 3 panel, with results shown as orange curves. Similar plots for other observed SNP sets and imputed SNP MAFs can be found in File S3.