Fig. 2

Comparison of sequencing errors with known somatic mutations in deep sequencing data generated from diluted COLO829 cancer cell line. a Error rate (y-axis) in BRAF V600 amplicon (x-axis: chr7 positions) under standard pileup (top) and CleanDeepSeq (bottom). A>T errors are shown in red and other errors shown in gray. Known somatic mutation BRAF V600E is shown in purple. Also shown are error rates summarized at sample level by pileup (left panels, “Methods”) or CleanDeepSeq (right panels) for 1:1000 dilution (b) and 1:5000 dilution (c). The 12 possible substitution patterns (first parenthesis) are depicted in rows. Median error rates (log10 scale) are indicated on the left, and sample sizes (number of genomic sites) for the histogram are indicated on the right in the second parenthesis. The x-axis displays the error rate in log10 scale. The designed MAF ladders for the known somatic mutations were depicted using red, blue, and black lines labeled on top, and the known somatic mutations were colored according to their expected MAF. Black arrow: BRAF V600E, which has 4 mutant alleles and 2 wildtype alleles in COLO829, so that at 1:1000 dilution and 1:5000 dilution the expected MAF are 0.002 and 0.0004, respectively (“Methods”)