The x axis represents the samples. The y axis represents the exons, one row per exon, and they are sorted by average coverage across samples. For exons with exactly the same average coverage, they are sorted next by the %GC of the exon. (The secondary sort is especially useful for the zero-coverage exons at the bottom).

Figure 1. 

The mutation spectrum is depicted in the lego plots below in which the 96 possible mutation types are subdivided into six large blocks, color-coded to reflect the base substitution type. Each large block is further subdivided into the 16 possible pairs of 5' and 3' neighbors, as listed in the 4x4 trinucleotide context legend. The height of each block corresponds to the mutation frequency for that kind of mutation (counts of mutations normalized by the base coverage in a given bin). The shape of the spectrum is a signature for dominant mutational mechanisms in different tumor types.

Figure 3.  Get High-res Image SNV Mutation rate lego plot for entire set. Each bin is normalized by base coverage for that bin. Colors represent the six SNV types on the upper right. The three-base context for each mutation is labeled in the 4x4 legend on the lower right. The fractional breakdown of SNV counts is shown in the pie chart on the upper left. If this figure is blank, not enough information was provided in the MAF to generate it.

Figure 4.  Get High-res Image SNV Mutation rate lego plots for 4 slices of mutation allele fraction (0<=AF<0.1, 0.1<=AF<0.25, 0.25<=AF<0.5, & 0.5<=AF) . The color code and three-base context legends are the same as the previous figure. If this figure is blank, not enough information was provided in the MAF to generate it.

Column Descriptions:

• N = number of sequenced bases in this gene across the individual set

• n = number of (nonsilent) mutations in this gene across the individual set

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

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

• nsil = number of silent mutations in this gene across the individual set

• n1 = number of nonsilent mutations of type: *CpG->(A/T)

• n2 = number of nonsilent mutations of type: *Cp(A/C/T)->(A/T)

• n3 = number of nonsilent mutations of type: A->(C/G)

• n4 = number of nonsilent mutations of type: flip

• n5 = number of nonsilent mutations of type: indel+null

• n6 = number of nonsilent mutations of type: double_null

• p_cons = p-value for enrichment of mutations at evolutionarily most-conserved sites in gene

• p_joint = p-value for clustering + conservation

• p = p-value (overall)

• q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

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CTNNB1

Figure S1.  This figure depicts the distribution of mutations and mutation types across the CTNNB1 significant gene.

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SPOP

Figure S2.  This figure depicts the distribution of mutations and mutation types across the SPOP significant gene.

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PTEN

Figure S3.  This figure depicts the distribution of mutations and mutation types across the PTEN significant gene.

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PCDHAC2

Figure S4.  This figure depicts the distribution of mutations and mutation types across the PCDHAC2 significant gene.

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FOXA1

Figure S5.  This figure depicts the distribution of mutations and mutation types across the FOXA1 significant gene.

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TP53

Figure S6.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

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TMEM216

Figure S7.  This figure depicts the distribution of mutations and mutation types across the TMEM216 significant gene.

In this analysis, COSMIC is used as a filter to increase power by restricting the territory of each gene. Cosmic version: v48.

Note:

n - number of (nonsilent) mutations in this gene across the individual set.

cos = number of unique mutated sites in this gene in COSMIC

n_cos = overlap between n and cos.

N_cos = number of individuals times cos.

cos_ev = total evidence: number of reports in COSMIC for mutations seen in this gene.

p = p-value for seeing the observed amount of overlap in this gene)

q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)