Fig. 3.

Cutoff thresholds for copy number variant (CNV) confirmation. A Boxplot displays of the cutoffs used to confirm deletions and duplications across 50 samples and 56 CNVs (including the false-positive CNV). The cutoff thresholds for CNVs were set at three standard deviations from the mean of either the mean depth ratios of the five control regions or the mean depth ratios of the five control regions and two pad regions, whichever was larger or smaller for deletions and duplications, respectively. ^***, p < 0.001. The dashed gray line denotes a mean depth ratio of 1, which would be the expected mean depth ratio for a region not affected by a CNV. B Scatter plot of the difference between the CNV mean depth ratio and its dynamically determined cutoff for each of the 56 deletion, duplication, or control variants. The difference for deletions was calculated as the CNV depth ratio subtracted from the deletion depth ratio cutoff, and the difference for duplications was calculated as the duplication depth ratio cutoff subtracted from the CNV depth ratio, such that confirmed CNVs appear above zero, denoted by the red dashed line