Fig. 5

Analysis of the PCAWG consensus calls with CNAqc. a QC for simple CNAs in \(n=2589\) PCAWG samples (median coverage 45 ×), using consensus CNAs and mutation calls. The plot shows the percentage of cases with pass status, split by segment type, multiplicity, and tumor type, with sample size shown with the asterisks. b Proportion of cases that pass QC, split by purity (low, mid and high) and median depth of sequencing (removing outliers with depth < 24 × or > 129 ×). c QC for \(n=570\) PCAWG samples with complex CNAs and > 150 mutations per segment, with tumor types ranked by number of cases. Numbers report the absolute number of cases. d Best evolution model used to analyze \(n=538\) PCAWG samples with subclonal CNAs and > 150 mutations per segment, with tumor types ranked by number of cases. e Regression of tumor purity against the proportion of segments with unassigned CCF values using the entropy method in CNAqc