Figure 3 : Completeness of additional variant genotyping.

From: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

Figure 3

We calculated the fraction of variants in the WGS and WES panel that were captured via either imputation or exome array genotyping, respectively. (a) The mean imputation quality of variants in the WGS panel, as a function of their allele count in the WGS panel. Green circles show imputation quality in Finnish individuals, while green crosses show imputation quality in British individuals. For comparison, blue circles and crosses show imputation quality using the 1000G Phase 1 dataset as a reference panel (instead of the WGS panel). (b) The number of coding variants in the WES panel present on the exome array. Variants are stratified by annotation and frequency, and sensitivity calculations are shown for variants in each ancestry group as well as overall. Panel (b) is reproduced from Supplementary Fig. 17 in Fuchsberger et al.8.