Fig. 5. WGS mutations in exonic regions not captured by WES.

a A sunburst diagram provides a breakdown of variants that are removed during the coverage step of the tool. The innermost circle represents the total number of variants identified upon filtering for exome beds used by MC3. Then, we restrict PCAWG variants to well-covered MC3 regions for each sample. The majority of gencode.v19 annotated and the BROAD target bed file of exonic regions are sufficiently covered by PCAWG in flanking regions: 3’UTRs, 5’UTR, and 5’Flanking. The outermost ring illustrates the number mutations identified by PCAWG that were poorly covered by MC3. b A density plot illustrates the density of percent GC-content from a 100 bp window surrounding a variant. Four variant-sets are displayed: matched, private to MC3, private to PCAWG, and we extend our dataset to include exonic variants not covered by WES but sufficiently covered in WGS (Covered by PCAWG only). c A scatter plot displays mean sequence depth (y-axis) by increasing GC-content bins (x-axis). Points are colored according to variant set (same as panel b). d–f Total annotated mutations counts from 3 different annotated regions are shown for 5UTR, 3UTR, and missense mutations, respectively. g Expression Z−Scores for 3’UTR using all TCGA-UCEC samples. Cis-RNAseq expression violin plots are displayed for 13 genes. On top of the gene-level distribution violin plot, box and whisker plots display sample expression based on mutation classification (box include 25th quantile to 75th quantiles, and whiskers extend to 1.5 times the interquartile range).