Fig. 3: Recoverability simulation and effects of subclones on mutation concordance.

a Observed recovery rate of PCAWG variants in MC3 (red) and of MC3 variants in PCAWG (blue), alongside sequencing noise simulations calculated from random draws of a binomial model that incorporates the VAF and estimated read depth at each site (light red simulates PCAWG recoverability of MC3 variants, and light blue simulated MC3 recoverability of PCAWG variants). Y-axis is described with legend. X-axis displays VAF of the comparative data set in regard to Y. b A stacked bar chart displays the proportion of matched and unique variants (y-axis) for different VAF bins (x-axis). 180 variants did not provide read count information and were removed from this figure. c Stacked proportional histogram shows the fractions of PCAWG matched mutations (purple) and PCAWG-unique mutations (red). Mutations were restricted to SNVs, and subclonality predictions are indicated as either ‘Clonal’ or ‘Sub-clonal’. Columns 2–4 reflect sub-clonal assignment provided by PCAWG (Note: only a few samples reported five predicted subclones and were not included in this analysis). The number of variants represented for each clonal assignment is shown on the x-axis. d Similar to panel c, a stacked proportional histogram illustrates the proportion of matched and unique variants for MC3 which provide estimates of total number of matched or unique variants called by MC3.