Results from DFE-alpha.

nt is the total number of sites in the reference genome corresponding to each mutually exclusive site class (including non-canonical spliceforms in the case of protein-coding exons). Nes (the product of the mean homozygous effect of a deleterious mutation and the effective population size) and β (the gamma shape parameter, which has a lower estimable value of 0.05 within DFE-alpha) are the inferred parameters of the DFE, from which we calculate the mean fixation probability of a deleterious mutation relative to a neutral mutation (un) and estimates of the proportion of deleterious mutations in three ranges of fitness effects (on a scale of Nes = 0–1, 1–10 and 10+). From estimates of divergence from rat at selected and neutral sites, we calculate estimates of the proportion of adaptive substitutions (α) and the rate of adaptive substitution relative to the rate of synonymous substitution (ωa) (results are shown for non-CpG-prone sites). na is an estimate of the total number of adaptive substitutions between mouse and rat attributable to each site class and is calculated from na = ωa nt ds, where ds = 0.18, an estimate of divergence for synonymous sites. 95% confidence limits are shown in square brackets.