Figure 3.

Scenario 2, experiments 9–12: Training models using 1000 UKB AFR samples and testing on 2,960 independent UKB AFR samples, for all variants with WES available

(A and B) Performance comparison between Rsq and MagicalRsq in terms of squared Pearson correlation with true R² for (A) 1000G-based imputation; (B) TOPMed-based imputation.

(C) Smooth scatterplot showing Rsq or MagicalRsq (x axis) calculated from both matched (second row) and mis-matched (third row) models against true R² (y axis) for both 1000G-based (left) and TOPMed-based (right) imputation, for all low-frequency variants with WES available.