Fig 2. A summary and comparison of per-site and per-individual imputation accuracy from Beagle and glmnet imputation.

(A and B) The x- and y-axes report estimates of imputation accuracy for glmnet and Beagle, respectively. Each point represents the estimated accuracy for a single site (A) and individual (B). (C) Both Beagle and glmnet produced bimodal distributions of per-site accuracies, with median per-site imputation accuracies of 0.76 (black vertical line) and 0.82 (red vertical line), respectively. (D) Both methods produced left-skewed distributions of per-individual accuracies, with median per-individual accuracies of 0.991 and 0.992 for Beagle and glmnet, respectively.