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Table 1 Empirical accuracies (R2dose, R2gt, CR) and model-based (Rsq) imputation quality score from Minimac3 using different reference panels

From: Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome

  Size of the reference panel
250 500 1000 2000
Rsq Low-frequency (MAF < 5%) 0.829 0.856 0.871 0.876
Common (MAF > 5%) 0.942 0.960 0.971 0.978
Global 0.909 0.928 0.938 0.944
R2dose Low-frequency (MAF < 5%) 0.688 0.737 0.778 0.818
Common (MAF > 5%) 0.909 0.936 0.953 0.965
Global 0.845 0.874 0.897 0.917
R2gt Low-frequency (MAF < 5%) 0.690 0.746 0.792 0.832
Common (MAF > 5%) 0.887 0.920 0.941 0.956
Global 0.832 0.868 0.895 0.917
CR Low-frequency (MAF < 5%) 0.992 0.995 0.996 0.997
Common (MAF > 5%) 0.962 0.973 0.98 0.985
Global 0.971 0.980 0.986 0.989