Fig. 3

Scatter plot between Rsq-score/Info-score and average Hellinger score of GQ SNPs. In the three sub-figures, imputation results of AfAm obtained with the three software packages MaCH, MaCH-minimac and IMPUTE2 are presented. Color represents results after imputation with one of the four reference panels CEU, CHB_JPT, MEX and YRI. Results are smoothed by loess estimators. For a particular value of MaCH-Rsq/IMPUTE-info, Hellinger scores obtained by using a genetically similar reference panel are higher than those obtained from mismatching reference panels (p-value < 0.001 for all three scenarios, based on a regression analysis considering the software-specific score as covariable)