Mutation Analysis (MutSig v2.0)
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
Maintained by David Heiman (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C11V5D6J
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:KIRP-TP.final_analysis_set.maf

  • Blacklist used for this analysis: pancan_mutation_blacklist.v14.hg19.txt

  • Significantly mutated genes (q ≤ 0.1): 23

  • Mutations seen in COSMIC: 56

  • Significantly mutated genes in COSMIC territory: 4

  • Significantly mutated genesets: 0

  • Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing
  • Read 161 MAFs of type "maf1"

  • Total number of mutations in input MAFs: 15585

  • After removing 512 blacklisted mutations: 15073

  • After removing 403 noncoding mutations: 14670

  • After collapsing adjacent/redundant mutations: 14636

Mutation Filtering
  • Number of mutations before filtering: 14636

  • After removing 901 mutations outside gene set: 13735

  • After removing 38 mutations outside category set: 13697

  • After removing 1 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 12757

- Results
+ Breakdown of Mutations by Type
+ Breakdown of Mutation Rates by Category Type
+ Target Coverage for Each Individual
+ Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples
+ Lego Plots
+ CoMut Plot
+ Significantly Mutated Genes
+ COSMIC analyses
+ Geneset Analyses
+ Methods & Data