Fig. 2
Relating evolutionary history to contemporary selective constraint on human promoters. a The relative rate of rare (red; derived allele frequency <1.5%) and common (blue; >5%) derived alleles for human substitution polymorphisms across all promoters (top panel) and promoters stratified by evolutionary history (lower panels). Rates are normalised to the −4 to −2 kb upstream of the TSS, indicated as the neutral proxy (N.proxy) region and calculated as the rolling average of 250 bp windows. 95% bootstrap confidence intervals are indicated by light outer curves. The number of polymorphisms contributing to the red and blue curve for each analysis are indicated. b–c As for (a) but showing derived human insertion and deletion polymorphisms respectively. d Summary odds ratios for rare versus common derived alleles in promoter regions compared to the N.proxy. Positive values have a relatively higher rate of rare than common polymorphisms indicative of negative (purifying) selection in promoter regions. Symbols are coloured black where a statistically significant difference is found in the rare to common ratio between the promoter and N.proxy regions (Bonferroni corrected pcor < 0.05; confidence intervals shown are 99.7%, the equivalent of 95% after correcting for n=15 tests)