Figure 1

Overall allelic r2 for FImpute, Beagle and Impute2 across different imputation scenarios. There were 2000 and 500 young target individuals for imputation from 3 k/6 k to 50 k and from 50 k to 300 k, respectively. In scenarios A and F, reference groups with different sizes were randomly chosen after excluding parents and grandparents. The reference group in scenarios B and C included only parents and grandparents, in scenarios D and E it included all genotyped males and in scenarios G and H it included all genotyped individuals. Pedigree information was considered in scenarios C, E and H and was disregarded in scenarios B, C and G.