Fig. 2

Comparison of the neoantigen repertoire derived from SVs to that from SNVs and indels. a Venn diagram of the intersection of neoantigen repertoire from SVs, SNVs, and indels. b, c Boxplots of the neoantigen load (b) and per-mutation neoantigenic rate (c) of every patient for SVs, SNVs, and indels (two-sided Wilcoxon rank-sum test). Boxplot hinges represent the 25th to 75th percentiles, and central lines represent median values; violin plots refer to the kernel probability densities. d Relative contributions of SVs, SNVs, and indels to the neoantigen repertoires of 4 representative cancer types. e Proportions of neoantigens with high or low self-similarity from SVs, SNVs, and indels (two-sided Fisher’s exact test)