Figure S7.

Variant Allele Fraction Distribution Plots for Cell Line Clones, Related to Figure 3, Figure 4, Figure 5

(A and B) Distribution plots showing frequencies of the variant alleles fractions (VAFs) of mutations that remain after the filtering steps (STAR Methods) in indicated clones analyzed by whole-exome (panel A) or whole-genome sequencing (panel B). VAF peaks often deviate from 50%, expected for clonal heterozygous somatic mutations in a diploid genome, because cancer cell lines are often polyploid and heterozygous copy number changes across the genome can further modulate the distribution of the VAF. Bimodal distributions and subclonal peaks can arise from mixed effects of mutations being acquired on different copy number states of the genome and/or subclonally. Minor proportion of mutations presenting at 100% of the reads in some clones can reflect loss of heterozygosity at the loci of the newly acquired mutations or residual germline variants, mainly in parent clones that were compared against the unmatched normal human genome (STAR Methods).