Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	TTotCov	TVarCov	NTotCov	NVarCov	TVarRat	NVarRat	dbSNP_AF	dbSNP_PopFreq	dbSNP_Strength	COSMIC_Codon	COSMIC_Gene	COSMIC_Gene_Freq	COSMIC_Site_Freq	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	Confidence	Algorithm
GPR25	2848	hgsc.bcm.edu	37	1	200843152	200843178	+	In_Frame_Del	DEL	GGCGCGAAGGATCAGCTCAGCCTCCTC	GGCGCGAAGGATCAGCTCAGCCTCCTC	-	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	GGCGCGAAGGATCAGCTCAGCCTCCTC	GGCGCGAAGGATCAGCTCAGCCTCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	99	15	100	0	0.151515	0	.	.	none	.	GPR25	23	.	NM_005298	exon1	c.986_1012del	p.329_338del	.	.	PASS	Atlas-Indel
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056512	26056513	+	Frame_Shift_Ins	INS	-	-	CA	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	73	12	76	0	0.164384	0	.	.	none	.	HIST1H1C	80	.	NM_005319	exon1	c.145_146insTG	p.A49fs	.	.	PASS	Atlas-Indel
DGKB	1607	hgsc.bcm.edu	37	7	14775822	14775822	+	Splice_Site	DEL	G	G	-	rs139628753	bycluster;by1000genomes	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	170	62	219	0	0.364706	0	G|0.405;-|0.595	0.595	strong	.	DGKB	166	.	NM_004080	exon5	c.169-2C>-	.	.	.	PASS	Atlas-Indel
USP9Y	8287	hgsc.bcm.edu	37	Y	14968773	14968773	+	Splice_Site	DEL	A	A	-	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	53	11	25	0	0.207547	0	.	.	none	.	USP9Y	49	.	NM_004654	exon44	c.7434+2A>-	.	.	.	PASS	Atlas-Indel
CUBN	8029	hgsc.bcm.edu	37	10	16883024	16883024	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	75	10	73	0	0.133333	0	.	.	none	.	CUBN	515	.	NM_001081	exon61	c.9687delT	p.N3229fs	.	.	PASS	Atlas-Indel
PCDH1	5097	hgsc.bcm.edu	37	5	141248200	141248200	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	62	10	84	.	0.161	.	.	.	none	.	PCDH1	119	.	NM_032420	exon2	c.838delT	p.F280fs	.	.	PASS	Pindel,Atlas-Indel
SLC16A7	9194	hgsc.bcm.edu	37	12	60168856	60168856	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	137	23	130	.	0.168	.	.	.	none	SLC16A7,NS,carcinoma,-1,1	SLC16A7	82	1	NM_001270623	exon5	c.779delG	p.G260fs	.	.	PASS	Pindel,Atlas-Indel
MAZ	4150	hgsc.bcm.edu	37	16	29819056	29819064	+	In_Frame_Del	DEL	AGCGCAAGG	AGCGCAAGG	-	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	AGCGCAAGG	AGCGCAAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	74	13	82	0	0.175676	0	.	.	none	.	MAZ	48	.	NM_002383	exon2	c.949_957del	p.317_319del	.	.	PASS	Atlas-Indel
PLEKHD1	400224	hgsc.bcm.edu	37	14	69966878	69966879	+	Frame_Shift_Ins	INS	-	-	AAAA	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	66	12	61	0	0.181818	0	.	.	none	.	PLEKHD1	24	.	NM_001161498	exon2	c.196_197insAAAA	p.E66fs	.	.	PASS	Atlas-Indel
CRELD2	79174	hgsc.bcm.edu	37	22	50315936	50315973	+	Frame_Shift_Del	DEL	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	-	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	39	10	28	0	0.25641	0	.	.	none	.	CRELD2	57	.	NM_001135101	exon6	c.593_620del	p.198_207del	.	.	PASS	Atlas-Indel
RTCA	8634	hgsc.bcm.edu	37	1	100731979	100731985	+	Splice_Site	DEL	GAGTACA	GAGTACA	-	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	GAGTACA	GAGTACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	105	12	98	0	0.114286	0	.	.	none	.	.	.	.	.	.	.	.	.	.	PASS	Atlas-Indel
HIST1H3F	8968	hgsc.bcm.edu	37	6	26250470	26250480	+	Frame_Shift_Del	DEL	GCATGATAGTC	GCATGATAGTC	-	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	GCATGATAGTC	GCATGATAGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	69	14	94	.	0.203	.	.	.	none	.	HIST1H3F	16	.	NM_021018	exon1	c.355_365del	p.119_122del	.	.	PASS	Pindel,Atlas-Indel
KRTAP5-3	387266	hgsc.bcm.edu	37	11	1629430	1629431	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	136	25	199	0	0.183824	0	.	.	none	.	KRTAP5-3	33	.	NM_001012708	exon1	c.186_187insG	p.G62fs	.	.	PASS	Atlas-Indel
DSPP	1834	hgsc.bcm.edu	37	4	88537205	88537213	+	In_Frame_Del	DEL	GACAGCAGT	GACAGCAGT	-	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	GACAGCAGT	GACAGCAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	87	77	71	0	0.885057	0	.	.	none	.	DSPP	174	.	NM_014208	exon5	c.3390_3398del	p.1130_1133del	.	.	PASS	Atlas-Indel
CRIP1	1396	hgsc.bcm.edu	37	14	105954680	105954681	+	Frame_Shift_Del	DEL	CC	CC	-	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	101	15	136	0	0.148515	0	.	.	none	.	CRIP1	1	.	NM_001311	exon4	c.147_148del	p.49_50del	.	.	PASS	Atlas-Indel
EHD1	10938	hgsc.bcm.edu	37	11	64645661	64645661	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	67	12	82	0	0.179104	0	.	.	none	.	EHD1	31	.	NM_006795	exon1	c.277delA	p.T93fs	.	.	PASS	Atlas-Indel
HIST1H4E	8367	hgsc.bcm.edu	37	6	26204831	26204967	+	Frame_Shift_Del	DEL	GTTTTTCAGATTTTTGCGGCTATTTTCGTTGGTGTGTTGGTCATGTCTGGTCGCGGCAAAGGCGGAAAGGGACTGGGTAAAGGAGGCGCTAAGCGTCACCGTAAGGTCCTGCGAGATAACATCCAGGGCATTACCAA	GTTTTTCAGATTTTTGCGGCTATTTTCGTTGGTGTGTTGGTCATGTCTGGTCGCGGCAAAGGCGGAAAGGGACTGGGTAAAGGAGGCGCTAAGCGTCACCGTAAGGTCCTGCGAGATAACATCCAGGGCATTACCAA	-	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	GTTTTTCAGATTTTTGCGGCTATTTTCGTTGGTGTGTTGGTCATGTCTGGTCGCGGCAAAGGCGGAAAGGGACTGGGTAAAGGAGGCGCTAAGCGTCACCGTAAGGTCCTGCGAGATAACATCCAGGGCATTACCAA	GTTTTTCAGATTTTTGCGGCTATTTTCGTTGGTGTGTTGGTCATGTCTGGTCGCGGCAAAGGCGGAAAGGGACTGGGTAAAGGAGGCGCTAAGCGTCACCGTAAGGTCCTGCGAGATAACATCCAGGGCATTACCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	56	12	69	.	0.214	.	.	.	none	.	HIST1H4E	22	.	NM_003545	wholegene	.	.	.	.	PASS	Pindel
CCDC66	285331	hgsc.bcm.edu	37	3	56650051	56650052	+	In_Frame_Ins	INS	-	-	CTT	rs77152637	bycluster;by1000genomes	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	115	39	121	.	0.339	.	-|0.298;CTT|0.702	0.702	strong	.	CCDC66	145	.	NM_001141947	exon13	c.1813_1814insCTT	p.T605delinsTS	.	.	PASS	Pindel
PCDHB2	56133	hgsc.bcm.edu	37	5	140476411	140476411	+	Silent	SNP	A	A	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	84	4	76	3	0.047619	0.0394737	.	.	none	PCDHB2,NS,carcinoma,0,1	PCDHB2	163	1	NM_018936	exon1	c.A2037C	p.A679A	GGCGGCACCGGCC	.	scavenged	Atlas-SNP
POM121	9883	hgsc.bcm.edu	37	7	72413472	72413472	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	226	4	285	4	0.0176991	0.0140351	.	.	none	POM121_ENST00000395270,NS,carcinoma,0,2	POM121	131	2	NM_172020	exon11	c.G2145A	p.P715P	GCCACCGGGGGCC	.	scavenged	Atlas-SNP
LPHN2	23266	hgsc.bcm.edu	37	1	82415874	82415874	+	Silent	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	120	27	116	0	0.225	0	.	.	none	.	LPHN2	464	.	NM_012302	exon6	c.G1200T	p.V400V	CATAGTGCCTACC	.	PASS	Atlas-SNP
ANKS6	203286	hgsc.bcm.edu	37	9	101518730	101518730	+	Silent	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	42	6	69	0	0.142857	0	.	.	none	.	ANKS6	59	.	NM_173551	exon12	c.C2298A	p.G766G	GCTGGAGCCCCCA	.	PASS	Atlas-SNP
RGMB	285704	hgsc.bcm.edu	37	5	98115299	98115299	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	95	2	108	0	0.0210526	0	.	.	none	RGMB,NS,carcinoma,-1,1	RGMB	29	1	NM_001012761	exon4	c.C275T	p.P92L	AACAGCCAGCCCA	.	scavenged	Atlas-SNP
OSBPL10	114884	hgsc.bcm.edu	37	3	32022446	32022446	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	50	6	43	0	0.12	0	.	.	none	.	OSBPL10	160	.	NM_017784	exon1	c.G226A	p.A76T	CGAGCGCCGGCTC	.	PASS	Atlas-SNP
SLC12A6	9990	hgsc.bcm.edu	37	15	34628685	34628685	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	76	11	93	0	0.144737	0	.	.	none	.	SLC12A6	205	.	NM_133647	exon1	c.C197T	p.A66V	GTGGTGGCCCCAG	.	PASS	Atlas-SNP
AGGF1	55109	hgsc.bcm.edu	37	5	76332463	76332463	+	Missense_Mutation	SNP	C	C	A	rs78273685	bycluster	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	124	6	150	1	0.0483871	0.00666667	A|0.001;C|0.999	0.001	weak	AGGF1,NS,carcinoma,0,1	AGGF1	71	1	NM_018046	exon4	c.C599A	p.A200E	CAGAAGCGGCTGT	.	scavenged	Atlas-SNP
C17orf97	400566	hgsc.bcm.edu	37	17	263682	263682	+	Missense_Mutation	SNP	G	G	A	rs181299622	bycluster;by1000genomes	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	238	5	282	3	0.0210084	0.0106383	G|0.978;A|0.022	0.022	strong	C17orf97_ENST00000360127,NS,carcinoma,0,2	C17orf97	76	2	NM_001013672	exon2	c.G1048A	p.E350K	GACCCCGAGGCCC	.	scavenged	Atlas-SNP
TMC6	11322	hgsc.bcm.edu	37	17	76113396	76113396	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	113	3	128	0	0.0265487	0	.	.	none	TMC6,NS,carcinoma,+1,2	TMC6	42	2	NM_001127198	exon18	c.G2231A	p.R744Q	TGGCCCCGCACCA	.	scavenged	Atlas-SNP
LIMD1	8994	hgsc.bcm.edu	37	3	45636656	45636656	+	Silent	SNP	C	C	T	rs143647674	alternate_allele	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	29	6	39	0	0.206897	0	C|1.000;G|0.000	.	alt	.	LIMD1	34	.	NM_014240	exon1	c.C285T	p.S95S	GGGCAGCAAGCTG	.	PASS	Atlas-SNP
ALX3	257	hgsc.bcm.edu	37	1	110607400	110607400	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	119	26	150	0	0.218487	0	.	.	none	.	ALX3	16	.	NM_006492	exon2	c.C403T	p.P135S	AAAGAGGAAGATG	.	PASS	Atlas-SNP
NFKB2	4791	hgsc.bcm.edu	37	10	104157819	104157819	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	114	16	143	0	0.140351	0	.	.	none	.	NFKB2	48	.	NM_001077494	exon9	c.T743A	p.L248Q	TTTATCTGCTTTG	.	PASS	Atlas-SNP
ABCA10	10349	hgsc.bcm.edu	37	17	67178333	67178333	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	256	48	302	0	0.1875	0	.	.	none	.	ABCA10	209	.	NM_080282	exon23	c.C2730A	p.F910L	CTCCGTGAAGTTA	.	PASS	Atlas-SNP
FAM179B	23116	hgsc.bcm.edu	37	14	45433254	45433254	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	58	9	85	0	0.155172	0	.	.	none	.	FAM179B	115	.	NM_015091	exon1	c.G1630A	p.G544S	GGCTCAGGTAAAA	.	PASS	Atlas-SNP
CAMSAP3	57662	hgsc.bcm.edu	37	19	7670117	7670117	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	69	4	83	0	0.057971	0	.	.	none	KIAA1543,rectum,carcinoma,-2,4	CAMSAP3	131	4	NM_020902	exon2	c.G154T	p.V52L	GAGCACGTGCCCC	.	PASS	Atlas-SNP
SRRM5	100170229	hgsc.bcm.edu	37	19	44118178	44118178	+	Silent	SNP	T	T	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	40	8	55	0	0.2	0	.	.	none	.	SRRM5	38	.	NM_001145641	exon1	c.T1905C	p.S635S	AACCTCTAGCAAG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239047	31239047	+	Missense_Mutation	SNP	G	G	A	rs281860470		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	150	23	133	0	0.153333	0	.	.	weak	.	HLA-C	92	.	NM_002117	exon3	c.C422T	p.A141V	TCGTAGGCGGACT	.	PASS	Atlas-SNP
PCDH15	65217	hgsc.bcm.edu	37	10	55698632	55698632	+	Nonsense_Mutation	SNP	G	G	A	rs202033121	bycluster	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	43	10	44	0	0.232558	0	.	.	weak	PCDH15_ENST00000417177,NS,malignant_melanoma,0,8	PCDH15	1715	8	NM_001142763	exon26	c.C3331T	p.R1111X	GGACTCGAAGTAC	.	PASS	Atlas-SNP
HIST1H2AG	8969	hgsc.bcm.edu	37	6	27100963	27100963	+	Missense_Mutation	SNP	G	G	A	rs201426448		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	111	21	95	0	0.189189	0	G|0.999;A|0.001	0.001	weak	.	HIST1H2AG	37	.	NM_021064	exon1	c.G113A	p.G38D	GCAAAGGCAACTA	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190883051	190883051	+	Missense_Mutation	SNP	G	G	A	rs1803593	bycluster;bysubmitter	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	320	46	393	39	0.14375	0.0992366	G|1.000;|0.000	.	weak	FRG1,NS,carcinoid-endocrine_tumour,0,1	FRG1	76	1	NM_004477	exon8	c.G704A	p.R235Q	AGGCTCGGAAAGA	.	scavenged	Atlas-SNP
PRMT10	90826	hgsc.bcm.edu	37	4	148594981	148594981	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	108	21	102	0	0.194444	0	.	.	none	.	PRMT10	68	.	NM_138364	exon3	c.T383G	p.V128G	AGCTTCACTGCTT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506983	195506983	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	51	6	70	1	0.117647	0.0142857	.	.	none	MUC4_ENST00000463781,NS,carcinoma,+1,2	MUC4	1505	2	NM_018406	exon2	c.C11468T	p.T3823I	AGAGGGGTGGTGT	.	scavenged	Atlas-SNP
CCND2	894	hgsc.bcm.edu	37	12	4383364	4383364	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	177	26	194	0	0.146893	0	.	.	none	.	CCND2	50	.	NM_001759	exon1	c.C158T	p.P53L	TCCAACCCTACAT	.	PASS	Atlas-SNP
SPTLC3	55304	hgsc.bcm.edu	37	20	13107302	13107302	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	82	17	83	0	0.207317	0	.	.	none	.	SPTLC3	78	.	NM_018327	exon9	c.C1217T	p.P406L	GCCCACCGATAGC	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1895963	1895963	+	Missense_Mutation	SNP	A	A	G	rs17855613	bycluster	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	104	13	132	17	0.125	0.128788	.	.	weak	SIRPA,brain,glioma,-2,4	SIRPA	83	4	NM_001040022	exon3	c.A298G	p.N100D	AAGAGAAACAACA	.	scavenged	Atlas-SNP
ANKS1A	23294	hgsc.bcm.edu	37	6	34857318	34857318	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	12	10	6	0	0.833333	0	.	.	none	ANKS1A,NS,carcinoma,0,1	ANKS1A	123	1	NM_015245	exon1	c.A139G	p.S47G	GGCGGCAGCGGCG	.	scavenged	Atlas-SNP
IRF4	3662	hgsc.bcm.edu	37	6	393222	393222	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	205	79	155	0	0.385366	0	.	.	none	.	IRF4	65	.	NM_001195286	exon2	c.C70G	p.L24V	GGGAAGCTCCGCC	.	PASS	Atlas-SNP
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056391	26056391	+	Missense_Mutation	SNP	C	C	T	rs370479531	alternate_allele	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	83	12	114	0	0.144578	0	.	.	alt	.	HIST1H1C	80	.	NM_005319	exon1	c.G266A	p.S89N	CCCTTGCTCACCA	.	PASS	Atlas-SNP
OR7G3	390883	hgsc.bcm.edu	37	19	9236917	9236917	+	Missense_Mutation	SNP	G	G	A	rs61730387	bycluster;byfrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	104	6	142	0	0.0576923	0	G|0.935;A|0.065	0.065	strong	.	OR7G3	41	.	NM_001001958	exon1	c.C710T	p.A237V	GAAAAAGCTTTAT	.	PASS	Atlas-SNP
TRIM49	57093	hgsc.bcm.edu	37	11	89531510	89531510	+	Missense_Mutation	SNP	C	C	T	rs570208	bycluster	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	135	7	120	6	0.0518519	0.05	C|0.500;T|0.500	0.500	weak	TRIM49,extremity,malignant_melanoma,0,1	TRIM49	45	1	NM_020358	exon8	c.G1147A	p.V383I	TCTTAACACACCC	.	scavenged	Atlas-SNP
HIBADH	11112	hgsc.bcm.edu	37	7	27702327	27702327	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	135	25	158	0	0.185185	0	.	.	none	.	HIBADH	28	.	NM_152740	exon1	c.C81T	p.S27S	TGCAAAGCTGCCG	.	PASS	Atlas-SNP
ITGA4	3676	hgsc.bcm.edu	37	2	182322531	182322531	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	70	12	82	0	0.171429	0	.	.	none	ITGA4,colon,carcinoma,+1,1	ITGA4	142	1	NM_000885	exon1	c.G150A	p.T50T	CAACACGCTGTTC	.	PASS	Atlas-SNP
TFAP2D	83741	hgsc.bcm.edu	37	6	50712940	50712940	+	Missense_Mutation	SNP	A	A	G	rs201424626	by1000genomes	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	182	39	198	1	0.214286	0.00505051	A|1.000;G|0.000	0.000	strong	TFAP2D,NS,carcinoma,0,1	TFAP2D	144	1	NM_172238	exon6	c.A1004G	p.K335R	CAAGAAAAAAGAT	.	scavenged	Atlas-SNP
ANXA11	311	hgsc.bcm.edu	37	10	81930597	81930597	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	42	13	68	1	0.309524	0.0147059	.	.	none	ANXA11,right_upper_lobe,carcinoma,0,1	ANXA11	32	1	NM_145868	exon4	c.A130T	p.T44S	CATAGGTGGCCAC	.	scavenged	Atlas-SNP
PRAMEF1	65121	hgsc.bcm.edu	37	1	12855647	12855647	+	Silent	SNP	C	C	T	rs200536957		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	193	15	210	5	0.0777202	0.0238095	C|0.999;T|0.001	0.001	weak	PRAMEF1,NS,carcinoma,+2,2	PRAMEF1	78	2	NM_023013	exon4	c.C927T	p.D309D	AGAAGACATGAAG	.	scavenged	Atlas-SNP
GDI1	2664	hgsc.bcm.edu	37	X	153670076	153670076	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	137	29	105	0	0.211679	0	.	.	none	.	GDI1	36	.	NM_001493	exon8	c.A926G	p.K309R	CCATCAAGAACAC	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152671306	152671306	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	61	13	83	0	0.213115	0	.	.	none	.	SYNE1	3227	.	NM_182961	exon72	c.C11898G	p.H3966Q	TACCTTGTGGTGG	.	PASS	Atlas-SNP
TBP	6908	hgsc.bcm.edu	37	6	170871055	170871055	+	Silent	SNP	G	G	A	rs112928724		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	32	6	42	2	0.1875	0.047619	G|0.500;A|0.500	0.500	weak	TBP,colon,carcinoma,0,2	TBP	58	2	NM_003194	exon3	c.G231A	p.Q77Q	GCAGCAGCAGCAG	.	scavenged	Atlas-SNP
SCRN2	90507	hgsc.bcm.edu	37	17	45915662	45915662	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	48	14	72	0	0.291667	0	.	.	none	.	SCRN2	35	.	NM_138355	exon7	c.G1093T	p.A365S	CCAGGGCTGCCTG	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88956767	88956767	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	94	12	90	0	0.12766	0	.	.	none	.	ZNF804B	322	.	NM_181646	exon3	c.A359C	p.E120A	TGGCTGAGTTAAG	.	PASS	Atlas-SNP
PRCC	5546	hgsc.bcm.edu	37	1	156737930	156737930	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	39	6	46	0	0.153846	0	.	.	none	.	PRCC	39	.	NM_005973	exon1	c.C367T	p.P123S	AATCTGCCCCCTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508903	195508903	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	54	9	79	2	0.166667	0.0253165	.	.	none	MUC4_ENST00000463781,NS,malignant_melanoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C9548T	p.T3183M	AGAGGCGTGGTGT	.	scavenged	Atlas-SNP
C1S	716	hgsc.bcm.edu	37	12	7173133	7173133	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	91	11	108	0	0.120879	0	.	.	none	.	C1S	93	.	NM_201442	exon7	c.G730C	p.D244H	GCAGGAGATCGGC	.	PASS	Atlas-SNP
MST1	4485	hgsc.bcm.edu	37	3	49723881	49723881	+	Missense_Mutation	SNP	G	G	C	rs6777426	bycluster;byfrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	137	7	182	5	0.0510949	0.0274725	G|0.986;C|0.014	0.014	strong	MST1,extremity,malignant_melanoma,0,1	MST1	84	1	NM_020998	exon8	c.C881G	p.T294S	CTGACAGTTGTGG	.	scavenged	Atlas-SNP
SLC13A5	284111	hgsc.bcm.edu	37	17	6607294	6607294	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	23	6	48	0	0.26087	0	.	.	none	.	SLC13A5	57	.	NM_001143838	exon4	c.C450T	p.P150P	CACGATGGGCACC	.	PASS	Atlas-SNP
NOX4	50507	hgsc.bcm.edu	37	11	89059934	89059934	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	101	21	128	0	0.207921	0	.	.	none	.	NOX4	101	.	NM_016931	exon18	c.C1727A	p.S576Y	CTGAAAGACTCTT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515304	195515304	+	Silent	SNP	T	T	A	rs202019266		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	42	3	60	0	0.0714286	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.A3147T	p.A1049A	TGTGGATGCTGAG	.	scavenged	Atlas-SNP
MN1	4330	hgsc.bcm.edu	37	22	28194930	28194930	+	Silent	SNP	C	C	T	rs45463091	byfrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	52	8	65	1	0.153846	0.0153846	C|0.958;T|0.042	0.042	strong	MN1,colon,carcinoma,0,4	MN1	122	4	NM_002430	exon1	c.G1602A	p.Q534Q	CTGCTGCTGTTGC	.	scavenged	Atlas-SNP
HIST4H4	121504	hgsc.bcm.edu	37	12	14923952	14923952	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	59	12	63	0	0.20339	0	.	.	none	.	HIST4H4	13	.	NM_175054	exon1	c.C67A	p.L23M	CCCGCAGCACCTT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508982	195508982	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	67	11	60	3	0.164179	0.05	.	.	none	MUC4_ENST00000463781,NS,malignant_melanoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G9469A	p.D3157N	AAGTGTCGGTGAC	.	scavenged	Atlas-SNP
KLF2	10365	hgsc.bcm.edu	37	19	16436806	16436806	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	31	9	35	0	0.290323	0	.	.	none	.	KLF2	10	.	NM_016270	exon2	c.G855C	p.K285N	CACCAAGAGTTCG	.	PASS	Atlas-SNP
OR10X1	128367	hgsc.bcm.edu	37	1	158549535	158549535	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	89	8	89	0	0.0898876	0	.	.	none	.	OR10X1	96	.	NM_001004477	exon1	c.T155C	p.L52P	GTGAGAAGGTAGA	.	PASS	Atlas-SNP
HIST1H3I	8354	hgsc.bcm.edu	37	6	27839875	27839875	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	154	60	151	0	0.38961	0	.	.	none	.	HIST1H3I	28	.	NM_003533	exon1	c.G219A	p.R73R	GATCTCCCGTACC	.	PASS	Atlas-SNP
GADD45B	4616	hgsc.bcm.edu	37	19	2476602	2476602	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	66	12	76	0	0.181818	0	.	.	none	.	GADD45B	6	.	NM_015675	exon2	c.G120A	p.V40V	GGGGGTGTACGAG	.	PASS	Atlas-SNP
HIST1H2BN	8341	hgsc.bcm.edu	37	6	27806574	27806574	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	113	22	108	0	0.19469	0	.	.	none	.	HIST1H2BN	11	.	NM_003520	exon1	c.G135A	p.V45V	CAAGGTGCTGAAG	.	PASS	Atlas-SNP
PTPN6	5777	hgsc.bcm.edu	37	12	7061240	7061240	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	83	11	112	0	0.13253	0	.	.	none	.	PTPN6	42	.	NM_080548	exon3	c.G232C	p.V78L	GAGCTGGTGGAGT	.	PASS	Atlas-SNP
ANK2	287	hgsc.bcm.edu	37	4	114290944	114290944	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	84	15	90	0	0.178571	0	.	.	none	.	ANK2	576	.	NM_001148	exon43	c.G11593A	p.D3865N	GATGAAGATGCAG	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525060	248525060	+	Missense_Mutation	SNP	T	T	A	rs28491677	bycluster;byfrequency;by1000genomes	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	241	3	351	4	0.0124481	0.011396	T|0.787;A|0.213	0.213	strong	OR2T4,NS,carcinoma,-1,1	OR2T4	126	1	NM_001004696	exon1	c.T178A	p.C60S	CTACTTTGTGTGG	.	scavenged	Atlas-SNP
RIMS2	9699	hgsc.bcm.edu	37	8	105263908	105263908	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	130	23	125	0	0.176923	0	.	.	none	.	RIMS2	1357	.	NM_001100117	exon24	c.G3910C	p.E1304Q	GAACTAGAGCTAT	.	PASS	Atlas-SNP
IRF4	3662	hgsc.bcm.edu	37	6	393348	393348	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	117	49	96	0	0.418803	0	.	.	none	.	IRF4	65	.	NM_001195286	exon2	c.G196A	p.E66K	CGCGAGGAGGACG	.	PASS	Atlas-SNP
HIST1H4H	8365	hgsc.bcm.edu	37	6	26285420	26285420	+	Missense_Mutation	SNP	C	C	T	rs377418572	alternate_allele	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	95	38	89	0	0.4	0	.	.	alt	.	HIST1H4H	16	.	NM_003543	exon1	c.G308A	p.G103D	CCTTAGCCACCGA	.	PASS	Atlas-SNP
KLF2	10365	hgsc.bcm.edu	37	19	16436833	16436833	+	Silent	SNP	C	C	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	28	9	33	0	0.321429	0	.	.	none	.	KLF2	10	.	NM_016270	exon2	c.C882G	p.R294R	TCTGCGCACGCAC	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017974	1017974	+	Missense_Mutation	SNP	C	C	G	rs200353019	bycluster	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	245	5	306	8	0.0204082	0.0261438	.	.	weak	MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.G4827C	p.Q1609H	TGTGGTCTGAGGG	.	scavenged	Atlas-SNP
CHIT1	1118	hgsc.bcm.edu	37	1	203186950	203186950	+	Nonsense_Mutation	SNP	C	C	T	rs201320385	bycluster;byfrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	74	9	48	0	0.121622	0	C|0.989;T|0.011	0.011	strong	CHIT1,colon,carcinoma,0,2	CHIT1	61	2	NM_003465	exon10	c.G1073A	p.W358X	AGTGCCCAGACCA	.	PASS	Atlas-SNP
IFT88	8100	hgsc.bcm.edu	37	13	21237643	21237643	+	Missense_Mutation	SNP	G	G	A	rs143840290		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	31	6	51	1	0.193548	0.0196078	G|1.000;A|0.000	0.000	weak	IFT88,caecum,carcinoma,0,1	IFT88	83	1	NM_175605	exon25	c.G2102A	p.R701H	GTCTGCGTTTCTT	.	scavenged	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186039858	186039858	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	131	23	126	0	0.175573	0	.	.	none	.	HMCN1	797	.	NM_031935	exon52	c.C8108A	p.S2703Y	TTCCTTCTGCCTC	.	PASS	Atlas-SNP
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234570	26234570	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	117	35	98	0	0.299145	0	.	.	none	.	HIST1H1D	40	.	NM_005320	exon1	c.C592T	p.P198S	CCTTGGGCTTAGG	.	PASS	Atlas-SNP
RHBG	57127	hgsc.bcm.edu	37	1	156347192	156347192	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	76	12	90	0	0.157895	0	.	.	none	.	RHBG	133	.	NM_020407	exon2	c.G288A	p.L96L	CCTCCTGGCCGCC	.	PASS	Atlas-SNP
NOTCH2	4853	hgsc.bcm.edu	37	1	120539668	120539668	+	Missense_Mutation	SNP	T	T	A	rs200464440	bycluster	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	196	4	242	4	0.0204082	0.0165289	.	.	weak	NOTCH2_ENST00000369342,NS,carcinoma,0,2	NOTCH2	348	2	NM_001200001	exon4	c.A703T	p.T235S	GACAGGTGCCTCC	.	scavenged	Atlas-SNP
SEMA3D	223117	hgsc.bcm.edu	37	7	84629120	84629120	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	62	12	89	0	0.193548	0	.	.	none	.	SEMA3D	177	.	NM_152754	exon17	c.A1970G	p.K657R	TCCTTCTTCTGCA	.	PASS	Atlas-SNP
KCNN3	3782	hgsc.bcm.edu	37	1	154842244	154842244	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	55	13	65	1	0.236364	0.0153846	.	.	none	KCNN3,NS,carcinoma,+1,3	KCNN3	141	3	NM_001204087	exon1	c.T197A	p.L66H	TGCTGAAGCTGCG	.	scavenged	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537078	88537078	+	Silent	SNP	T	T	C	rs373805744	bycluster	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	41	28	18	7	0.682927	0.388889	.	.	weak	DSPP,colon,carcinoma,0,1	DSPP	174	1	NM_014208	exon5	c.T3264C	p.S1088S	TAGCAGTGACAGC	.	scavenged	Atlas-SNP
TAGAP	117289	hgsc.bcm.edu	37	6	159463199	159463199	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	78	11	89	1	0.141026	0.011236	.	.	none	TAGAP,NS,carcinoma,+1,1	TAGAP	75	1	NM_138810	exon5	c.G226A	p.A76T	CCAAAGCCCCAGA	.	scavenged	Atlas-SNP
TBP	6908	hgsc.bcm.edu	37	6	170871067	170871067	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	34	9	39	4	0.264706	0.102564	.	.	none	TBP,NS,carcinoma,0,1	TBP	58	1	NM_003194	exon3	c.G243A	p.Q81Q	GCAGCAGCAGCAG	.	scavenged	Atlas-SNP
ESPN	83715	hgsc.bcm.edu	37	1	6504644	6504644	+	Missense_Mutation	SNP	C	C	T	rs201251427		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	113	26	125	0	0.230089	0	C|0.999;T|0.001	0.001	weak	ESPN,NS,carcinoma,+1,1	ESPN	32	1	NM_031475	exon6	c.C1094T	p.P365L	TCCAGCCGCTGAA	.	PASS	Atlas-SNP
PDE4D	5144	hgsc.bcm.edu	37	5	58334737	58334737	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	72	13	87	0	0.180556	0	.	.	none	.	PDE4D	345	.	NM_001104631	exon6	c.G870A	p.Q290Q	CTCTAGCTGGTCC	.	PASS	Atlas-SNP
NOX4	50507	hgsc.bcm.edu	37	11	89069055	89069055	+	Missense_Mutation	SNP	C	C	A	rs147166939	alternate_allele	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	445	92	523	0	0.206742	0	C|1.000;T|0.000	.	alt	NOX4,colon,carcinoma,0,1	NOX4	101	1	NM_016931	exon17	c.G1574T	p.R525L	TTCCACCGAGGAC	.	PASS	Atlas-SNP
SUV420H2	84787	hgsc.bcm.edu	37	19	55853653	55853653	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	91	5	100	0	0.0549451	0	.	.	none	.	SUV420H2	20	.	NM_032701	exon3	c.C181A	p.L61M	CGGGACCTGGAGG	.	PASS	Atlas-SNP
ADAM9	8754	hgsc.bcm.edu	37	8	38899582	38899582	+	Silent	SNP	C	C	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	194	45	212	0	0.231959	0	.	.	none	.	ADAM9	66	.	NM_003816	exon12	c.C1248A	p.S416S	TCCCTCCTGTGGT	.	PASS	Atlas-SNP
C5orf46	389336	hgsc.bcm.edu	37	5	147286021	147286021	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	281	42	293	0	0.149466	0	.	.	none	.	C5orf46	8	.	NM_206966	exon1	c.T44G	p.L15R	AAGACAAGCAGTC	.	PASS	Atlas-SNP
SLC23A3	151295	hgsc.bcm.edu	37	2	220033469	220033469	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	73	14	112	0	0.191781	0	.	.	none	.	SLC23A3	60	.	NM_001144890	exon5	c.G603A	p.G201G	CAGGGGCCCACAG	.	PASS	Atlas-SNP
ALG9	79796	hgsc.bcm.edu	37	11	111657183	111657183	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	120	5	110	0	0.0416667	0	.	.	none	.	ALG9	77	.	NM_024740	exon16	c.G1795A	p.V599I	AGTTTACGTACAC	.	PASS	Atlas-SNP
CUX2	23316	hgsc.bcm.edu	37	12	111744875	111744875	+	Missense_Mutation	SNP	G	G	A	rs201601231	bycluster;by1000genomes	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	49	10	57	0	0.204082	0	G|1.000;A|0.000	0.000	strong	.	CUX2	145	.	NM_015267	exon11	c.G1009A	p.D337N	ATCGCCGACCTGG	.	PASS	Atlas-SNP
KCNC2	3747	hgsc.bcm.edu	37	12	75436936	75436936	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	102	19	148	0	0.186275	0	.	.	none	.	KCNC2	239	.	NM_139137	exon5	c.C1866T	p.N622N	AGGAGAGTTGTAG	.	PASS	Atlas-SNP
ZNF799	90576	hgsc.bcm.edu	37	19	12501852	12501852	+	Missense_Mutation	SNP	C	C	T	rs200077318		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	113	4	112	2	0.0353982	0.0178571	.	.	weak	ZNF799_ENST00000430385,head_neck,carcinoma,0,2	ZNF799	111	2	NM_001080821	exon4	c.G1360A	p.G454R	CTTTCCCACATTT	.	scavenged	Atlas-SNP
EHMT2	10919	hgsc.bcm.edu	37	6	31856190	31856190	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	83	5	66	0	0.060241	0	.	.	none	.	EHMT2	45	.	NM_006709	exon12	c.C1459A	p.R487S	CCATGCGGGCGCG	.	PASS	Atlas-SNP
PARD3	56288	hgsc.bcm.edu	37	10	34626206	34626206	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	62	10	78	0	0.16129	0	.	.	none	.	PARD3	131	.	NM_001184787	exon17	c.G2566A	p.G856S	CACTACCTAAATC	.	PASS	Atlas-SNP
OR51G2	81282	hgsc.bcm.edu	37	11	4936072	4936072	+	Silent	SNP	G	G	A	rs199760109	by1000genomes	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	79	22	83	0	0.278481	0	G|1.000;A|0.000	0.000	strong	.	OR51G2	70	.	NM_001005238	exon1	c.C822T	p.P274P	CAGGTGGGGTGCC	.	PASS	Atlas-SNP
CAST	831	hgsc.bcm.edu	37	5	96076487	96076487	+	Silent	SNP	G	G	A	rs7724759	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	293	5	361	1	0.0170648	0.00277008	G|0.780;A|0.220	0.220	strong	CAST,NS,carcinoma,+1,2	CAST	58	2	NM_001042440	exon11	c.G795A	p.S265S	CTCTTCGGTGAGT	.	scavenged	Atlas-SNP
HOMEZ	57594	hgsc.bcm.edu	37	14	23744829	23744829	+	Silent	SNP	C	C	T	rs79723196	bycluster	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	40	5	25	0	0.125	0	.	.	weak	.	HOMEZ	80	.	NM_020834	exon2	c.G1608A	p.E536E	ATCTTCCTCCTCC	.	PASS	Atlas-SNP
PRR5-ARHGAP8	553158	hgsc.bcm.edu	37	22	45241156	45241156	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	54	14	47	0	0.259259	0	.	.	none	.	PRR5-ARHGAP8	53	.	NM_181334	exon11	c.G970C	p.D324H	CTCAAAGACAAAA	.	PASS	Atlas-SNP
AKAP17A	8227	hgsc.bcm.edu	37	X	1718203	1718203	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	113	20	93	0	0.176991	0	.	.	none	.	AKAP17A	46	.	NM_005088	exon4	c.C1030G	p.L344V	GAGAAGCTGCAGG	.	PASS	Atlas-SNP
PPFIA2	8499	hgsc.bcm.edu	37	12	81769580	81769580	+	Missense_Mutation	SNP	G	G	A	rs370246827		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	81	12	105	0	0.148148	0	.	.	weak	.	PPFIA2	207	.	NM_001220476	exon9	c.C1126T	p.R376W	CCTGCCGCAGGAT	.	PASS	Atlas-SNP
SLC9A7	84679	hgsc.bcm.edu	37	X	46618168	46618168	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	47	19	41	0	0.404255	0	.	.	none	.	SLC9A7	73	.	NM_001257291	exon1	c.G297A	p.L99L	CTCGTGCAGAAAG	.	PASS	Atlas-SNP
TNFRSF8	943	hgsc.bcm.edu	37	1	12123708	12123708	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	84	20	101	0	0.238095	0	.	.	none	.	TNFRSF8	70	.	NM_001243	exon1	c.C53T	p.A18V	TACGAGCCTTCCC	.	PASS	Atlas-SNP
MGA	23269	hgsc.bcm.edu	37	15	42003386	42003386	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	65	9	55	0	0.138462	0	.	.	none	.	MGA	264	.	NM_001080541	exon8	c.C2923T	p.Q975X	GCACAGCAGCAGC	.	PASS	Atlas-SNP
CCNT1	904	hgsc.bcm.edu	37	12	49110308	49110308	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	107	3	108	0	0.0280374	0	.	.	none	CCNT1,NS,carcinoma,+1,1	CCNT1	55	1	NM_001240	exon1	c.C151A	p.R51S	TAAGACGCTGCCC	.	scavenged	Atlas-SNP
PRB2	653247	hgsc.bcm.edu	37	12	11546314	11546314	+	Missense_Mutation	SNP	T	T	C	rs34305575	bycluster;byfrequency;by1000genomes	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	153	4	207	1	0.0261438	0.00483092	T|0.891;C|0.109	0.109	strong	PRB2_ENST00000389362,NS,carcinoma,0,2	PRB2	168	2	NM_006248	exon3	c.A698G	p.Q233R	GCACTTTGGGACT	.	scavenged	Atlas-SNP
HIST1H2BC	8347	hgsc.bcm.edu	37	6	26123770	26123770	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	107	20	106	0	0.186916	0	.	.	none	.	HIST1H2BC	35	.	NM_003526	exon1	c.G363A	p.K121K	GGTGTACTTGGTG	.	PASS	Atlas-SNP
BRS3	680	hgsc.bcm.edu	37	X	135574270	135574270	+	Silent	SNP	C	C	T	rs369993360	alternate_allele	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	64	32	70	0	0.5	0	.	.	alt	.	BRS3	62	.	NM_001727	exon3	c.C936T	p.T312T	TTTCACCATTTTC	.	PASS	Atlas-SNP
HIST1H4I	8294	hgsc.bcm.edu	37	6	27107282	27107282	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	140	49	132	0	0.35	0	.	.	none	.	HIST1H4I	26	.	NM_003495	exon1	c.C195T	p.N65N	GGAGAACGTGATC	.	PASS	Atlas-SNP
TREML2	79865	hgsc.bcm.edu	37	6	41166025	41166025	+	Silent	SNP	G	G	A	rs113267424	bycluster;byfrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	64	8	48	1	0.125	0.0208333	G|0.996;A|0.004	0.004	strong	TREML2,caecum,carcinoma,0,1	TREML2	41	1	NM_024807	exon2	c.C198T	p.G66G	GGCAAAGCCAGGC	.	scavenged	Atlas-SNP
TUBB8	347688	hgsc.bcm.edu	37	10	93797	93797	+	Missense_Mutation	SNP	C	C	T	rs71485064		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	93	5	82	3	0.0537634	0.0365854	T|1.000;|0.000	1.000	weak	TUBB8,NS,carcinoma,0,1	TUBB8	62	1	NM_177987	exon4	c.G535A	p.V179M	CCACCACGGTGTC	.	scavenged	Atlas-SNP
JMJD7-PLA2G4B	8681	hgsc.bcm.edu	37	15	42139859	42139859	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	67	19	87	0	0.283582	0	.	.	none	.	JMJD7-PLA2G4B	90	.	NM_005090	exon25	c.C2840A	p.T947K	GGCGGACACCCGA	.	PASS	Atlas-SNP
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124565	26124565	+	Silent	SNP	C	C	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	81	12	121	0	0.148148	0	.	.	none	.	HIST1H2AC	29	.	NM_003512	exon1	c.C105A	p.L35L	CCTGCTCCGTAAA	.	PASS	Atlas-SNP
LOR	4014	hgsc.bcm.edu	37	1	153233701	153233701	+	Silent	SNP	A	A	C	rs1143390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	16	11	7	0	0.6875	0	A|0.594;C|0.406	0.406	strong	.	LOR	19	.	NM_000427	exon2	c.A276C	p.G92G	CTCCGGAGGCGGC	.	PASS	Atlas-SNP
ATAD3B	83858	hgsc.bcm.edu	37	1	1431048	1431048	+	Missense_Mutation	SNP	A	A	G	rs201429000		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	56	4	69	1	0.0714286	0.0144928	.	.	weak	ATAD3B,NS,neuroblastoma,0,1	ATAD3B	68	1	NM_031921	exon16	c.A1798G	p.T600A	CTGGCCACGGACC	.	scavenged	Atlas-SNP
NINJ1	4814	hgsc.bcm.edu	37	9	95887259	95887259	+	Silent	SNP	C	C	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	54	10	65	0	0.185185	0	.	.	none	.	NINJ1	7	.	NM_004148	exon3	c.G390T	p.V130V	GACTACCACGATG	.	PASS	Atlas-SNP
KLF2	10365	hgsc.bcm.edu	37	19	16436027	16436027	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	35	6	17	0	0.171429	0	.	.	none	.	KLF2	10	.	NM_016270	exon2	c.C76T	p.R26C	CCGCAGCGCTGGC	.	PASS	Atlas-SNP
MN1	4330	hgsc.bcm.edu	37	22	28194933	28194933	+	Silent	SNP	T	T	C	rs373314940		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	51	9	67	1	0.176471	0.0149254	.	.	weak	MN1,caecum,carcinoma,0,2	MN1	122	2	NM_002430	exon1	c.A1599G	p.Q533Q	CTGCTGTTGCTGC	.	scavenged	Atlas-SNP
EIF2B5	8893	hgsc.bcm.edu	37	3	183855505	183855505	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	88	25	117	0	0.284091	0	.	.	none	.	EIF2B5	62	.	NM_003907	exon3	c.G418T	p.A140S	GTTGATGCCAAGG	.	PASS	Atlas-SNP
RGS7	6000	hgsc.bcm.edu	37	1	241032080	241032080	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	88	14	100	0	0.159091	0	.	.	none	.	RGS7	308	.	NM_002924	exon8	c.G523A	p.A175T	ACTTTGCTTGTGC	.	PASS	Atlas-SNP
BMP15	9210	hgsc.bcm.edu	37	X	50659592	50659592	+	Silent	SNP	T	T	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	64	33	72	0	0.515625	0	.	.	none	.	BMP15	62	.	NM_005448	exon2	c.T1164C	p.S388S	TGAGTCTTGTACA	.	PASS	Atlas-SNP
TMSB4X	7114	hgsc.bcm.edu	37	X	12994468	12994468	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	146	55	170	0	0.376712	0	.	.	none	.	TMSB4X	3	.	NM_021109	exon2	c.C88A	p.P30T	CCACTGCCTTCCA	.	PASS	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	37	19	52131127	52131127	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	110	20	128	0	0.181818	0	.	.	none	SIGLEC5,NS,carcinoma,0,2	SIGLEC5	67	2	NM_003830	exon5	c.G957A	p.P319P	GCCCAGCGGGTGC	.	PASS	Atlas-SNP
ZNF530	348327	hgsc.bcm.edu	37	19	58117726	58117726	+	Missense_Mutation	SNP	G	G	A	rs201516823		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	62	10	108	0	0.16129	0	G|0.999;A|0.001	0.001	weak	.	ZNF530	71	.	NM_020880	exon3	c.G833A	p.R278H	TTAGTCGCAAAAC	.	PASS	Atlas-SNP
TBP	6908	hgsc.bcm.edu	37	6	170871061	170871061	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	34	8	41	5	0.235294	0.121951	.	.	none	TBP,caecum,carcinoma,0,5	TBP	58	5	NM_003194	exon3	c.G237A	p.Q79Q	GCAGCAGCAGCAG	.	scavenged	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141819821	141819821	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	56	13	59	0	0.232143	0	.	.	none	.	LRP1B	1315	.	NM_018557	exon8	c.C1035T	p.Y345Y	ATTCCCGTAGTCA	.	PASS	Atlas-SNP
PAX5	5079	hgsc.bcm.edu	37	9	37002696	37002696	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	159	32	169	0	0.201258	0	.	.	none	.	PAX5	250	.	NM_016734	exon5	c.C553G	p.L185V	TGCCCAGGATGCC	.	PASS	Atlas-SNP
SSTR4	6754	hgsc.bcm.edu	37	20	23016253	23016253	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	66	20	59	1	0.30303	0.0169492	.	.	none	SSTR4,NS,carcinoma,-1,1	SSTR4	83	1	NM_001052	exon1	c.G133A	p.A45T	CGGGCGGCGGGCA	.	scavenged	Atlas-SNP
SRRM1	10250	hgsc.bcm.edu	37	1	24993386	24993386	+	Missense_Mutation	SNP	G	G	T	rs78787676	bycluster;byfrequency;alternate_allele	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	266	5	291	1	0.018797	0.00343643	G|0.999;A|0.001	.	alt	SRRM1,bladder,carcinoma,0,2	SRRM1	81	2	NM_005839	exon13	c.G1709T	p.R570L	GACGGCGCAGGAC	.	scavenged	Atlas-SNP
KCNK3	3777	hgsc.bcm.edu	37	2	26951314	26951314	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	44	9	48	0	0.204545	0	.	.	none	.	KCNK3	43	.	NM_002246	exon2	c.G1063A	p.D355N	TACAGCGACACGC	.	PASS	Atlas-SNP
ATF4	468	hgsc.bcm.edu	37	22	39917610	39917610	+	Missense_Mutation	SNP	G	G	A	rs148038848		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	99	23	118	0	0.232323	0	G|1.000;A|0.000	0.000	weak	.	ATF4	27	.	NM_001675	exon1	c.G160A	p.A54T	GACAAGGCTAAGG	.	PASS	Atlas-SNP
PHLPP1	23239	hgsc.bcm.edu	37	18	60497429	60497429	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	125	3	114	0	0.024	0	.	.	none	PHLPP1_ENST00000262719,NS,haematopoietic_neoplasm,0,3	PHLPP1	164	3	NM_194449	exon2	c.G1738A	p.G580R	TTGACCGGAAAGA	.	scavenged	Atlas-SNP
RBMXL1	494115	hgsc.bcm.edu	37	1	89448812	89448812	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	209	5	201	1	0.0239234	0.00497512	.	.	none	CCBL2,NS,carcinoma,0,3	.	.	3	NM_001162536	exon3	c.A698C	p.D233A	GCATAATCTCTTG	.	scavenged	Atlas-SNP
FUT4	2526	hgsc.bcm.edu	37	11	94278849	94278849	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	32	7	39	0	0.21875	0	.	.	none	.	FUT4	17	.	NM_002033	exon1	c.G1550A	p.R517Q	GGGACCGGCCCAA	.	PASS	Atlas-SNP
UACA	55075	hgsc.bcm.edu	37	15	70960860	70960860	+	Silent	SNP	T	T	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	55	10	75	0	0.181818	0	.	.	none	.	UACA	235	.	NM_018003	exon16	c.A2163G	p.K721K	ATAAACTTTTTCA	.	PASS	Atlas-SNP
MBTD1	54799	hgsc.bcm.edu	37	17	49281177	49281177	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	197	47	197	0	0.238579	0	.	.	none	.	MBTD1	44	.	NM_017643	exon8	c.C714T	p.S238S	TTTTCCGCTGGCT	.	PASS	Atlas-SNP
TREML2	79865	hgsc.bcm.edu	37	6	41166021	41166021	+	Missense_Mutation	SNP	C	C	T	rs61736679	bycluster;byfrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	64	8	48	1	0.125	0.0208333	C|0.989;T|0.011	0.011	strong	TREML2,caecum,carcinoma,0,1	TREML2	41	1	NM_024807	exon2	c.G202A	p.A68T	CTCGGGCAAAGCC	.	scavenged	Atlas-SNP
CORO1A	11151	hgsc.bcm.edu	37	16	30198463	30198463	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	46	10	52	0	0.217391	0	.	.	none	.	CORO1A	36	.	NM_001193333	exon6	c.C555T	p.S185S	CTGGAGCCGAGAT	.	PASS	Atlas-SNP
AIFM2	84883	hgsc.bcm.edu	37	10	71880315	71880315	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	50	7	63	0	0.14	0	.	.	none	.	AIFM2	33	.	NM_001198696	exon5	c.C455T	p.S152L	CCAGCCGAGCCTC	.	PASS	Atlas-SNP
PCMTD1	115294	hgsc.bcm.edu	37	8	52732958	52732958	+	Missense_Mutation	SNP	G	G	A	rs200497338		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	106	4	95	3	0.0377358	0.0315789	.	.	weak	PCMTD1,trunk,malignant_melanoma,0,2	PCMTD1	73	2	NM_052937	exon6	c.C1027T	p.L343F	CAGGGAGGGGCAG	.	scavenged	Atlas-SNP
PLD2	5338	hgsc.bcm.edu	37	17	4711711	4711711	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	45	13	62	0	0.288889	0	.	.	none	.	PLD2	138	.	NM_001243108	exon4	c.G383A	p.R128Q	TGGCTCGGTGAGG	.	PASS	Atlas-SNP
STAT3	6774	hgsc.bcm.edu	37	17	40474419	40474419	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	93	14	154	0	0.150538	0	.	.	none	STAT3,skin,lymphoid_neoplasm,-1,42	STAT3	268	42	NM_003150	exon21	c.A1982T	p.D661V	GTAGCATCCATGA	.	PASS	Atlas-SNP
PLG	5340	hgsc.bcm.edu	37	6	161173935	161173935	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	283	58	352	0	0.204947	0	.	.	none	.	PLG	150	.	NM_000301	exon19	c.G2275A	p.D759N	TAGGGTGACAGTG	.	PASS	Atlas-SNP
IER5L	389792	hgsc.bcm.edu	37	9	131940019	131940019	+	Missense_Mutation	SNP	G	G	A	rs184457	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	6	5	1	0	0.833333	0	G|0.700;A|0.300	0.300	strong	.	IER5L	4	.	NM_203434	exon1	c.C313T	p.P105S	CGGCCGGCTCGCG	.	PASS	Atlas-SNP
BRAP	8315	hgsc.bcm.edu	37	12	112082105	112082105	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	47	12	79	0	0.255319	0	.	.	none	.	BRAP	42	.	NM_006768	exon12	c.G1677A	p.E559E	CTGTCCCTCCTGG	.	PASS	Atlas-SNP
OR52I2	143502	hgsc.bcm.edu	37	11	4608393	4608393	+	Silent	SNP	A	A	G	rs56002758	bycluster;byfrequency;by1000genomes	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	108	9	99	2	0.0833333	0.020202	A|0.972;G|0.028	0.028	strong	OR52I2,NS,carcinoma,0,1	OR52I2	50	1	NM_001005170	exon1	c.A351G	p.S117S	CTGCTCAGGAGAC	.	scavenged	Atlas-SNP
FPGT	8790	hgsc.bcm.edu	37	1	74670119	74670119	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	86	11	112	0	0.127907	0	.	.	none	FPGT,NS,carcinoma,0,1	FPGT	77	1	NM_001199328	exon4	c.A388C	p.I130L	GGAAAAATTTTCA	.	PASS	Atlas-SNP
SOWAHD	347454	hgsc.bcm.edu	37	X	118893023	118893023	+	Missense_Mutation	SNP	G	G	C	rs373940647		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	26	5	25	0	0.192308	0	.	.	weak	.	.	.	.	NM_001105576	exon1	c.G393C	p.E131D	GCGGGAGCTGCTG	.	PASS	Atlas-SNP
ICOSLG	23308	hgsc.bcm.edu	37	21	45656994	45656994	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	95	4	102	0	0.0421053	0	.	.	none	.	ICOSLG	20	.	NM_015259	exon3	c.G162A	p.W54X	GGTTTGCCAATAT	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254124	39254124	+	Silent	SNP	C	C	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	52	3	35	1	0.0576923	0.0285714	.	.	none	KRTAP4-8,colon,carcinoma,0,2	KRTAP4-8	57	2	NM_031960	exon1	c.G213C	p.V71V	GCTGGACACACAG	.	scavenged	Atlas-SNP
OTOP1	133060	hgsc.bcm.edu	37	4	4228479	4228479	+	Missense_Mutation	SNP	G	G	C	rs199890951		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	33	4	30	1	0.121212	0.0333333	.	.	weak	OTOP1,NS,carcinoma,0,1	OTOP1	118	1	NM_177998	exon1	c.C113G	p.S38C	TCCGGGGACCTCG	.	scavenged	Atlas-SNP
SMC4	10051	hgsc.bcm.edu	37	3	160130162	160130162	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	312	118	294	0	0.378205	0	.	.	none	SMC4,mouth,carcinoma,0,1	SMC4	135	1	NM_005496	exon6	c.G901A	p.E301K	GAAGGAGAGAAAA	.	PASS	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52887146	52887146	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	209	9	262	0	0.0430622	0	.	.	none	ZNF880,colon,carcinoma,-1,1	ZNF880	45	1	NM_001145434	exon4	c.A313T	p.K105X	TCTCTTAAAAATC	.	scavenged	Atlas-SNP
LINGO4	339398	hgsc.bcm.edu	37	1	151774688	151774688	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	57	9	64	0	0.157895	0	.	.	none	.	LINGO4	51	.	NM_001004432	exon2	c.G493T	p.D165Y	GGTTGTCCCCAAC	.	PASS	Atlas-SNP
LTA4H	4048	hgsc.bcm.edu	37	12	96396751	96396751	+	Silent	SNP	G	G	T	rs376007921	alternate_allele	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	122	3	112	0	0.0245902	0	.	.	alt	LTA4H,colon,carcinoma,+1,1	LTA4H	38	1	NM_000895	exon18	c.C1705A	p.R569R	AGGGCCGGGTAAA	.	scavenged	Atlas-SNP
CEP55	55165	hgsc.bcm.edu	37	10	95276727	95276727	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	160	2	166	0	0.0125	0	.	.	none	CEP55,NS,carcinoma,0,2	CEP55	35	2	NM_018131	exon6	c.G715T	p.D239Y	TACAACGATCTCT	.	scavenged	Atlas-SNP
EPHB1	2047	hgsc.bcm.edu	37	3	134670283	134670283	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	84	31	114	0	0.369048	0	.	.	none	.	EPHB1	519	.	NM_004441	exon3	c.A194G	p.E65G	TCTTCGAGCCCAA	.	PASS	Atlas-SNP
ATG2B	55102	hgsc.bcm.edu	37	14	96779678	96779678	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	334	4	351	0	0.011976	0	.	.	none	ATG2B,NS,carcinoma,-1,1	ATG2B	169	1	NM_018036	exon24	c.C3737A	p.A1246E	TCAAGTGCACAGC	.	scavenged	Atlas-SNP
LGALS8	3964	hgsc.bcm.edu	37	1	236703874	236703874	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	53	9	41	0	0.169811	0	.	.	none	.	LGALS8	42	.	NM_006499	exon6	c.A356G	p.N119S	CTGTAAATGGAAA	.	PASS	Atlas-SNP
COX10	1352	hgsc.bcm.edu	37	17	14095348	14095348	+	Silent	SNP	G	G	A	rs34362247	byfrequency;alternate_allele	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	67	5	53	2	0.0746269	0.0377358	T|0.054;A|0.946	0.946	alt	COX10,NS,carcinoma,+1,1	COX10	36	1	NM_001303	exon6	c.G738A	p.P246P	TGTTCCGGGAGTT	.	scavenged	Atlas-SNP
PHIP	55023	hgsc.bcm.edu	37	6	79671508	79671508	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	245	11	271	0	0.044898	0	.	.	none	.	PHIP	177	.	NM_017934	exon31	c.G3555A	p.V1185V	GGGGGCCACAAAT	.	PASS	Atlas-SNP
CFB	629	hgsc.bcm.edu	37	6	31918104	31918104	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	67	5	66	0	0.0746269	0	.	.	none	.	CFB	33	.	NM_001710	exon12	c.G1548A	p.V516V	TGTGGTGTCTGAG	.	PASS	Atlas-SNP
OR51M1	390059	hgsc.bcm.edu	37	11	5410941	5410941	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	41	8	53	0	0.195122	0	.	.	none	.	OR51M1	60	.	NM_001004756	exon1	c.T313C	p.Y105H	AGTATCTACTTTG	.	PASS	Atlas-SNP
KAT2A	2648	hgsc.bcm.edu	37	17	40267789	40267789	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	52	8	70	0	0.153846	0	.	.	none	.	KAT2A	54	.	NM_021078	exon12	c.C1827T	p.Y609Y	GAGGAAGTAGAGA	.	PASS	Atlas-SNP
ACTB	60	hgsc.bcm.edu	37	7	5568064	5568064	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	69	14	99	0	0.202899	0	.	.	none	.	ACTB	45	.	NM_001101	exon4	c.G650A	p.C217Y	ACGTAGCACAGCT	.	PASS	Atlas-SNP
TAS2R31	259290	hgsc.bcm.edu	37	12	11183305	11183305	+	Missense_Mutation	SNP	C	C	G	rs200367513	bycluster	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	170	11	197	3	0.0647059	0.0152284	.	.	weak	TAS2R31,NS,carcinoma,-2,1	TAS2R31	24	1	NM_176885	exon1	c.G630C	p.Q210H	ATGGAGCTGCATC	.	scavenged	Atlas-SNP
CLK1	1195	hgsc.bcm.edu	37	2	201721689	201721689	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	56	16	64	0	0.285714	0	.	.	none	.	CLK1	103	.	NM_001162407	exon8	c.G978A	p.L326L	GTGAGTCAACTTA	.	PASS	Atlas-SNP
PCDHA9	9752	hgsc.bcm.edu	37	5	140229745	140229745	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	92	15	122	0	0.163043	0	.	.	none	.	PCDHA9	373	.	NM_031857	exon1	c.G1665A	p.V555V	GTTCGTGCTGGAC	.	PASS	Atlas-SNP
C5orf46	389336	hgsc.bcm.edu	37	5	147286047	147286047	+	Silent	SNP	A	A	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	271	39	284	0	0.143911	0	.	.	none	.	C5orf46	8	.	NM_206966	exon1	c.T18C	p.L6L	CAGGCGAAGTACT	.	PASS	Atlas-SNP
TMEM135	65084	hgsc.bcm.edu	37	11	87024503	87024503	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	231	41	265	0	0.177489	0	.	.	none	.	TMEM135	40	.	NM_022918	exon11	c.G973A	p.D325N	AACTTAGATGATG	.	PASS	Atlas-SNP
FLJ25363	0	hgsc.bcm.edu	37	3	109195589	109195589	+	Silent	SNP	A	A	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	62	16	84	0	0.258065	0	.	.	none	.	.	.	.	NM_001145553	exon4	c.A267G	p.Q89Q	GCCTCAAGAACAG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284823	152284823	+	Missense_Mutation	SNP	A	A	G	rs74129459	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	81	5	78	2	0.0617284	0.025641	A|0.984;T|0.016	.	alt	FLG,NS,carcinoma,0,1	FLG	900	1	NM_002016	exon3	c.T2539C	p.S847P	TGCTTGACCCCGG	.	scavenged	Atlas-SNP
ZNF208	7757	hgsc.bcm.edu	37	19	22157028	22157028	+	Missense_Mutation	SNP	C	C	A	rs202182420		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	42	6	40	0	0.142857	0	C|0.996;A|0.004	0.004	weak	.	ZNF208	817	.	NM_007153	exon4	c.G808T	p.A270S	GGATTGCAGATTG	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017068	1017068	+	Silent	SNP	C	C	T	rs78992004		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	252	39	303	53	0.154762	0.174917	C|0.500;T|0.500	0.500	weak	MUC6,NS,carcinoma,-1,1	MUC6	408	1	NM_005961	exon31	c.G5733A	p.T1911T	TTTGGCCGTGCTA	.	scavenged	Atlas-SNP
DGKI	9162	hgsc.bcm.edu	37	7	137080402	137080402	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	62	9	55	0	0.145161	0	.	.	none	DGKI_ENST00000288490,NS,carcinoma,-1,2	DGKI	335	2	NM_004717	exon33	c.G3023T	p.R1008L	ACAGCCCGGTTCC	.	PASS	Atlas-SNP
GAS6	2621	hgsc.bcm.edu	37	13	114530106	114530106	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	62	9	90	0	0.145161	0	.	.	none	GAS6_ENST00000327773,colon,carcinoma,-1,2	GAS6	75	2	NM_000820	exon12	c.G1340A	p.S447N	TTCCAGCTCCTCA	.	PASS	Atlas-SNP
TNRC6C	57690	hgsc.bcm.edu	37	17	76045908	76045908	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	61	25	63	0	0.409836	0	.	.	none	TNRC6C,NS,carcinoma,+1,1	TNRC6C	173	1	NM_018996	exon4	c.C765T	p.N255N	AGGTAACCCTGCC	.	PASS	Atlas-SNP
HIF3A	64344	hgsc.bcm.edu	37	19	46832549	46832549	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	90	18	109	0	0.2	0	.	.	none	.	HIF3A	154	.	NM_152795	exon12	c.C1526T	p.P509L	AGCTACCCAGGGC	.	PASS	Atlas-SNP
ZNF570	148268	hgsc.bcm.edu	37	19	37975034	37975034	+	Silent	SNP	T	T	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	81	18	79	0	0.222222	0	.	.	none	.	ZNF570	58	.	NM_144694	exon5	c.T510C	p.S170S	GGGAAGTTTTCAT	.	PASS	Atlas-SNP
HIST1H2AK	8330	hgsc.bcm.edu	37	6	27805883	27805883	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	149	22	148	0	0.147651	0	.	.	none	HIST1H2AK,NS,carcinoma,0,1	HIST1H2AK	28	1	NM_003510	exon1	c.A235G	p.I79V	GGATGATGCGGGT	.	PASS	Atlas-SNP
KCNU1	157855	hgsc.bcm.edu	37	8	36694417	36694417	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	86	16	88	0	0.186047	0	.	.	none	.	KCNU1	359	.	NM_001031836	exon14	c.G1472A	p.G491D	TGCCAGGCTTGTG	.	PASS	Atlas-SNP
CHD5	26038	hgsc.bcm.edu	37	1	6189098	6189098	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	43	7	52	0	0.162791	0	.	.	none	.	CHD5	267	.	NM_015557	exon23	c.A3419T	p.N1140I	TTCTTGTTCTGGC	.	PASS	Atlas-SNP
SMARCA5	8467	hgsc.bcm.edu	37	4	144467950	144467950	+	Silent	SNP	A	A	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	101	27	141	0	0.267327	0	.	.	none	SMARCA5,rectum,carcinoma,-1,1	SMARCA5	73	1	NM_003601	exon20	c.A2542C	p.R848R	AATAAGAGAGATT	.	PASS	Atlas-SNP
PATZ1	23598	hgsc.bcm.edu	37	22	31741415	31741415	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	70	9	114	0	0.128571	0	.	.	none	.	PATZ1	24	.	NM_032050	exon1	c.G174A	p.V58V	GGCCAGCACGGCG	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919589	12919589	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	222	10	237	5	0.045045	0.021097	.	.	none	PRAMEF2,NS,carcinoma,+1,1	PRAMEF2	85	1	NM_023014	exon3	c.A329G	p.E110G	TTGATGAGAATTT	.	scavenged	Atlas-SNP
TMSB4X	7114	hgsc.bcm.edu	37	X	12994364	12994364	+	Splice_Site	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	90	26	123	0	0.288889	0	.	.	none	.	TMSB4X	3	.	.	.	.	.	CCTGCAGCTTTTC	.	PASS	Atlas-SNP
NLN	57486	hgsc.bcm.edu	37	5	65054569	65054569	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	135	3	147	0	0.0222222	0	.	.	none	NLN,NS,carcinoma,0,1	NLN	51	1	NM_020726	exon2	c.G217T	p.D73Y	GTGTACGATGCTG	.	scavenged	Atlas-SNP
ANKS1A	23294	hgsc.bcm.edu	37	6	34857324	34857324	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	10	7	4	0	0.7	0	.	.	none	ANKS1A,NS,carcinoma,0,1	ANKS1A	123	1	NM_015245	exon1	c.G145A	p.G49S	AGCGGCGGCGGCG	.	scavenged	Atlas-SNP
SYNPR	132204	hgsc.bcm.edu	37	3	63466620	63466620	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	41	8	47	0	0.195122	0	.	.	none	SYNPR,NS,carcinoma,+1,4	SYNPR	38	4	NM_001130003	exon3	c.C197T	p.A66V	CGTTTGCCTACCC	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25016911	25016911	+	Missense_Mutation	SNP	C	C	T	rs199703506	bycluster;byfrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	230	10	288	7	0.0434783	0.0243056	C|0.996;T|0.004	0.004	strong	GGT1,NS,carcinoma,0,1	GGT1	68	1	NM_013430	exon9	c.C607T	p.R203W	GTGCTTCGGGAGG	.	scavenged	Atlas-SNP
SSTR4	6754	hgsc.bcm.edu	37	20	23016714	23016714	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	16	5	11	0	0.3125	0	.	.	none	.	SSTR4	83	.	NM_001052	exon1	c.C594A	p.C198X	GGCCTGCAACCTG	.	PASS	Atlas-SNP
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234687	26234687	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	87	12	82	0	0.137931	0	.	.	none	HIST1H1D,NS,carcinoma,0,1	HIST1H1D	40	1	NM_005320	exon1	c.G475T	p.V159L	TCTTTACCTTCTT	.	PASS	Atlas-SNP
HIST1H2AM	8336	hgsc.bcm.edu	37	6	27860749	27860749	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	161	32	135	0	0.198758	0	.	.	none	.	HIST1H2AM	27	.	NM_003514	exon1	c.C179T	p.T60I	TCGGCAGTTAGGT	.	PASS	Atlas-SNP
TREML2	79865	hgsc.bcm.edu	37	6	41166017	41166017	+	Missense_Mutation	SNP	C	C	T	rs77093113	bycluster;byfrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	64	8	53	1	0.125	0.0188679	C|0.995;T|0.005	0.005	strong	TREML2,caecum,carcinoma,0,2	TREML2	41	2	NM_024807	exon2	c.G206A	p.R69Q	CAGACTCGGGCAA	.	scavenged	Atlas-SNP
TNNT1	7138	hgsc.bcm.edu	37	19	55645539	55645539	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	40	7	61	0	0.175	0	.	.	none	.	TNNT1	28	.	NM_003283	exon12	c.C645T	p.P215P	GCAGGAGGGCTGT	.	PASS	Atlas-SNP
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234812	26234812	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	80	20	70	0	0.25	0	.	.	none	.	HIST1H1D	40	.	NM_005320	exon1	c.G350A	p.G117D	GGTTTGCCTTCCC	.	PASS	Atlas-SNP
CXCR4	7852	hgsc.bcm.edu	37	2	136872627	136872627	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	151	28	179	0	0.18543	0	.	.	none	.	CXCR4	51	.	NM_001008540	exon1	c.G883A	p.A295T	AGAAAGCTAGGGC	.	PASS	Atlas-SNP
EIF4A2	1974	hgsc.bcm.edu	37	3	186502355	186502355	+	Missense_Mutation	SNP	C	C	G	rs371691662	alternate_allele	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	109	21	151	0	0.192661	0	.	.	alt	.	EIF4A2	55	.	NM_001967	exon3	c.C78G	p.S26R	ACAGAGCAACTGG	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17086183	17086183	+	Splice_Site	SNP	T	T	G	rs61769735	bycluster;byfrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	114	16	164	22	0.140351	0.134146	T|0.988;G|0.011	0.011	strong	Q13209_HUMAN,NS,carcinoma,0,6	.	.	6	NM_001271733	exon8	c.716-2A>C	.	GGACCCTTAGATG	.	scavenged	Atlas-SNP
WDR96	80217	hgsc.bcm.edu	37	10	105923874	105923874	+	Missense_Mutation	SNP	G	G	A	rs146455280	bycluster;by1000genomes;alternate_allele	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	71	22	80	0	0.309859	0	G|1.000;T|0.000	.	alt	.	WDR96	183	.	NM_025145	exon24	c.C3224T	p.T1075M	ACAAGCGTTCTCT	.	PASS	Atlas-SNP
ZNF474	133923	hgsc.bcm.edu	37	5	121488255	121488255	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	70	17	74	0	0.242857	0	.	.	none	.	ZNF474	43	.	NM_207317	exon2	c.G570T	p.K190N	GCCAAAGGGTGAG	.	PASS	Atlas-SNP
KRTAP5-2	440021	hgsc.bcm.edu	37	11	1619234	1619234	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	102	19	118	0	0.186275	0	.	.	none	.	KRTAP5-2	38	.	NM_001004325	exon1	c.G247A	p.G83S	TGGAGCCCCCACA	.	PASS	Atlas-SNP
PRB1	5542	hgsc.bcm.edu	37	12	11506288	11506288	+	Missense_Mutation	SNP	T	T	C	rs140825288	bycluster	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	140	7	168	4	0.05	0.0238095	.	.	weak	PRB1,NS,carcinoma,0,2	PRB1	33	2	NM_199353	exon4	c.A350G	p.K117R	TGAGGTTTGTTGC	.	scavenged	Atlas-SNP
CPA2	1358	hgsc.bcm.edu	37	7	129916536	129916536	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	88	5	115	0	0.0568182	0	.	.	none	CPA2,NS,carcinoma,0,1	CPA2	36	1	NM_001869	exon7	c.G654A	p.L218L	CCTCCTGCCAGTC	.	PASS	Atlas-SNP
LIPN	643418	hgsc.bcm.edu	37	10	90537944	90537944	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	95	21	98	0	0.221053	0	.	.	none	.	LIPN	28	.	NM_001102469	exon9	c.A1142G	p.D381G	GCCTCGATGCCCC	.	PASS	Atlas-SNP
RPL35A	6165	hgsc.bcm.edu	37	3	197678057	197678057	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	70	15	88	0	0.214286	0	.	.	none	.	RPL35A	9	.	NM_000996	exon3	c.C39T	p.G13G	TGCTGGCTATAAG	.	PASS	Atlas-SNP
PCDHGA12	26025	hgsc.bcm.edu	37	5	140810511	140810511	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	102	12	109	0	0.117647	0	.	.	none	PCDHGA12_ENST00000252085,NS,carcinoma,+1,4	PCDHGA12	271	4	NM_032094	exon1	c.G185A	p.R62H	CGGAGCGCGGAGT	.	PASS	Atlas-SNP
A2M	2	hgsc.bcm.edu	37	12	9266020	9266020	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	144	28	135	0	0.194444	0	.	.	none	.	A2M	180	.	NM_000014	exon2	c.G206A	p.G69E	CTGTTTCCCCTGA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9072256	9072256	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	67	11	90	0	0.164179	0	.	.	none	.	MUC16	4315	.	NM_024690	exon3	c.C15190A	p.L5064I	AGGAGAGCTTATC	.	PASS	Atlas-SNP
ABCC10	89845	hgsc.bcm.edu	37	6	43399895	43399895	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	46	6	48	0	0.130435	0	.	.	none	.	ABCC10	118	.	NM_001198934	exon3	c.C177T	p.I59I	TTACATCCTACCC	.	PASS	Atlas-SNP
HNRNPD	3184	hgsc.bcm.edu	37	4	83294756	83294756	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	23	6	18	0	0.26087	0	.	.	none	.	HNRNPD	23	.	NM_031370	exon1	c.C76T	p.Q26X	CCTCCTGCTCGCC	.	PASS	Atlas-SNP
HEMK1	51409	hgsc.bcm.edu	37	3	50609175	50609175	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	74	21	98	0	0.283784	0	.	.	none	.	HEMK1	17	.	NM_016173	exon3	c.C263T	p.P88L	CCCAGCCCTTGAC	.	PASS	Atlas-SNP
ACADM	34	hgsc.bcm.edu	37	1	76228440	76228440	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	367	71	406	0	0.19346	0	.	.	none	.	ACADM	50	.	NM_001127328	exon12	c.A1270G	p.K424E	AAGTACAAAAATT	.	PASS	Atlas-SNP
NDUFV2	4729	hgsc.bcm.edu	37	18	9122638	9122638	+	Missense_Mutation	SNP	G	G	C	rs148158107	bycluster;byfrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	142	7	164	6	0.0492958	0.0365854	G|0.996;C|0.005	0.005	strong	NDUFV2,colon,carcinoma,+1,3	NDUFV2	17	3	NM_021074	exon5	c.G428C	p.R143P	TGCTTCGAAACTC	.	scavenged	Atlas-SNP
LYVE1	10894	hgsc.bcm.edu	37	11	10580685	10580685	+	Silent	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	124	2	130	0	0.016129	0	.	.	none	LYVE1,brain,glioma,0,1	LYVE1	19	1	NM_006691	exon6	c.C942A	p.T314T	TCGCACGGTAGTT	.	scavenged	Atlas-SNP
GPR34	2857	hgsc.bcm.edu	37	X	41555136	41555136	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	106	44	110	0	0.415094	0	.	.	none	.	GPR34	42	.	NM_001097579	exon3	c.C250T	p.R84C	ATTCACCGTAAAA	.	PASS	Atlas-SNP
IRS1	3667	hgsc.bcm.edu	37	2	227663446	227663446	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	74	14	73	0	0.189189	0	.	.	none	.	IRS1	141	.	NM_005544	exon1	c.C9T	p.S3S	CGGAGGGCTCGCC	.	PASS	Atlas-SNP
EFHC1	114327	hgsc.bcm.edu	37	6	52344443	52344443	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	98	17	96	0	0.173469	0	.	.	none	.	EFHC1	68	.	NM_018100	exon9	c.G1498T	p.G500C	GTGTTTGGTCACC	.	PASS	Atlas-SNP
MCM4	4173	hgsc.bcm.edu	37	8	48889332	48889332	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	51	10	48	0	0.196078	0	.	.	none	.	MCM4	97	.	NM_182746	exon17	c.G2586A	p.L862L	GCGCTTGCTCTGA	.	PASS	Atlas-SNP
DUSP2	1844	hgsc.bcm.edu	37	2	96810559	96810559	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	60	10	54	0	0.166667	0	.	.	none	.	DUSP2	20	.	NM_004418	exon2	c.C451G	p.L151V	GCGGCAGCGCAGG	.	PASS	Atlas-SNP
ARHGAP21	57584	hgsc.bcm.edu	37	10	24909112	24909112	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	87	20	93	0	0.229885	0	.	.	none	.	ARHGAP21	185	.	NM_020824	exon9	c.G1712A	p.R571Q	CTCATTCGCCTGT	.	PASS	Atlas-SNP
ANAPC1	64682	hgsc.bcm.edu	37	2	112608394	112608394	+	Missense_Mutation	SNP	T	T	C	rs12466309	bycluster;byfrequency;byhapmap	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	485	23	556	4	0.0474227	0.00719424	T|0.500;C|0.500	0.500	strong	ANAPC1,NS,carcinoma,0,9	ANAPC1	116	9	NM_022662	exon14	c.A1609G	p.T537A	TTGGAGTACTAAC	.	scavenged	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1018511	1018511	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	143	2	185	1	0.013986	0.00540541	.	.	none	MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.C4290T	p.T1430T	GGTAGTGGTGGCA	.	scavenged	Atlas-SNP
CA4	762	hgsc.bcm.edu	37	17	58227428	58227428	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	53	5	46	0	0.0943396	0	.	.	none	.	CA4	20	.	NM_000717	exon1	c.C33T	p.S11S	CCTCTCCGCGGCG	.	PASS	Atlas-SNP
IL2RA	3559	hgsc.bcm.edu	37	10	6104051	6104051	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	93	16	113	0	0.172043	0	.	.	none	.	IL2RA	37	.	NM_000417	exon1	c.G64A	p.E22K	CCTTACCTGCCTG	.	PASS	Atlas-SNP
HTR1B	3351	hgsc.bcm.edu	37	6	78172576	78172576	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	95	14	92	0	0.147368	0	.	.	none	.	HTR1B	55	.	NM_000863	exon1	c.T545C	p.L182P	GGCGGCAGCGAGA	.	PASS	Atlas-SNP
MAML2	84441	hgsc.bcm.edu	37	11	95825386	95825386	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	54	6	63	0	0.111111	0	.	.	none	MAML2,NS,carcinoma,0,2	MAML2	94	2	NM_032427	exon2	c.G1809A	p.Q603Q	CTGCTGCTGCTGC	.	PASS	Atlas-SNP
MYC	4609	hgsc.bcm.edu	37	8	128751032	128751032	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	52	10	69	0	0.192308	0	.	.	none	MYC_ENST00000377970,NS,lymphoid_neoplasm,0,2	MYC	168	2	NM_002467	exon2	c.G569A	p.S190N	CCTCCAGCTTGTA	.	PASS	Atlas-SNP
ZNF367	195828	hgsc.bcm.edu	37	9	99180102	99180102	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	46	6	59	0	0.130435	0	.	.	none	.	ZNF367	27	.	NM_153695	exon1	c.G213A	p.W71X	CCAGCGCCACGGG	.	PASS	Atlas-SNP
IGSF3	3321	hgsc.bcm.edu	37	1	117158745	117158745	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	133	9	212	4	0.0676692	0.0188679	.	.	none	IGSF3,extremity,malignant_melanoma,0,1	IGSF3	294	1	NM_001542	exon3	c.T378G	p.D126E	TTGCTTATCAGTG	.	scavenged	Atlas-SNP
CRIP1	1396	hgsc.bcm.edu	37	14	105954689	105954689	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	108	17	149	0	0.157407	0	.	.	none	.	CRIP1	1	.	NM_001311	exon4	c.A157C	p.N53H	TACTGCAACCACC	.	PASS	Atlas-SNP
GZMM	3004	hgsc.bcm.edu	37	19	549011	549011	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	103	11	94	0	0.106796	0	.	.	none	GZMM,bladder,carcinoma,+1,1	GZMM	11	1	NM_005317	exon4	c.C438T	p.S146S	GTGCAGCATGGCC	.	PASS	Atlas-SNP
CYB5R4	51167	hgsc.bcm.edu	37	6	84569547	84569547	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	76	14	84	0	0.184211	0	.	.	none	.	CYB5R4	72	.	NM_016230	exon1	c.C46G	p.Q16E	TCGCAGCAGCGTG	.	PASS	Atlas-SNP
FANCG	2189	hgsc.bcm.edu	37	9	35077020	35077020	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	80	19	85	0	0.2375	0	.	.	none	.	FANCG	56	.	NM_004629	exon6	c.G725A	p.R242Q	ACAGGCCGTGGAC	.	PASS	Atlas-SNP
HIST1H3F	8968	hgsc.bcm.edu	37	6	26250506	26250506	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	75	18	87	0	0.24	0	.	.	none	.	HIST1H3F	16	.	NM_021018	exon1	c.C328T	p.L110L	CACACAGGTTGGT	.	PASS	Atlas-SNP
SIPA1	6494	hgsc.bcm.edu	37	11	65416900	65416900	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	59	12	78	0	0.20339	0	.	.	none	.	SIPA1	45	.	NM_006747	exon10	c.C2474T	p.A825V	ATCTGGCCGAGGA	.	PASS	Atlas-SNP
AKAP8	10270	hgsc.bcm.edu	37	19	15484046	15484046	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	97	17	105	0	0.175258	0	.	.	none	.	AKAP8	68	.	NM_005858	exon5	c.G477A	p.G159G	GTCGGACCCCAGG	.	PASS	Atlas-SNP
DHRS4	10901	hgsc.bcm.edu	37	14	24424420	24424420	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	117	7	160	4	0.0598291	0.025	.	.	none	DHRS4,NS,carcinoma,0,5	DHRS4	22	5	NM_021004	exon2	c.C305T	p.T102M	TGGCCACGGTGAG	.	scavenged	Atlas-SNP
TAF5L	27097	hgsc.bcm.edu	37	1	229730826	229730826	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	37	18	30	0	0.486486	0	.	.	none	.	TAF5L	76	.	NM_014409	exon5	c.A988C	p.N330H	CTGCATTATCATC	.	PASS	Atlas-SNP
TAF1B	9014	hgsc.bcm.edu	37	2	10008516	10008516	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	269	50	259	0	0.185874	0	.	.	none	.	TAF1B	62	.	NM_005680	exon6	c.C511G	p.H171D	GACATCCACACTC	.	PASS	Atlas-SNP
HIST1H4F	8361	hgsc.bcm.edu	37	6	26240823	26240823	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	103	15	128	0	0.145631	0	.	.	none	HIST1H4F,colon,carcinoma,0,1	HIST1H4F	9	1	NM_003540	exon1	c.G170A	p.G57D	CCCGCGGTGTTCT	.	PASS	Atlas-SNP
ZC2HC1A	51101	hgsc.bcm.edu	37	8	79629693	79629693	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	80	17	80	0	0.2125	0	.	.	none	.	.	.	.	NM_016010	exon9	c.T943C	p.C315R	AAATTTTGCTGTG	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152486080	152486080	+	Silent	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	66	13	62	0	0.19697	0	.	.	none	.	NEB	1697	.	NM_001271208	exon68	c.C9804A	p.A3268A	GGCCTTGGCAGCC	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190878658	190878658	+	Splice_Site	SNP	G	G	A	rs76810924		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	417	13	421	3	0.0311751	0.00712589	G|0.875;A|0.125	0.125	weak	FRG1,right_upper_lobe,carcinoma,0,1	FRG1	76	1	NM_004477	exon6	c.537+1G>A	.	ATCAAGGTAATGA	.	scavenged	Atlas-SNP
SNX1	6642	hgsc.bcm.edu	37	15	64410372	64410372	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	140	35	202	0	0.25	0	.	.	none	.	SNX1	36	.	NM_003099	exon3	c.G328A	p.A110T	GTGCTAGCCAAAA	.	PASS	Atlas-SNP
RXFP2	122042	hgsc.bcm.edu	37	13	32376518	32376518	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	95	22	107	0	0.231579	0	.	.	none	.	RXFP2	95	.	NM_130806	exon18	c.C2241G	p.D747E	TGGAGACAGTATA	.	PASS	Atlas-SNP
ZMYM2	7750	hgsc.bcm.edu	37	13	20641392	20641392	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	80	19	78	0	0.2375	0	.	.	none	.	ZMYM2	191	.	NM_001190964	exon22	c.G3315A	p.K1105K	AGTAAAGTTAAAA	.	PASS	Atlas-SNP
CHIT1	1118	hgsc.bcm.edu	37	1	203186947	203186947	+	Missense_Mutation	SNP	G	G	C	rs201682373	byfrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	74	9	48	0	0.121622	0	G|0.988;C|0.012	0.012	strong	CHIT1,NS,carcinoma,0,1	CHIT1	61	1	NM_003465	exon10	c.C1076G	p.A359G	TCCAGTGCCCAGA	.	PASS	Atlas-SNP
EIF4A2	1974	hgsc.bcm.edu	37	3	186502430	186502430	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	95	20	110	0	0.210526	0	.	.	none	.	EIF4A2	55	.	NM_001967	exon3	c.C153T	p.Y51Y	TGCTTACGGTTTT	.	PASS	Atlas-SNP
IRF4	3662	hgsc.bcm.edu	37	6	393209	393209	+	Silent	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	180	73	135	0	0.405556	0	.	.	none	.	IRF4	65	.	NM_001195286	exon2	c.C57T	p.C19C	GAGCTGCGGCAAC	.	PASS	Atlas-SNP
TREML2	79865	hgsc.bcm.edu	37	6	41166022	41166022	+	Silent	SNP	A	A	G	rs139267947		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	63	8	47	1	0.126984	0.0212766	A|0.997;G|0.003	0.003	weak	TREML2,caecum,carcinoma,0,1	TREML2	41	1	NM_024807	exon2	c.T201C	p.F67F	TCGGGCAAAGCCA	.	scavenged	Atlas-SNP
HIST2H2BE	8349	hgsc.bcm.edu	37	1	149858111	149858111	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	88	16	97	0	0.181818	0	.	.	none	HIST2H2BE,NS,carcinoma,0,2	HIST2H2BE	33	2	NM_003528	exon1	c.G80C	p.G27A	TTCTTGCCGTCTT	.	PASS	Atlas-SNP
TMEM132A	54972	hgsc.bcm.edu	37	11	60699343	60699343	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	104	20	137	0	0.192308	0	.	.	none	.	TMEM132A	135	.	NM_017870	exon6	c.T1202C	p.I401T	CCCTTATCCCACT	.	PASS	Atlas-SNP
MAML2	84441	hgsc.bcm.edu	37	11	95825374	95825374	+	Silent	SNP	T	T	C	rs112603485		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	56	3	67	1	0.0535714	0.0149254	C|1.000;|0.000	1.000	weak	MAML2,NS,carcinoma,0,1	MAML2	94	1	NM_032427	exon2	c.A1821G	p.Q607Q	CTGCTGTTGCTGC	.	scavenged	Atlas-SNP
SCN4A	6329	hgsc.bcm.edu	37	17	62045701	62045701	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	80	6	107	0	0.075	0	.	.	none	.	SCN4A	205	.	NM_000334	exon6	c.G718A	p.V240M	CCCCCACGATCGT	.	PASS	Atlas-SNP
BTBD9	114781	hgsc.bcm.edu	37	6	38545397	38545397	+	Missense_Mutation	SNP	T	T	C	rs373363401		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	51	21	54	0	0.411765	0	.	.	weak	.	BTBD9	85	.	NM_052893	exon7	c.A1133G	p.Y378C	GGAAAATATAATT	.	PASS	Atlas-SNP
AGGF1	55109	hgsc.bcm.edu	37	5	76332530	76332530	+	Silent	SNP	T	T	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	117	5	113	1	0.042735	0.00884956	.	.	none	AGGF1,NS,carcinoma,+2,1	AGGF1	71	1	NM_018046	exon4	c.T666G	p.G222G	CACTGGTTTCTAT	.	scavenged	Atlas-SNP
PLD6	201164	hgsc.bcm.edu	37	17	17106346	17106346	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	105	21	161	0	0.2	0	.	.	none	.	PLD6	9	.	NM_178836	exon2	c.G494C	p.R165T	AGCACCCTCTTGT	.	PASS	Atlas-SNP
CHEK2	11200	hgsc.bcm.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs74751600		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	248	10	304	5	0.0403226	0.0164474	.	.	weak	CHEK2,NS,carcinoma,0,36	CHEK2	438	36	NM_001005735	exon12	c.A1246G	p.K416E	AAATCTTGGAGTG	.	scavenged	Atlas-SNP
TMEM135	65084	hgsc.bcm.edu	37	11	87024484	87024484	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	227	46	260	0	0.202643	0	.	.	none	.	TMEM135	40	.	NM_022918	exon11	c.G954A	p.L318L	CTTCCTGCGCTGG	.	PASS	Atlas-SNP
HIST1H2BG	8339	hgsc.bcm.edu	37	6	26216544	26216544	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	76	7	69	0	0.0921053	0	.	.	none	.	HIST1H2BG	25	.	NM_003518	exon1	c.C328T	p.H110Y	CTGCGTGCTTGGC	.	PASS	Atlas-SNP
TRPM6	140803	hgsc.bcm.edu	37	9	77400960	77400960	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	132	27	158	0	0.204545	0	.	.	none	TRPM6_ENST00000451710,axilla,malignant_melanoma,+1,2	TRPM6	377	2	NM_017662	exon21	c.G2749C	p.A917P	CAATGGCCACAGT	.	PASS	Atlas-SNP
KCNN3	3782	hgsc.bcm.edu	37	1	154842243	154842243	+	Silent	SNP	A	A	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	54	13	64	4	0.240741	0.0625	.	.	none	KCNN3,NS,carcinoma,0,3	KCNN3	141	3	NM_001204087	exon1	c.T198G	p.L66L	CTGCTGAAGCTGC	.	scavenged	Atlas-SNP
ZNF846	162993	hgsc.bcm.edu	37	19	9868728	9868728	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	80	15	81	0	0.1875	0	.	.	none	.	ZNF846	61	.	NM_001077624	exon6	c.A1025G	p.E342G	CCACACTCCTTAC	.	PASS	Atlas-SNP
ISLR2	57611	hgsc.bcm.edu	37	15	74426853	74426853	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	75	8	95	0	0.106667	0	.	.	none	.	ISLR2	78	.	NM_001130138	exon4	c.G1758T	p.E586D	GAAGGAGCTCCCA	.	PASS	Atlas-SNP
PIK3C2A	5286	hgsc.bcm.edu	37	11	17167456	17167456	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	75	15	83	0	0.2	0	.	.	none	.	PIK3C2A	148	.	NM_002645	exon6	c.A1594C	p.K532Q	GGTGTTTGTTTAA	.	PASS	Atlas-SNP
ZNF534	147658	hgsc.bcm.edu	37	19	52941505	52941505	+	Silent	SNP	T	T	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	65	15	82	0	0.230769	0	.	.	none	.	ZNF534	105	.	NM_001143939	exon4	c.T831C	p.H277H	AATTCATACTGGA	.	PASS	Atlas-SNP
LRRFIP2	9209	hgsc.bcm.edu	37	3	37151161	37151161	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	218	42	198	0	0.192661	0	.	.	none	.	LRRFIP2	71	.	NM_006309	exon11	c.A547G	p.T183A	TATATGTTGCCAG	.	PASS	Atlas-SNP
ATN1	1822	hgsc.bcm.edu	37	12	7045891	7045891	+	Silent	SNP	A	A	G	rs150855426	bycluster;byfrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	73	17	76	0	0.232877	0	A|0.990;G|0.010	0.010	strong	ATN1,NS,carcinoma,0,3	ATN1	95	3	NM_001007026	exon5	c.A1461G	p.Q487Q	ACAGCAACAGCAG	.	PASS	Atlas-SNP
NAT8L	339983	hgsc.bcm.edu	37	4	2062888	2062888	+	Silent	SNP	C	C	T	rs376253416		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	115	19	125	0	0.165217	0	.	.	weak	.	NAT8L	23	.	NM_178557	exon2	c.C540T	p.P180P	GCCGCCCGGTGAG	.	PASS	Atlas-SNP
PCMTD1	115294	hgsc.bcm.edu	37	8	52733196	52733196	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	199	6	220	1	0.0301508	0.00454545	.	.	none	PCMTD1,NS,carcinoma,0,1	PCMTD1	73	1	NM_052937	exon6	c.G789T	p.M263I	GGCCTGCATCTCA	.	scavenged	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190878625	190878625	+	Missense_Mutation	SNP	A	A	G	rs373840195		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	519	18	506	5	0.0346821	0.00988142	.	.	weak	FRG1,NS,carcinoma,0,3	FRG1	76	3	NM_004477	exon6	c.A505G	p.S169G	GCAAAAAGTAAAA	.	scavenged	Atlas-SNP
SPRY4	81848	hgsc.bcm.edu	37	5	141694497	141694497	+	Silent	SNP	G	G	A	novel		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	96	22	117	0	0.229167	0	.	.	none	.	SPRY4	31	.	NM_030964	exon3	c.C246T	p.A82A	GGTCAGGGCCAGG	.	PASS	Atlas-SNP
