File Description *_sorted_anz2.txt "MAF file with mutations sorted by Tumor_Sample_Barcode, Chromosome, and Start_position. Contains additional columns identifying complex mutations and mutation clusters as well as columns describing the content of mutation clusters" *_sorted_anz3.txt "MAF file with columns immediately relevant to APOBEC ( and colocalization analyses added, when available)" *_sorted_anz4.txt "MAF file, similar to _anz3 with more columns beyond immediately relevant to APOBEC and colocalization analyses" *_sorted_anz5.txt "MAF file, similar to _anz3 with additional columns containing metrics describing the amount and statistical evalution of APOBEC mutagenesis in individual samples." *_sorted_clusterSum.txt summary of cluster finding (and cluster-to-breakpoint colocalization analysis when available) *_sorted_graph1.png Figure 1. Fold-enrichment of APOBEC mutagenesis signature over the expected for random mutagenesis. *_sorted_graph2.png Figure 2. Fold enrichment of the APOBEC mutagenesis signature over the expected for random mutagenesis in individual samples. *_sorted_graph3.png Figure 3. Relative and absolute load of APOBEC signature mutations. *_sorted_graph4.png Figure 4. Numbers of APOBEC and non-APOBEC mutations in each sample. *_sorted_graph5.png Figure 5. Numbers of different types of mutation clusters. *_sorted_graph6.png Figure 6. The number of C- or G-coordinated clustered mutations occurring in different known C- or G-specific mutation signatures. Counts are totaled among all samples. *_sorted_graph7.png Figure 7. The number of the three possible substitutions at the tCw motif (complementary mutations included) within C- or G-coordinated clusters. *_sorted_graph8.png Figure 8. Fold enrichment of the APOBEC mutation signature in clusters of different sizes and in non-clustered (scattered) mutations. *_sorted_sum_all.txt sample-specific results of analyses for all post-filtering mutations in the MAF *_sorted_sum_all_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in the MAF including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum_all_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in the MAF including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum_clusters.txt sample-specific results of analyses for all post-filtering mutations in all clusters *_sorted_sum_clusters_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in all clusters including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum_clusters_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in all clusters including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum_G_C_clusters.txt sample-specific results of analyses for all post-filtering mutations in C- and G-coordinated clusters *_sorted_sum_G_C_clusters_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum_G_C_clusters_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum_non_clusters.txt sample-specific results of analyses for all post-filtering mutations in non-coordinated clusters *_sorted_sum_non_clusters_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum_non_clusters_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum_scattered.txt sample-specific results of analyses for all post-filtering mutations in the MAF not belonging to any cluster *_sorted_sum_scattered_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in the MAF not belonging to any cluster including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum_scattered_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in the MAF not belonging to any cluster including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum01a.txt sample-specific results of analyses for all post-filtering mutations in non-coordinated clusters consisting of 2 mutations *_sorted_sum01a_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of 2 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum01a_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of 2 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum01b.txt sample-specific results of analyses for all post-filtering mutations in non-coordinated clusters consisting of 3 mutations *_sorted_sum01b_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of 3 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum01b_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of 3 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum01c.txt sample-specific results of analyses for all post-filtering mutations in non-coordinated clusters consisting of >3 mutations *_sorted_sum01c_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of >3 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum01c_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of >3 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum01f.txt sample-specific results of analyses for all post-filtering mutations in non-coordinated clusters consisting of 4 mutations *_sorted_sum01f_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of 4 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum01f_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of 4 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum01g.txt sample-specific results of analyses for all post-filtering mutations in non-coordinated clusters consisting of >4 mutations *_sorted_sum01g_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of >4 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum01g_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of >4 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum01h.txt sample-specific results of analyses for all post-filtering mutations in non-coordinated clusters consisting of 5 mutations *_sorted_sum01h_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of 5 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum01h_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of 5 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum01i.txt sample-specific results of analyses for all post-filtering mutations in non-coordinated clusters consisting of >5 mutations *_sorted_sum01i_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of >5 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum01i_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in non-coordinated clusters consisting of >5 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum04a.txt sample-specific results of analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of 2 mutations *_sorted_sum04a_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of 2 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum04a_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of 2 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum04b.txt sample-specific results of analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of 3 mutations *_sorted_sum04b_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of 3 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum04b_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of 3 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum04c.txt sample-specific results of analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of >3 mutations *_sorted_sum04c_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of >3 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum04c_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of >3 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum04f.txt sample-specific results of analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of 4 mutations *_sorted_sum04f_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of 4 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum04f_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of 4 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum04g.txt sample-specific results of analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of >4 mutations *_sorted_sum04g_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of >4 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum04g_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of >4 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum04h.txt sample-specific results of analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of 5 mutations *_sorted_sum04h_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of 5 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum04h_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of 5 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum04i.txt sample-specific results of analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of >5 mutations *_sorted_sum04i_fisher.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of >5 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments *_sorted_sum04i_fisher_Pcorr.txt sample-specific results of APOBEC-related analyses for all post-filtering mutations in C- and G-coordinated clusters consisting of >5 mutations including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing *_sorted_sum10c.txt "sample-specific results of analyses for all post-filtering mutations in the MAF not belonging to any cluster. Identical to *_sorted_sum_scattered.txt, but generated by a rule-based naming conventions" *_sorted_sum10c_fisher.txt "sample-specific results of APOBEC-related analyses for all post-filtering mutations in the MAF not belonging to any cluster including Fisher's Exact Test statistical evaluation of APOBEC enrichments. Identical to *_sorted_sum_scattered_fisher.txt, but generated by a rule-based naming conventions" *_sorted_sum10c_fisher_Pcorr.txt "sample-specific results of APOBEC-related analyses for all post-filtering mutations in the MAF not belonging to any cluster including Fisher's Exact Test statistical evaluation of APOBEC enrichments corrected for multiple testing. Identical to *_sorted_sum_scattered_fisher_Pcorr.txt, but generated by a rule-based naming conventions" *_sorted_sum_APOBECenrich_ClustSize.txt Summary table containing values that underline Figure 8. Fold enrichment with tCw mutation motif in C-mutations within clusters of different sizes and in non-clustered (scattered) mutations.