Figure 3.

Selection pressure against INDELs

(A) The ratio of the number of INDELs to the number of SNVs per cell.

(B) The fraction of mutations (SNVs and INDELs combined) at evolutionarily conserved and accelerated sites out of total mutations (wild type and Msh2^−/− combined). The fractions of SNVs and INDELs at conserved and accelerated sites by chance alone were estimated based on randomly generated mutations using SigProfilerSimulator.³¹ We randomly generated the same number of SNVs and INDELs as the observed numbers with also the same mutation signature, performed the same analysis of their conservation scores, and repeated the above two steps 2,000 times to reach stable estimations. Because there is no difference between the values of SNVs and INDELs expected by chance alone, we merged them into two single values as indicated by the two dashed lines (for conserved and accelerated sites separately).

Boxplot elements are defined as follows: center line indicates median, box limits indicate upper and lower quartiles, and whiskers indicate 1.5× interquartile range.