Evidence for gene conversion from a linked germline variant. (A–E) The process of producing clear evidence for gene conversion under a model with two sites, site-S and site-G. Zero and one represent the original and derived alleles. See text for details. (F) An example case (Patient ID, TCGA-AX-A2HC) with strong evidence for gene conversion. Short-reads of normal cells and tumor cells in regions Chr 2: 216,205,235–216,205,285 regions are shown. The figure was made using the Integrative Genomics Viewer (IGV) (Robinson et al. 2011). (G) The proportion of sites with evidence for gene conversion was confirmed by a linked germline variant, as a function of the distance to the germline variant site. The error bars represent the 95% confidence intervals.