Supplementary Figure 7: X-chromosome variant pathogenicity prediction comparison for CCR versus other metrics.
From: A map of constrained coding regions in the human genome
a, Enrichment of 166 pathogenic de novo mutations on the X chromosome in the most constrained X-CCRs and 43 benign mutations in the least constrained X-CCRs. The error bars represent 95% confidence intervals of 0.043–0.226 for the 0–20 bin, 0.46–2.07 for the 20–80 bin, 0.85–16.5 for the 80–90 bin, 0.69–41.1 for the 90–95 bin, and 1.35–77.2 for the 95–100 bin. b, ROC curve for the developmental disorder de novo variant evaluation set. The true positives are 166 missense-only de novo variants from patients with developmental disorders. The true negatives are 43 missense de novo variants from the unaffected siblings of autism patients. c, PR curve for X-CCR versus other metrics for the de novo set. The dots in b and c indicate the score cutoff with the maximal Youden J statistic for each tool. Values in parentheses indicate AUC and peak J score (respectively) for b and the F1 score, the weighted average of recall and precision, at the J-score cutoff for c.
