Supplementary Figure 1: Evaluation of CCR models by sequencing coverage threshold.
From: A map of constrained coding regions in the human genome
Evaluation of CCR models constructed using different coverage thresholds and different thresholds for the percentage of gnomAD individuals meeting the minimum coverage depth. For example, ‘10x.5 CCR’ reflects a CCR model where every position in a CCR region was required to have 10× coverage in at least 50% of gnomAD individuals. a, ROC curve based on the ClinVar variant set. b, PR curve based on ClinVar. True positives are pathogenic variants and likely pathogenic variants from ClinVar. True negatives are variants labeled as benign from ClinVar. The performance of each model is clearly very similar, and the ‘10x.5 CCR’ model imposed the most relaxed coverage requirement while exhibiting the highest performance. It was therefore chosen as the coverage threshold for the final model. 24,554 pathogenic variants from ClinVar were used, and 4,689 benign variants were used for the evaluation dataset.
