Dots and bars represent the point estimate and 95% CI, respectively, for MAPS and proportion singletons. a, b, Fathmm-MKL (a) and Genomiser (b) separate benign variation (low MAPS score) from likely damaging variation (high MAPS score), but do not identify any classes of variation under strong selective constraint. c, There was no significant difference in the strength of purifying selection measured by MAPS between sites predicted to result in loss, gain, or no change in transcription factor binding. d, Validation of Fig. 1c using whole-genome data from the UK10K project. While CADD can identify coding variation under strong selective constraint (as measured by the proportion of singletons), CADD is unable to identify strongly constrained non-coding variants. e, f, The subset of CNEs sequenced in the DDD cohort that are predicted to be inactive in all 111 Roadmap Tissues (n = 261) exhibit a similar degree of evolutionary conservation (e) but lower selective constraint (f) in a healthy population compared to CNEs active in at least one tissue (n = 4,046).