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	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	Algorithm
ZYG11A	440590	hgsc.bcm.edu	37	1	53343407	53343409	+	In_Frame_Del	DEL	CTT	CTT	-	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	ZYG11A	NM_001004339	exon9	c.1595_1597del	p.532_533del	.	.	155.0	28.0	90.0	0.0	.	46	.	Pindel,Atlas-Indel
GNL3	26354	hgsc.bcm.edu	37	3	52721395	52721396	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.,1	GNL3	NM_014366	exon3	c.205_206del	p.69_69del	.	.	230.0	46.0	181.0	0.0	.	37	.	Pindel,Atlas-Indel
AKAP11	11215	hgsc.bcm.edu	37	13	42876257	42876257	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_016248	exon8	c.G3375T	p.K1125N	GCTCAAGGGAGAA	.	91.0	4.0	136.0	0.0	.	.	.	Atlas-SNP
ATG2A	23130	hgsc.bcm.edu	37	11	64662855	64662855	+	Silent	SNP	C	C	A	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_015104	exon40	c.G5487T	p.L1829L	ATCCTGCAGGGAG	.	62.0	27.0	55.0	0.0	.	.	.	Atlas-SNP
KRT85	3891	hgsc.bcm.edu	37	12	52758951	52758951	+	Missense_Mutation	SNP	G	G	A	rs148274330		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_002283	exon2	c.C424T	p.R142C	GGAAGCGCACCTG	.	92.0	17.0	65.0	0.0	.	.	.	Atlas-SNP
KANK1	23189	hgsc.bcm.edu	37	9	745199	745199	+	Silent	SNP	G	G	A	rs148157700		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	KANK1_ENST00000382303,NS,carcinoma,0,2	KANK1_ENST00000382303	NM_001256876	exon16	c.G4023A	p.T1341T	GAAGACGTCTCCT	.	124.0	54.0	158.0	0.0	0.000	0	2	Atlas-SNP
PPT2-EGFL8	0	hgsc.bcm.edu	37	6	32123363	32123363	+	RNA	SNP	G	G	C	rs111653317	bycluster	TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	.	.	.	.	GTCTCTGTGTGTG	.	35.0	4.0	21.0	0.0	0.500	.	.	Atlas-SNP
GLT1D1	144423	hgsc.bcm.edu	37	12	129467613	129467613	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_144669	exon8	c.T779C	p.L260P	GGAAGCTGGAAGG	.	62.0	20.0	49.0	0.0	.	.	.	Atlas-SNP
PNMAL2	57469	hgsc.bcm.edu	37	19	46997528	46997528	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_020709	exon1	c.G1195A	p.A399T	CCACGGCGTCCAC	.	35.0	9.0	27.0	0.0	.	.	.	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093393	1093393	+	Missense_Mutation	SNP	G	G	A	rs199525790		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2_ENST00000441003	NM_002457	exon30	c.G5212A	p.G1738S	CCCACCGGCACAC	.	43.0	5.0	28.0	0.0	.	0	2	Atlas-SNP
MERTK	10461	hgsc.bcm.edu	37	2	112760766	112760766	+	Splice_Site	SNP	T	T	C	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_006343	exon12	c.1786+2T>C	.	TGAAGGTAAGCAA	.	160.0	42.0	114.0	0.0	.	.	.	Atlas-SNP
TCOF1	6949	hgsc.bcm.edu	37	5	149767638	149767638	+	Silent	SNP	G	G	A	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_001135243	exon18	c.G3033A	p.Q1011Q	TACACAGTGCTTG	.	156.0	7.0	155.0	0.0	.	.	.	Atlas-SNP
FAM126A	84668	hgsc.bcm.edu	37	7	23016321	23016321	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_032581	exon6	c.C521T	p.A174V	TTCTGTGCTGTCA	.	113.0	29.0	81.0	0.0	.	.	.	Atlas-SNP
MTERFD1	51001	hgsc.bcm.edu	37	8	97263294	97263294	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_015942	exon4	c.C517T	p.P173S	CTTCTGGATGTTT	.	52.0	14.0	38.0	0.0	.	.	.	Atlas-SNP
RPL14	9045	hgsc.bcm.edu	37	3	40503518	40503518	+	Missense_Mutation	SNP	G	G	C	rs199894150	alternate_allele	TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_003973	exon6	c.G443C	p.G148A	CTAAGGGTACTGC	.	90.0	7.0	76.0	0.0	.	.	.	Atlas-SNP
ETV3	2117	hgsc.bcm.edu	37	1	157094985	157094985	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_001145312	exon5	c.C1187T	p.S396L	CGTGCCGACTGCC	.	92.0	5.0	55.0	0.0	.	.	.	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274343	39274343	+	Silent	SNP	A	A	G	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	KRTAP4-11,NS,malignant_melanoma,0,2	KRTAP4-11	NM_033059	exon1	c.T225C	p.C75C	GGGGCGACAGCAG	.	52.0	3.0	48.0	0.0	.	0	2	Atlas-SNP
FLNA	2316	hgsc.bcm.edu	37	X	153583390	153583390	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_001110556	exon31	c.G5020C	p.V1674L	TGTCCACAGTGAT	.	118.0	53.0	90.0	0.0	.	.	.	Atlas-SNP
C12orf52	84934	hgsc.bcm.edu	37	12	113629502	113629502	+	Silent	SNP	G	G	A	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_032848	exon4	c.G690A	p.T230T	TTCCACGTCAGGG	.	111.0	30.0	68.0	0.0	.	.	.	Atlas-SNP
RAB12	201475	hgsc.bcm.edu	37	18	8609900	8609900	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_001025300	exon1	c.A175T	p.M59L	AGCCTGATGGAGC	.	101.0	48.0	120.0	0.0	.	.	.	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510724	195510724	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4_ENST00000463781	NM_018406	exon2	c.C7727T	p.P2576L	GGAAGAGGGGTGG	.	99.0	16.0	74.0	0.0	.	-1	1	Atlas-SNP
SOX13	9580	hgsc.bcm.edu	37	1	204092277	204092277	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_005686	exon11	c.G1172T	p.R391L	AGGAGCGGCTGGA	.	137.0	82.0	98.0	0.0	.	.	.	Atlas-SNP
DNM2	1785	hgsc.bcm.edu	37	19	10908073	10908073	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_001005361	exon10	c.C1214G	p.P405R	TCACCCCCGACAT	.	64.0	17.0	36.0	0.0	.	.	.	Atlas-SNP
ABCA11P	79963	hgsc.bcm.edu	37	4	466474	466474	+	RNA	SNP	C	C	T	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	.	.	.	.	ACATCCCTGAATG	.	119.0	7.0	113.0	0.0	.	.	.	Atlas-SNP
ASTN1	460	hgsc.bcm.edu	37	1	176853487	176853487	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_004319	exon19	c.A3214T	p.K1072X	CCACTTTGGAGTG	.	167.0	42.0	84.0	0.0	.	.	.	Atlas-SNP
ATP6V0D1	9114	hgsc.bcm.edu	37	16	67473035	67473035	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_004691	exon6	c.C655T	p.R219C	AGGCGCGGCGGTC	.	47.0	21.0	40.0	0.0	.	.	.	Atlas-SNP
LRRC8B	23507	hgsc.bcm.edu	37	1	90058405	90058405	+	Missense_Mutation	SNP	A	A	T	rs201504233		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_015350	exon6	c.A2215T	p.N739Y	TTGATGAATTTGT	.	138.0	32.0	70.0	0.0	0.001	.	.	Atlas-SNP
SPACA1	81833	hgsc.bcm.edu	37	6	88757823	88757823	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_030960	exon1	c.C200A	p.T67N	CTGAAACCGAGGA	.	107.0	31.0	96.0	0.0	.	.	.	Atlas-SNP
CNTN5	53942	hgsc.bcm.edu	37	11	99715691	99715691	+	Missense_Mutation	SNP	C	C	T	rs201512506		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	.	.	NM_001243270	exon4	c.C385T	p.P129S	GGCAATCCAGTTC	.	126.0	27.0	94.0	0.0	.	.	.	Atlas-SNP
MAP3K3	4215	hgsc.bcm.edu	37	17	61767648	61767648	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2G-AAL5-01A-11D-A42Y-10	TCGA-2G-AAL5-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	171689da-01a4-40f0-81f1-2e31c2e22def	89d0a1e3-1b77-413f-aa1f-f31cc665e959	MAP3K3,NS,carcinoma,0,2	MAP3K3	NM_203351	exon13	c.G1181T	p.R394L	ACTGGCGCCGGGG	.	48.0	3.0	44.0	0.0	.	0	2	Atlas-SNP
