Fig. 1: Overview of phasing approach using Expectation-Maximization method in gnomAD.

a, Schematic of phasing approach. b, Histogram of ${\mathrm{P}}_{\mathrm{t}\mathrm{r}\mathrm{a}\mathrm{n}\mathrm{s}}$ scores for variant pairs in cis (top, blue) and in trans (bottom, red). c, Proportion of variant pairs in each ${\mathrm{P}}_{\mathrm{t}\mathrm{r}\mathrm{a}\mathrm{n}\mathrm{s}}$ bin that are in trans. Each point represents variant pairs with ${\mathrm{P}}_{\mathrm{t}\mathrm{r}\mathrm{a}\mathrm{n}\mathrm{s}}$ bin size of 0.01. Blue dashed line at 10% indicates the ${\mathrm{P}}_{\mathrm{t}\mathrm{r}\mathrm{a}\mathrm{n}\mathrm{s}}$ threshold at which ≥ 90% of variant pairs in bin are on the same haplotype (${\mathrm{P}}_{\mathrm{t}\mathrm{r}\mathrm{a}\mathrm{n}\mathrm{s}}\le 0.02$). Red dashed line at 90% indicates the ${\mathrm{P}}_{\mathrm{t}\mathrm{r}\mathrm{a}\mathrm{n}\mathrm{s}}$ threshold at which ≥ 90% of variant pairs in bin are on opposite haplotypes (${\mathrm{P}}_{\mathrm{t}\mathrm{r}\mathrm{a}\mathrm{n}\mathrm{s}}\ge 0.55$). Calculations are performed using variant pairs with population AF ≥ 1×10⁻⁴. d, Performance of ${\mathrm{P}}_{\mathrm{t}\mathrm{r}\mathrm{a}\mathrm{n}\mathrm{s}}$ for distinguishing variant pairs in cis and trans. Accuracy is calculated as the proportion of variant pairs correctly phased (green bars) divided by the proportion of variant pairs phased using ${\mathrm{P}}_{\mathrm{t}\mathrm{r}\mathrm{a}\mathrm{n}\mathrm{s}}$ (orange plus green bars). b-d, ${\mathrm{P}}_{\mathrm{t}\mathrm{r}\mathrm{a}\mathrm{n}\mathrm{s}}$ scores are population-specific.