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
ADAM15	8751	hgsc.bcm.edu	hg19	1	155032387	155032387	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	ADAM15	NM_001261464	exon17	c.A2035T	p.S679C	TGTGACAGCAACA	.	458.0	179.0	406.0	0.0	.	92	.	.	.	none	.	.	PASS	Atlas-SNP
ASH1L	55870	hgsc.bcm.edu	hg19	1	155408153	155408153	+	Silent	SNP	T	T	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	ASH1L	NM_018489	exon5	c.A5793T	p.P1931P	TGGTAATGGCTTC	.	228.0	76.0	331.0	0.0	.	279	.	.	.	none	.	.	PASS	Atlas-SNP
ISG20L2	81875	hgsc.bcm.edu	hg19	1	156693972	156693972	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	ISG20L2	NM_030980	exon2	c.C916T	p.L306F	TGGTGAGATGCTT	.	226.0	21.0	239.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
IGSF9	57549	hgsc.bcm.edu	hg19	1	159898194	159898194	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	IGSF9	NM_001135050	exon19	c.C2984A	p.P995H	GTGTAAGGGGGCT	.	15.0	8.0	26.0	0.0	.	123	.	.	.	none	.	.	PASS	Atlas-SNP
PROX1	5629	hgsc.bcm.edu	hg19	1	214178606	214178606	+	Silent	SNP	C	C	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	PROX1,NS,carcinoma,0,2	PROX1	NM_001270616	exon3	c.C1824T	p.S608S	CTTCTCCGACGTA	.	91.0	29.0	148.0	0.0	.	124	.	.	.	none	.	.	PASS	Atlas-SNP
BPNT1	10380	hgsc.bcm.edu	hg19	1	220232235	220232235	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	BPNT1	NM_006085	exon9	c.A878G	p.Y293C	GCATAGTAGTCAT	.	268.0	74.0	383.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
PRKCE	5581	hgsc.bcm.edu	hg19	2	46372319	46372319	+	Silent	SNP	T	T	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	PRKCE	NM_005400	exon12	c.T1680C	p.N560N	TCTGAATGGTGTG	.	266.0	108.0	264.0	1.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
DCTN1	1639	hgsc.bcm.edu	hg19	2	74589259	74589259	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	DCTN1	NM_004082	exon31	c.C3619G	p.L1207V	CCTTGAGGACCTC	.	80.0	41.0	89.0	0.0	.	110	.	.	.	none	.	.	PASS	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	hg19	2	107049613	107049613	+	Silent	SNP	A	A	G	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	RGPD3_ENST00000304514,NS,carcinoma,0,2	RGPD3	NM_001144013	exon16	c.T2334C	p.H778H	TGTAGAATGTTTT	.	381.0	104.0	593.0	0.0	.	316	.	.	.	none	.	.	PASS	Atlas-SNP
DPP10	57628	hgsc.bcm.edu	hg19	2	116598392	116598392	+	Missense_Mutation	SNP	C	C	A	rs201639501	bycluster;alternate_allele	TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	DPP10	NM_001178034	exon25	c.C2261A	p.T754N	ATTATACTATGCA	.	74.0	34.0	109.0	0.0	.	415	.	.	.	alt	C|0.999;G|0.001	.	PASS	Atlas-SNP
ITGB6	3694	hgsc.bcm.edu	hg19	2	160982928	160982928	+	Silent	SNP	T	T	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	ITGB6	NM_000888	exon11	c.A1845G	p.E615E	ACATCGTTCACAG	.	161.0	15.0	149.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
ACADL	33	hgsc.bcm.edu	hg19	2	211081149	211081149	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	ACADL	NM_001608	exon4	c.A458G	p.Q153R	TTAATCTGTTCTT	.	68.0	22.0	258.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
BARD1	580	hgsc.bcm.edu	hg19	2	215593624	215593624	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	BARD1	NM_000465	exon11	c.A2110C	p.S704R	TTCTACTGAGGAT	.	59.0	36.0	107.0	0.0	.	138	.	.	.	none	.	.	PASS	Atlas-SNP
STK25	10494	hgsc.bcm.edu	hg19	2	242437690	242437690	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	STK25	NM_006374	exon9	c.G992T	p.S331I	AGCTTGCTGTGTG	.	237.0	10.0	228.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
BHLHE40	8553	hgsc.bcm.edu	hg19	3	5024904	5024904	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	BHLHE40	NM_003670	exon5	c.A766T	p.S256C	TTGCGCAGTGAGC	.	146.0	92.0	98.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
SLC6A6	6533	hgsc.bcm.edu	hg19	3	14508150	14508150	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	SLC6A6	NM_003043	exon7	c.G859A	p.D287N	CTTGAGGACCCAC	.	191.0	115.0	121.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
BAP1	8314	hgsc.bcm.edu	hg19	3	52441417	52441417	+	Silent	SNP	G	G	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	BAP1	NM_004656	exon6	c.C435G	p.A145A	ACACCTGGCATGG	.	235.0	68.0	191.0	0.0	.	371	.	.	.	none	.	.	PASS	Atlas-SNP
PDZRN3	23024	hgsc.bcm.edu	hg19	3	73432828	73432828	+	Silent	SNP	C	C	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	PDZRN3,rectum,carcinoma,0,2	PDZRN3	NM_015009	exon10	c.G2889A	p.A963A	GCTCACCGCGTCG	.	278.0	79.0	147.0	0.0	.	196	.	.	.	none	.	.	PASS	Atlas-SNP
SLC2A2	6514	hgsc.bcm.edu	hg19	3	170732492	170732492	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	SLC2A2	NM_000340	exon3	c.T137C	p.L46S	ACACCCAAAACAT	.	201.0	53.0	238.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
EIF2B5	8893	hgsc.bcm.edu	hg19	3	183861938	183861938	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	EIF2B5,NS,carcinoma,0,1	EIF2B5	NM_003907	exon14	c.G1921A	p.D641N	GCAGCCGACCATT	.	515.0	142.0	410.0	1.0	.	62	.	.	.	none	.	.	PASS	Atlas-SNP
CD180	4064	hgsc.bcm.edu	hg19	5	66479676	66479676	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	CD180	NM_005582	exon3	c.A995G	p.H332R	TCGAAATGATTTA	.	210.0	89.0	286.0	1.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
SPINK5	11005	hgsc.bcm.edu	hg19	5	147505159	147505159	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	SPINK5	NM_001127698	exon29	c.G2812T	p.V938F	GCCTCTGTTGCCA	.	57.0	27.0	100.0	0.0	.	245	.	.	.	none	.	.	PASS	Atlas-SNP
MSH5	4439	hgsc.bcm.edu	hg19	6	31712029	31712029	+	Silent	SNP	A	A	G	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	MSH5	NM_025259	exon7	c.A651G	p.E217E	ACTGGAAGACTAT	.	195.0	63.0	211.0	0.0	.	108	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC1	55227	hgsc.bcm.edu	hg19	6	53787458	53787458	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	LRRC1	NM_018214	exon14	c.C1442A	p.P481Q	CCACTCCACACCC	.	214.0	189.0	237.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
BAI3	577	hgsc.bcm.edu	hg19	6	69759168	69759168	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	BAI3,colon,carcinoma,-1,3	BAI3	NM_001704	exon15	c.G2263C	p.D755H	GAATTAGATGAAT	.	27.0	2.0	112.0	0.0	.	451	.	.	.	none	.	.	PASS	Atlas-SNP
ARL4A	10124	hgsc.bcm.edu	hg19	7	12728407	12728407	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	ARL4A	NM_001037164	exon2	c.G528C	p.K176N	CCTAAAGGAAGGA	.	168.0	70.0	197.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
CAMK2B	816	hgsc.bcm.edu	hg19	7	44259810	44259810	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	CAMK2B	NM_001220	exon23	c.G1852A	p.A618T	TGTAAGCGATGCA	.	76.0	8.0	45.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
LANCL2	55915	hgsc.bcm.edu	hg19	7	55459595	55459595	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	LANCL2	NM_018697	exon2	c.G314C	p.G105A	ATACTGGCTGGAC	.	214.0	34.0	142.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
ABCB1	5243	hgsc.bcm.edu	hg19	7	87148688	87148688	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	ABCB1	NM_000927	exon24	c.G2881A	p.A961T	AGTAGGCTCCAAA	.	104.0	40.0	140.0	0.0	.	263	.	.	.	none	.	.	PASS	Atlas-SNP
CALD1	800	hgsc.bcm.edu	hg19	7	134618538	134618538	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	CALD1,NS,carcinoma,0,1	CALD1	NM_033138	exon5	c.G1018A	p.E340K	GCAGCAGAGGAGA	.	31.0	2.0	14.0	0.0	.	150	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM67	91147	hgsc.bcm.edu	hg19	8	94792858	94792858	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	TMEM67	NM_153704	exon8	c.A752C	p.N251T	TTGGAAATATGTG	.	291.0	134.0	444.0	1.0	.	187	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF658	26149	hgsc.bcm.edu	hg19	9	40774146	40774146	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	ZNF658	NM_033160	exon5	c.G1129T	p.E377X	TATCTTCTGTGTG	.	251.0	105.0	701.0	0.0	.	100	.	.	.	none	.	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	hg19	9	137714852	137714852	+	Silent	SNP	T	T	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	COL5A1	NM_000093	exon60	c.T4617C	p.P1539P	TCCGCCTGGTCCA	.	61.0	12.0	53.0	0.0	.	323	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF503	84858	hgsc.bcm.edu	hg19	10	77159027	77159027	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	ZNF503	NM_032772	exon2	c.C1421A	p.P474Q	TGCAGCGGGTGCG	.	50.0	32.0	20.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
CTBP2	1488	hgsc.bcm.edu	hg19	10	126715159	126715159	+	Silent	SNP	A	A	G	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.,1	CTBP2	NM_022802	exon1	c.T1170C	p.A390A	CAGAGGAGCCGCA	.	15.0	3.0	4.0	0.0	.	100	.	.	.	none	.	.	PASS	Atlas-SNP
KNDC1	85442	hgsc.bcm.edu	hg19	10	135009191	135009191	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	KNDC1	NM_152643	exon10	c.G1600A	p.V534I	GCCGCCGTTCTGT	.	55.0	21.0	44.0	0.0	.	155	.	.	.	none	.	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	hg19	11	7817940	7817940	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	OR5P2	NM_153444	exon1	c.T550A	p.S184T	AACAGGAGAGTTC	.	82.0	31.0	128.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
NXF1	10482	hgsc.bcm.edu	hg19	11	62567921	62567921	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	NXF1	NM_006362	exon10	c.T944C	p.L315P	AGCTTCAGCCCCT	.	80.0	27.0	92.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
LTBR	4055	hgsc.bcm.edu	hg19	12	6494285	6494285	+	Silent	SNP	C	C	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	LTBR	NM_002342	exon3	c.C291T	p.I97I	GACCATCTGCCAG	.	446.0	261.0	280.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
TM7SF3	51768	hgsc.bcm.edu	hg19	12	27156249	27156249	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	TM7SF3	NM_016551	exon2	c.C166A	p.H56N	TATCATGCAAAAT	.	65.0	23.0	103.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
TIMELESS	8914	hgsc.bcm.edu	hg19	12	56822670	56822670	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	TIMELESS	NM_003920	exon11	c.G1301A	p.R434H	CACCGGCGTGCCC	.	116.0	32.0	90.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
GRIP1	23426	hgsc.bcm.edu	hg19	12	66765685	66765685	+	Missense_Mutation	SNP	G	G	A	rs367781032		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	GRIP1,NS,carcinoma,0,1	GRIP1	NM_021150	exon22	c.C2645T	p.T882M	CTCATCGTGCTCC	.	187.0	51.0	133.0	0.0	.	106	.	.	.	weak	.	.	PASS	Atlas-SNP
SSH1	54434	hgsc.bcm.edu	hg19	12	109182194	109182194	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	SSH1	NM_018984	exon15	c.A2720T	p.H907L	CTGGTGTGGTCCA	.	200.0	133.0	94.0	0.0	.	144	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA0586	9786	hgsc.bcm.edu	hg19	14	58949256	58949256	+	Silent	SNP	C	C	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	KIAA0586	NM_001244189	exon23	c.C3129T	p.L1043L	CGCCCTCCAGCTT	.	55.0	26.0	77.0	0.0	.	180	.	.	.	none	.	.	PASS	Atlas-SNP
TRIP11	9321	hgsc.bcm.edu	hg19	14	92491671	92491671	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	TRIP11	NM_004239	exon3	c.C295G	p.Q99E	GAAGTTGATTTCG	.	53.0	28.0	116.0	0.0	.	184	.	.	.	none	.	.	PASS	Atlas-SNP
USP3	9960	hgsc.bcm.edu	hg19	15	63882867	63882867	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	USP3	NM_006537	exon15	c.T1405G	p.S469A	GTTGGTTCTGGAC	.	207.0	79.0	179.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
CRTC3	64784	hgsc.bcm.edu	hg19	15	91161146	91161146	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	CRTC3	NM_022769	exon8	c.G645C	p.E215D	AGAAGAGAATCTG	.	102.0	42.0	99.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
CACNA1H	8912	hgsc.bcm.edu	hg19	16	1263882	1263882	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	CACNA1H	NM_021098	exon27	c.T4880C	p.I1627T	TCATCATCTGTGT	.	34.0	21.0	20.0	0.0	.	317	.	.	.	none	.	.	PASS	Atlas-SNP
SRCAP	10847	hgsc.bcm.edu	hg19	16	30736125	30736125	+	Missense_Mutation	SNP	C	C	G	rs371358460		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	SRCAP	NM_006662	exon25	c.C5380G	p.P1794A	CCTGCCCCAGTTC	.	98.0	32.0	49.0	0.0	.	298	.	.	.	weak	.	.	PASS	Atlas-SNP
NEK8	284086	hgsc.bcm.edu	hg19	17	27067537	27067537	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	NEK8	NM_178170	exon11	c.C1474G	p.P492A	CCCATGCCCCCAG	.	324.0	87.0	202.0	0.0	.	76	.	.	.	none	.	.	PASS	Atlas-SNP
CACNB1	782	hgsc.bcm.edu	hg19	17	37331566	37331566	+	Silent	SNP	C	C	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	CACNB1	NM_000723	exon14	c.G1677A	p.L559L	GTCGGTCAGCTCT	.	853.0	268.0	575.0	1.0	.	89	.	.	.	none	.	.	PASS	Atlas-SNP
CDC6	990	hgsc.bcm.edu	hg19	17	38447499	38447499	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	CDC6	NM_001254	exon3	c.C368T	p.S123L	TTTCTTCAGTTAG	.	184.0	108.0	123.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
KCNJ2	3759	hgsc.bcm.edu	hg19	17	68171425	68171425	+	Missense_Mutation	SNP	G	G	A	rs199473653		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	KCNJ2	NM_000891	exon2	c.G245A	p.R82Q	GCTGGCGGTGGAT	.	310.0	108.0	256.0	0.0	.	74	.	.	.	weak	.	.	PASS	Atlas-SNP
RAB37	326624	hgsc.bcm.edu	hg19	17	72736931	72736931	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	RAB37	NM_001163989	exon2	c.G133A	p.V45I	ACAGGCGTCGGCA	.	508.0	34.0	351.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
ACOX1	51	hgsc.bcm.edu	hg19	17	73945931	73945931	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	ACOX1	NM_007292	exon10	c.G1346A	p.C449Y	ATGCCACACACCA	.	178.0	100.0	138.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
GAREM	64762	hgsc.bcm.edu	hg19	18	29867890	29867890	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	.	NM_022751	exon4	c.C670T	p.P224S	CCAGGGGACTTCG	.	139.0	55.0	187.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
HMSD	284293	hgsc.bcm.edu	hg19	18	61621714	61621714	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	HMSD	NM_001123366	exon3	c.A145G	p.I49V	GTTGCAATTAACA	.	156.0	13.0	269.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	hg19	19	10096525	10096525	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	COL5A3	NM_015719	exon31	c.G2399A	p.G800E	TTAGGTCCAGGGC	.	473.0	258.0	571.0	1.0	.	243	.	.	.	none	.	.	PASS	Atlas-SNP
SMARCA4	6597	hgsc.bcm.edu	hg19	19	11141551	11141551	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	SMARCA4	NM_003072	exon25	c.C3528G	p.S1176R	TGACAGCGACTGG	.	37.0	19.0	22.0	0.0	.	502	.	.	.	none	.	.	PASS	Atlas-SNP
PLEKHG2	64857	hgsc.bcm.edu	hg19	19	39915323	39915323	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	PLEKHG2	NM_022835	exon19	c.C3550T	p.P1184S	CCGGAGCCAAGCC	.	319.0	126.0	292.0	0.0	.	329	.	.	.	none	.	.	PASS	Atlas-SNP
MEGF8	1954	hgsc.bcm.edu	hg19	19	42872696	42872696	+	Silent	SNP	T	T	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	MEGF8	NM_001271938	exon36	c.T6363C	p.C2121C	GGGCTGTGCTCAG	.	29.0	13.0	28.0	0.0	.	358	.	.	.	none	.	.	PASS	Atlas-SNP
PPP1R12C	54776	hgsc.bcm.edu	hg19	19	55603617	55603617	+	Silent	SNP	G	G	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	PPP1R12C	NM_017607	exon19	c.C2133G	p.L711L	CACCTTGAGCTGC	.	18.0	5.0	16.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
FASTKD5	60493	hgsc.bcm.edu	hg19	20	3128940	3128940	+	Silent	SNP	A	A	G	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	FASTKD5	NM_021826	exon2	c.T777C	p.P259P	AAACCTAGGTACT	.	122.0	36.0	126.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
ZHX3	23051	hgsc.bcm.edu	hg19	20	39831715	39831715	+	Silent	SNP	G	G	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	ZHX3	NM_015035	exon3	c.C1842A	p.T614T	GTATTTGGTTGGT	.	281.0	176.0	164.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
DSCAM	1826	hgsc.bcm.edu	hg19	21	41710196	41710196	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	DSCAM	NM_001271534	exon8	c.A1615G	p.K539E	AGTTCTTGTACCA	.	103.0	80.0	235.0	0.0	.	347	.	.	.	none	.	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	hg19	22	23237695	23237695	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	IGLL5	NM_001178126	exon3	c.C466T	p.P156S	GGCAGCCCCGTCA	.	54.0	21.0	48.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
EIF4ENIF1	56478	hgsc.bcm.edu	hg19	22	31837941	31837941	+	Silent	SNP	T	T	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	EIF4ENIF1	NM_019843	exon17	c.A2370G	p.R790R	TGTTTTTCTCCCA	.	184.0	19.0	185.0	0.0	.	80	.	.	.	none	.	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	hg19	22	46931045	46931045	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	CELSR1	NM_014246	exon1	c.A2023G	p.I675V	CCGTGATGGACAC	.	43.0	13.0	26.0	0.0	.	242	.	.	.	none	.	.	PASS	Atlas-SNP
MBTPS2	51360	hgsc.bcm.edu	hg19	X	21857904	21857904	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	MBTPS2	NM_015884	exon1	c.T52C	p.Y18H	GTCGTCTACCTGA	.	5.0	5.0	9.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
SPIN3	169981	hgsc.bcm.edu	hg19	X	57021007	57021007	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	SPIN3	NM_001010862	exon2	c.C374G	p.A125G	ATTTCTGCCAAGT	.	217.0	11.0	287.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
ND1	10625	hgsc.bcm.edu	hg19	MT	3890	3890	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	.	ENST00000361390	exon1	c.G584A	p.R195Q	CCAACCGAACCCC	.	111.0	105.0	10.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
COX3	5742	hgsc.bcm.edu	hg19	MT	9612	9612	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	.	ENST00000362079	exon1	c.G406A	p.V136M	ACATCCGTATTAC	.	79.0	8.0	11.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	hg19	MT	12640	12640	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	.	ENST00000361567	exon1	c.G304A	p.E102K	ATCATAGAATTCT	.	61.0	7.0	15.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ND6	0	hgsc.bcm.edu	hg19	MT	14348	14348	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	.	ENST00000361681	exon1	c.A326G	p.Y109C	CCATCATACTCTT	.	91.0	6.0	19.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
BPNT1	10380	hgsc.bcm.edu	hg19	1	220232228	220232229	+	Frame_Shift_Ins	INS	-	-	GCATA	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	BPNT1	NM_006085	exon9	c.885_886insTATGC	p.A295fs	.	.	296.0	28.0	413.0	0.0	.	29	.	0.0945946	0	none	.	.	PASS	Atlas-INDEL
DDX5	1655	hgsc.bcm.edu	hg19	17	62500099	62500102	+	Frame_Shift_Del	DEL	ACAG	ACAG	-	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	ACAG	ACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	DDX5	NM_004396	exon4	c.441_441del	p.147_147del	.	.	179.0	45.0	294.0	0.0	.	101	.	0.251397	0	none	.	.	PASS	Atlas-INDEL
KCNS2	3788	hgsc.bcm.edu	hg19	8	99441466	99441466	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	KCNS2	NM_020697	exon2	c.1258delC	p.Q420fs	.	.	271.0	114.0	273.0	0.0	.	93	.	0.420664	0	none	.	.	PASS	Atlas-INDEL
CD248	57124	hgsc.bcm.edu	hg19	11	66082566	66082566	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	CD248	NM_020404	exon1	c.1934delT	p.I645fs	.	.	148.0	64.0	143.0	0.0	.	69	.	0.432432	0	none	.	.	PASS	Atlas-INDEL
EIF5	1983	hgsc.bcm.edu	hg19	14	103807312	103807312	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	EIF5	NM_183004	exon11	c.1218delG	p.S406fs	.	.	54.0	16.0	118.0	0.0	.	40	.	0.296296	0	none	.	.	PASS	Atlas-INDEL
ZNF17	7565	hgsc.bcm.edu	hg19	19	57931956	57931959	+	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	TTCT	TTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	ZNF17	NM_006959	exon3	c.1095_1098del	p.365_366del	.	.	145.0	15.0	245.0	0.0	.	49	.	0.103448	0	none	.	.	PASS	Atlas-INDEL
NXF1	10482	hgsc.bcm.edu	hg19	11	62567920	62567921	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	NXF1	NM_006362	exon10	c.945_946insC	p.L315fs	.	.	87.0	23.0	95.0	0.0	.	67	.	0.264368	0	none	.	.	PASS	Atlas-INDEL
ATP7B	540	hgsc.bcm.edu	hg19	13	52548120	52548120	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	ATP7B	NM_000053	exon2	c.1237delC	p.L413fs	.	.	147.0	59.0	163.0	0.0	.	123	.	0.401361	0	none	.	.	PASS	Atlas-INDEL
LY9	4063	hgsc.bcm.edu	hg19	1	160771585	160771585	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	LY9	NM_001033667	exon3	c.459delA	p.P153fs	.	.	284.0	121.0	251.0	0.0	.	115	.	0.426056	0	none	.	.	PASS	Atlas-INDEL
NR2F2	7026	hgsc.bcm.edu	hg19	15	96875754	96875755	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	NR2F2	NM_021005	exon1	c.420_421insT	p.L140fs	.	.	87.0	23.0	72.0	0.0	.	35	.	0.264368	0	none	.	.	PASS	Atlas-INDEL
OR2J3	442186	hgsc.bcm.edu	hg19	6	29080474	29080475	+	Frame_Shift_Del	DEL	TT	TT	-	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	OR2J3	NM_001005216	exon1	c.806_807del	p.269_269del	.	.	89.0	79.0	216.0	0.0	.	53	.	0.88764	0	none	.	.	PASS	Atlas-INDEL
PCSK2	5126	hgsc.bcm.edu	hg19	20	17207956	17207957	+	In_Frame_Ins	INS	-	-	GGT	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	PCSK2	NM_002594	exon1	c.6_7insGGT	p.K2delinsKG	.	.	218.0	92.0	193.0	0.0	.	112	.	0.422018	0	none	.	.	PASS	Atlas-INDEL
POLDIP3	84271	hgsc.bcm.edu	hg19	22	42998037	42998037	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	POLDIP3	NM_032311	exon3	c.477delA	p.P159fs	.	.	201.0	80.0	243.0	0.0	.	58	.	0.39801	0	none	.	.	PASS	Atlas-INDEL
SPATA31D1	389763	hgsc.bcm.edu	hg19	9	84609703	84609703	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	.	.	NM_001001670	exon4	c.4317delG	p.G1439fs	.	.	85.0	29.0	87.0	0.0	.	.	.	0.341176	0	none	.	.	PASS	Atlas-INDEL
