Fig. 2

Box plot of Hellinger scores of Germanic target population obtained from MaCH- imputation with four different reference panels. Results for correctly and wrongly imputed SNPs based on best-guess genotypes are presented separately. CEU achieves highest Hellinger scores for all, correctly and incorrectly imputed genotypes, i.e. performed best among reference panels. As one can see, applying a threshold of 0.45 for Hellinger scores almost ensures that the best-guess genotype is correct