Fig. 2

Ambiguous evidence for whether germline leakage explains some shared variants. Putative somatic variants are more likely to be shared with germline variants at sites with lower matched-normal read depth – which are just the sites with the lowest power to exclude germline leakage (a, black points). Alternatively, sites with lower matched-normal read-depth also happen to be sites with a high proportion of CpG dinucleotides, whose chemical instability could explain high rates of shared variants without appealing to germline leakage (a, gray points). In turn, the association between low read depth and high proportion of CpG dinucleotides may be related to the fact that CpG dinucleotides occur more frequently within GC-rich regions, and extreme GC content associates with low read depth (b)