Candidate variants per sample. (A-C) Bar plots of the number of candidate SNVs, indels, and CNVs per individual. (D) Scatterplot of the Bayes factor vs the observed over expected reads ratio for each CNV called by ExomeDepth and the thresholds distinguishing different levels of changes in zygosity. Note that the number of called CNVs is slightly biased upwards relative to the number of true CNVs because a single underlying CNV can sometimes be coded as multiple adjacent calls by the ExomeDepth algorithm. The number of CNVs surviving filtering is slightly elevated relative to the number of surviving indels, because we include CNV calls with a Bayes factor down to 4.5 for maximum sensitivity and because CNVs do not undergo any external cohort-based frequency filtering. Het, heterozygous.