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	TVarRat	NVarRat	dbSNP_Strength	dbSNP_AF	dbSNP_PopFreq	Confidence	Algorithm
MTOR	2475	hgsc.bcm.edu	hg19	1	11174395	11174395	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	MTOR,NS,carcinoma,+1,2	MTOR	NM_004958	exon53	c.T7280A	p.L2427Q	CAGTTCAGCAAGG	.	44.0	14.0	70.0	0.0	.	327	.	.	.	none	.	.	PASS	Atlas-SNP
DENND2C	163259	hgsc.bcm.edu	hg19	1	115130431	115130431	+	Silent	SNP	G	G	T	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	DENND2C	NM_001256404	exon19	c.C2574A	p.S858S	ACTTCGGGAGGTG	.	95.0	5.0	149.0	0.0	.	105	.	.	.	none	.	.	PASS	Atlas-SNP
LYST	1130	hgsc.bcm.edu	hg19	1	235827769	235827769	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	LYST	NM_000081	exon51	c.G11191T	p.V3731L	ACCTTACAATTCC	.	60.0	20.0	81.0	0.0	.	370	.	.	.	none	.	.	PASS	Atlas-SNP
B3GNT2	10678	hgsc.bcm.edu	hg19	2	62449390	62449390	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	B3GNT2	NM_006577	exon2	c.G35A	p.G12D	TGTTGGGTATCCT	.	99.0	31.0	179.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
ST3GAL6	10402	hgsc.bcm.edu	hg19	3	98512536	98512536	+	Silent	SNP	G	G	T	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	ST3GAL6	NM_001271145	exon10	c.G1086T	p.V362V	CAATGTGACTGCA	.	87.0	25.0	140.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	hg19	4	88537513	88537513	+	Missense_Mutation	SNP	A	A	C	rs112275895		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	DSPP	NM_014208	exon5	c.A3699C	p.E1233D	CAATGAAAGCAGC	.	88.0	13.0	116.0	0.0	.	174	.	.	.	weak	A|0.500;C|0.500	0.500	PASS	Atlas-SNP
PCDHA10	56139	hgsc.bcm.edu	hg19	5	140236456	140236456	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	PCDHA10	NM_031859	exon1	c.G823T	p.E275X	AACAAGGAAATGA	.	127.0	52.0	158.0	0.0	.	358	.	.	.	none	.	.	PASS	Atlas-SNP
ERGIC1	57222	hgsc.bcm.edu	hg19	5	172362237	172362237	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	ERGIC1	NM_001031711	exon9	c.G689T	p.W230L	CAATCTGGTTCCG	.	83.0	4.0	113.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
ATAT1	79969	hgsc.bcm.edu	hg19	6	30594987	30594987	+	Silent	SNP	T	T	C	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	ATAT1_ENST00000330083,NS,carcinoma,0,1	ATAT1	NM_001031722	exon1	c.T7C	p.L3L	ATGTGGTTGACCT	.	70.0	28.0	103.0	1.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
CDSN	1041	hgsc.bcm.edu	hg19	6	31085252	31085252	+	Missense_Mutation	SNP	C	C	T	rs370680006		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	CDSN	NM_001264	exon2	c.G140A	p.R47H	GTGATACGCGTGG	.	57.0	12.0	102.0	0.0	.	48	.	.	.	weak	.	.	PASS	Atlas-SNP
NPC1L1	29881	hgsc.bcm.edu	hg19	7	44561797	44561797	+	Silent	SNP	G	G	A	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	NPC1L1	NM_001101648	exon11	c.C2682T	p.F894F	CACCTCGAAGTAG	.	21.0	7.0	40.0	0.0	.	141	.	.	.	none	.	.	PASS	Atlas-SNP
SEMA3E	9723	hgsc.bcm.edu	hg19	7	83037688	83037688	+	Silent	SNP	C	C	T	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	SEMA3E	NM_012431	exon6	c.G666A	p.L222L	ACCTTTCAACAGA	.	108.0	27.0	171.0	0.0	.	125	.	.	.	none	.	.	PASS	Atlas-SNP
MLLT3	4300	hgsc.bcm.edu	hg19	9	20414373	20414373	+	Silent	SNP	G	G	A	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	MLLT3,NS,carcinoma,0,4	MLLT3	NM_004529	exon5	c.C471T	p.S157S	GCTGCTGCTACTG	.	96.0	6.0	110.0	1.0	.	125	.	.	.	none	.	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	hg19	10	29818641	29818641	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	SVIL	NM_021738	exon12	c.G2239A	p.A747T	TGGCTGCGATGAC	.	60.0	4.0	98.0	0.0	.	226	.	.	.	none	.	.	PASS	Atlas-SNP
PIWIL4	143689	hgsc.bcm.edu	hg19	11	94300728	94300728	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	PIWIL4	NM_152431	exon1	c.G44A	p.S15N	CCCGCAGCCCCAG	.	71.0	25.0	105.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
C2CD5	9847	hgsc.bcm.edu	hg19	12	22676361	22676361	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	.	NM_014802	exon7	c.G799A	p.E267K	CTTACTCCTTCAT	.	104.0	29.0	133.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
PTPRR	5801	hgsc.bcm.edu	hg19	12	71286725	71286725	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	PTPRR	NM_002849	exon2	c.G91A	p.A31T	TAATTGCCAAAAA	.	243.0	79.0	276.0	0.0	.	109	.	.	.	none	.	.	PASS	Atlas-SNP
RNF17	56163	hgsc.bcm.edu	hg19	13	25428149	25428149	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	RNF17	NM_031277	exon25	c.T3477G	p.F1159L	TGAATTTCAGGAG	.	98.0	27.0	121.0	0.0	.	259	.	.	.	none	.	.	PASS	Atlas-SNP
EML5	161436	hgsc.bcm.edu	hg19	14	89109293	89109293	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	EML5	NM_183387	exon30	c.G4181A	p.G1394D	TCATCACCATCAT	.	143.0	11.0	229.0	0.0	.	141	.	.	.	none	.	.	PASS	Atlas-SNP
CGNL1	84952	hgsc.bcm.edu	hg19	15	57815687	57815687	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	CGNL1	NM_001252335	exon12	c.G2716A	p.G906R	TTGCAGGGAAATC	.	53.0	17.0	87.0	0.0	.	125	.	.	.	none	.	.	PASS	Atlas-SNP
EPG5	57724	hgsc.bcm.edu	hg19	18	43534423	43534423	+	Silent	SNP	T	T	C	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	EPG5	NM_020964	exon2	c.A945G	p.T315T	ATCAGATGTCAGA	.	113.0	38.0	174.0	0.0	.	199	.	.	.	none	.	.	PASS	Atlas-SNP
MAG	4099	hgsc.bcm.edu	hg19	19	35802844	35802844	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	MAG	NM_080600	exon10	c.G1640A	p.S547N	GCCCCAGCTTCTC	.	83.0	37.0	140.0	0.0	.	172	.	.	.	none	.	.	PASS	Atlas-SNP
SCAF1	58506	hgsc.bcm.edu	hg19	19	50156129	50156129	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	SCAF1	NM_021228	exon7	c.C2483A	p.S828Y	GTTCTTCCCGGAA	.	26.0	9.0	57.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
COX1	5742	hgsc.bcm.edu	hg19	MT	6054	6054	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	.	ENST00000361624	exon1	c.G151A	p.D51N	GGTAACGACCACA	.	118.0	8.0	11.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
COX2	5743	hgsc.bcm.edu	hg19	MT	8075	8075	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	.	ENST00000361739	exon1	c.G490A	p.A164T	TCATGAGCTGTCC	.	80.0	6.0	14.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
MLL	4297	hgsc.bcm.edu	hg19	11	118377019	118377019	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	MLL	NM_001197104	exon27	c.10411delT	p.S3471fs	.	.	90.0	34.0	112.0	0.0	.	548	.	0.377778	0	none	.	.	PASS	Atlas-Indel,Pindel
EFHB	151651	hgsc.bcm.edu	hg19	3	19947241	19947250	+	Frame_Shift_Del	DEL	CCTGTGGAAA	CCTGTGGAAA	-	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	CCTGTGGAAA	CCTGTGGAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	EFHB	NM_144715	exon6	c.1289_1290del	p.430_430del	.	.	65.0	15.0	124.0	0.0	.	186	.	0.230769	0	none	.	.	PASS	Atlas-Indel,Pindel
NCOA6	23054	hgsc.bcm.edu	hg19	20	33329080	33329081	+	Frame_Shift_Del	DEL	AA	AA	-	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	NCOA6	NM_014071	exon11	c.4980_4981del	p.1660_1661del	.	.	68.0	23.0	109.0	0.0	.	219	.	0.338235	0	none	.	.	PASS	Atlas-Indel,Pindel
OBSCN	84033	hgsc.bcm.edu	hg19	1	228547456	228547466	+	Frame_Shift_Del	DEL	GCAGGCCGGAG	GCAGGCCGGAG	-	novel		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	GCAGGCCGGAG	GCAGGCCGGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	.	OBSCN	NM_052843	exon81	c.18862_18872del	p.6288_6291del	.	.	54.0	13.0	104.0	0.0	.	2142	.	0.240741	0	none	.	.	PASS	Atlas-Indel,Pindel
