Fig. 1

The histograms of true genotypes across all 19,530 SNPs and the histograms of genotype dosage values for coverage depth 10, 5, and 1 when MAFs are low (\(\hbox {MAF}<0.1\)), medium (\(0.1\le \hbox {MAF}<0.4\)), and high (\(\hbox {MAF}\ge 0.4\)). Genotypes dosage are the posterior mean of the genotype under additive coding. With values 0, 1 and 2 assigned to the genotypes (major, major), (major, minor) and (minor, minor), respectively, the genotype dosage, \({\text{ DS }} = \Pr (1 |{\text{ Data}})\) + 2\(\Pr (2 | {\text{ Data}})\), where \(\Pr (1 |{\text{ Data}})\) and \(\Pr (2 |{\text{ Data}})\) denote the conditional (“posterior”) probabilities for the genotypes (major, minor) and (minor, minor)