Figure 2

Sequencing coverage and read-mapping results for validated somatic mutations and false positives. (A) Log2-scaled read depths for sites harboring validated somatic mutations (red dots) and mutations that failed validation (black stars), in the tumor and normal samples from each individual predicted to harbor the mutation. (B) Fraction of reads containing the non-reference allele that mapped uniquely by BWA for validated somatic mutations (Somatic), mutations that were also detected in the germline sample during validation (Germline) and those that were not detected in either the tumor or the germline during validation (Did Not Validate; DNV). (C) Fraction of reads mapped by BWA using mate-pair rescue for validated somatic mutations (Somatic), mutations that were also detected in the germline sample during validation (Germline) and those that were not detected in either the tumor or the germline during validation (DNV). (B,C) Each box covers the interquartile range, with a horizontal line representing the median. Whiskers indicate the minimum and maximum values.