The density of variation in ExAC is not uniform across the genome, and the observation of variants depends on factors such as mutational properties and selective pressures. In the ~45M well covered (80% of individuals with a minimum of 10X coverage) positions in ExAC, there are ~18M possible synonymous variants, of which we observe 1.4M (7.5%). However, we observe 63.1% of possible CpG transitions (C to T variants, where the adjacent base is G), while only observing 3% of possible transversions and 9.2% of other possible transitions (Supplementary Information Table 9). A similar pattern is observed for missense and nonsense variants, with lower proportions due to selective pressures (Figure 1D). Of 123,629 HQ insertion/deletions (indels) called in coding exons, 117,242 (95%) have length <6 bases, with shorter deletions being the most common (Figure 1E). Frameshifts are found in smaller numbers and are more likely to be singletons than in-frame indels (Figure 1F), reflecting the influence of purifying selection.
