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.
