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). If the figure is unpopulated, then full coverage is assumed (e.g. MutSig CV doesn't use WIGs and assumes full coverage).

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: Tp*C->(T/G)

• n2 = number of nonsilent mutations of type: Tp*C->A

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

• n4 = number of nonsilent mutations of type: A->mut

• 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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PIK3CA

Figure S1.  This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

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TP53

Figure S2.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

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CDKN1A

Figure S3.  This figure depicts the distribution of mutations and mutation types across the CDKN1A significant gene.

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RB1

Figure S4.  This figure depicts the distribution of mutations and mutation types across the RB1 significant gene.

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ARID1A

Figure S5.  This figure depicts the distribution of mutations and mutation types across the ARID1A significant gene.

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MLL2

Figure S6.  This figure depicts the distribution of mutations and mutation types across the MLL2 significant gene.

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FBXW7

Figure S7.  This figure depicts the distribution of mutations and mutation types across the FBXW7 significant gene.

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KDM6A

Figure S8.  This figure depicts the distribution of mutations and mutation types across the KDM6A significant gene.

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ELF3

Figure S9.  This figure depicts the distribution of mutations and mutation types across the ELF3 significant gene.

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FGFR3

Figure S10.  This figure depicts the distribution of mutations and mutation types across the FGFR3 significant gene.

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FOXQ1

Figure S11.  This figure depicts the distribution of mutations and mutation types across the FOXQ1 significant gene.

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STAG2

Figure S12.  This figure depicts the distribution of mutations and mutation types across the STAG2 significant gene.

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NFE2L2

Figure S13.  This figure depicts the distribution of mutations and mutation types across the NFE2L2 significant gene.

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CDKN2A

Figure S14.  This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.

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KLF5

Figure S15.  This figure depicts the distribution of mutations and mutation types across the KLF5 significant gene.

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ASXL2

Figure S16.  This figure depicts the distribution of mutations and mutation types across the ASXL2 significant gene.

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TSC1

Figure S17.  This figure depicts the distribution of mutations and mutation types across the TSC1 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)