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. 

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: (C/T)p*C->T

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

• n3 = number of nonsilent mutations of type: A->G

• n4 = number of nonsilent mutations of type: transver

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

• n6 = number of nonsilent mutations of type: double_null

• p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene

• p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene

• 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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IDH1

Figure S1.  This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

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RAC1

Figure S2.  This figure depicts the distribution of mutations and mutation types across the RAC1 significant gene.

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ADAMTS9

Figure S3.  This figure depicts the distribution of mutations and mutation types across the ADAMTS9 significant gene.

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SERPINI2

Figure S4.  This figure depicts the distribution of mutations and mutation types across the SERPINI2 significant gene.

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EYA1

Figure S5.  This figure depicts the distribution of mutations and mutation types across the EYA1 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)

Note:

n - number of mutations in this gene in the individual set.

mindist - distance (in aa) between closest pair of mutations in this gene

npairs3 - how many pairs of mutations are within 3 aa of each other.

npairs12 - how many pairs of mutations are within 12 aa of each other.