patient samples, color-coded by type of mutation, for the significantly mutated genes.

The rate of synonymous and non-synonymous mutations is displayed at the top of the matrix. The barplot on

the left of the matrix shows the number of mutations in each gene. The percentages represent the fraction

of tumors with at least one mutation in the specified gene. The barplot to the right of the matrix displays

the q-values for the most significantly mutated genes. The purple boxplots below the

matrix (only displayed if required columns are present in the provided MAF) represent

the distributions of allelic fractions observed in each sample. The

plot at the bottom represents the base substitution distribution of individual samples,

using the same categories that were used to calculate significance.

nncd = number of noncoding mutations in this gene across the cohort

nsil = number of silent mutations in this gene across the cohort

nmis = number of missense mutations in this gene across the cohort

nstp = number of readthrough mutations in this gene across the cohort

nspl = number of splice site mutations in this gene across the cohort

nind = number of indels in this gene across the cohort

nnon = number of (nonsilent) mutations in this gene across the cohort

npat = number of patients (individuals) with at least one nonsilent mutation

nsite = number of unique sites having a non-silent mutation

Abundance (pCV) = Probability that the gene's overall

nonsilent mutation rate exceeds its inferred background

mutation rate (BMR), which is computed based on the

gene's own silent mutation rate plus silent mutation

rates of genes with similar covariates. BMR calculations

are normalized with respect to patient-specific and

Clustering (pCL) = Probability that recurrently mutated

loci in this gene have more mutations than expected by

chance. While pCV assesses the gene's overall mutation

burden, pCL assesses the burden of specific sites within

the gene. This allows MutSig to differentiate between

genes with uniformly distributed mutations and genes