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
DDI2	84301	hgsc.bcm.edu	hg19	1	15957021	15957021	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	DDI2	NM_032341	exon3	c.C470T	p.P157L	GCAATCCACCCCT	.	92.0	33.0	138.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
GALE	2582	hgsc.bcm.edu	hg19	1	24124297	24124297	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	GALE	NM_000403	exon6	c.C416A	p.P139H	TACTGGGGGTTCC	.	57.0	29.0	93.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
NUDC	10726	hgsc.bcm.edu	hg19	1	27250638	27250638	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	NUDC	NM_006600	exon2	c.A140G	p.E47G	GAGGAGAAGAAGG	.	74.0	31.0	71.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
PARS2	25973	hgsc.bcm.edu	hg19	1	55224237	55224237	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	PARS2	NM_152268	exon2	c.C598A	p.R200S	GGCCACGGAGAAG	.	98.0	4.0	127.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
DOCK7	85440	hgsc.bcm.edu	hg19	1	63119666	63119666	+	Silent	SNP	T	T	C	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	DOCK7	NM_001271999	exon3	c.A309G	p.V103V	TTCAGGTACAGCT	.	56.0	4.0	69.0	0.0	.	184	.	.	.	none	.	.	PASS	Atlas-SNP
CTH	1491	hgsc.bcm.edu	hg19	1	70877247	70877247	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	CTH	NM_153742	exon1	c.G149C	p.G50A	AGCAAGGGGCGCC	.	83.0	29.0	98.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
DNTTIP2	30836	hgsc.bcm.edu	hg19	1	94337674	94337674	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	DNTTIP2	NM_014597	exon5	c.G2021T	p.R674I	TAAAATCTTTTCG	.	302.0	135.0	338.0	1.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
SETDB1	9869	hgsc.bcm.edu	hg19	1	150936790	150936790	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	SETDB1	NM_001145415	exon22	c.G3826A	p.E1276K	GGCAAGGAGCTAC	.	63.0	16.0	88.0	0.0	.	204	.	.	.	none	.	.	PASS	Atlas-SNP
SLC27A3	11000	hgsc.bcm.edu	hg19	1	153752431	153752431	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	SLC27A3	NM_024330	exon10	c.A2146T	p.T716S	CCCCTCACAACTG	.	40.0	18.0	56.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
SLC4A5	57835	hgsc.bcm.edu	hg19	2	74458396	74458396	+	Silent	SNP	C	C	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	SLC4A5	NM_021196	exon20	c.G2814T	p.T938T	GATTCCCGTCAGG	.	103.0	5.0	131.0	0.0	.	215	.	.	.	none	.	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	hg19	2	109383218	109383218	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	RANBP2	NM_006267	exon20	c.A6223C	p.M2075L	ATGCTGATGCGAA	.	566.0	257.0	697.0	0.0	.	488	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	hg19	2	185802128	185802128	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	ZNF804A	NM_194250	exon4	c.G2005C	p.D669H	TTAAGTGACAATG	.	112.0	44.0	126.0	0.0	.	322	.	.	.	none	.	.	PASS	Atlas-SNP
ANKRD44	91526	hgsc.bcm.edu	hg19	2	198001337	198001337	+	Silent	SNP	C	C	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	ANKRD44	NM_153697	exon4	c.G240T	p.R80R	AACAGCCCGGTGC	.	67.0	30.0	86.0	0.0	.	281	.	.	.	none	.	.	PASS	Atlas-SNP
DCP1A	55802	hgsc.bcm.edu	hg19	3	53376261	53376261	+	Silent	SNP	G	G	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	DCP1A	NM_018403	exon3	c.C214A	p.R72R	TTAGTCGATTCAC	.	17.0	11.0	22.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
MORC1	27136	hgsc.bcm.edu	hg19	3	108703606	108703606	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	MORC1	NM_014429	exon23	c.G2281A	p.V761I	CTAGAACATCATT	.	33.0	12.0	47.0	0.0	.	211	.	.	.	none	.	.	PASS	Atlas-SNP
PLOD2	5352	hgsc.bcm.edu	hg19	3	145803003	145803003	+	Silent	SNP	A	A	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	PLOD2	NM_182943	exon11	c.T1185A	p.V395V	CAAAACAACATCT	.	54.0	21.0	83.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
TBL1XR1	79718	hgsc.bcm.edu	hg19	3	176767825	176767825	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	TBL1XR1	NM_024665	exon7	c.A662G	p.D221G	GGAACATCTTGCC	.	50.0	27.0	54.0	0.0	.	87	.	.	.	none	.	.	PASS	Atlas-SNP
MAP3K13	9175	hgsc.bcm.edu	hg19	3	185191375	185191375	+	Silent	SNP	G	G	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	MAP3K13	NM_004721	exon11	c.G2256A	p.G752G	AGTGGGGAGGAGC	.	185.0	10.0	219.0	0.0	.	209	.	.	.	none	.	.	PASS	Atlas-SNP
AHSG	197	hgsc.bcm.edu	hg19	3	186335047	186335047	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	AHSG	NM_001622	exon4	c.G481A	p.V161M	AGGGTGGTGCACG	.	120.0	63.0	164.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
NELFA	7469	hgsc.bcm.edu	hg19	4	1985129	1985129	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	.	NM_005663	exon11	c.G1537A	p.V513M	TGTCCACCAGCAT	.	180.0	81.0	255.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
COMMD8	54951	hgsc.bcm.edu	hg19	4	47462163	47462163	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	COMMD8	NM_017845	exon2	c.G220A	p.E74K	TTACCTCTTCATC	.	76.0	36.0	132.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
AASDH	132949	hgsc.bcm.edu	hg19	4	57204741	57204741	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	AASDH	NM_181806	exon15	c.T3124C	p.S1042P	CAGTAGATGCTGC	.	66.0	29.0	95.0	0.0	.	101	.	.	.	none	.	.	PASS	Atlas-SNP
TRMT10A	93587	hgsc.bcm.edu	hg19	4	100470297	100470297	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	.	NM_001134666	exon8	c.A968G	p.K323R	TCCTGCTTTTCTT	.	154.0	83.0	171.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
TET2	54790	hgsc.bcm.edu	hg19	4	106156045	106156045	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	TET2	NM_001127208	exon3	c.T946A	p.F316I	TGTTCCTTTCAGA	.	60.0	36.0	92.0	0.0	.	1762	.	.	.	none	.	.	PASS	Atlas-SNP
SLC12A7	10723	hgsc.bcm.edu	hg19	5	1064225	1064225	+	Silent	SNP	C	C	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	SLC12A7	NM_006598	exon19	c.G2580C	p.L860L	GGGCAGCAGCATG	.	40.0	19.0	32.0	0.0	.	97	.	.	.	none	.	.	PASS	Atlas-SNP
TNPO1	3842	hgsc.bcm.edu	hg19	5	72192301	72192301	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	TNPO1	NM_002270	exon19	c.A2160G	p.I720M	GCCAATATTGGGA	.	60.0	22.0	99.0	0.0	.	90	.	.	.	none	.	.	PASS	Atlas-SNP
TRAF3IP2	10758	hgsc.bcm.edu	hg19	6	111912700	111912700	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	TRAF3IP2	NM_147686	exon2	c.C590A	p.T197K	TATCCCGTGTCTA	.	107.0	12.0	145.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
LPL	4023	hgsc.bcm.edu	hg19	8	19816813	19816813	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	LPL	NM_000237	exon7	c.G1061C	p.S354T	CTGAGAGTGAAAC	.	61.0	26.0	62.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
EMC2	9694	hgsc.bcm.edu	hg19	8	109462083	109462083	+	Silent	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	.	NM_014673	exon2	c.A72G	p.E24E	GAGAGAAGAAAAC	.	82.0	36.0	119.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
AQP7	364	hgsc.bcm.edu	hg19	9	33385805	33385805	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	AQP7	NM_001170	exon7	c.C585A	p.N195K	TGCTGGGTTGTTC	.	130.0	39.0	198.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	hg19	11	1075662	1075662	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	MUC2	NM_002457	exon2	c.C88G	p.R30G	AGAACCCGAAACC	.	38.0	11.0	47.0	0.0	.	614	.	.	.	none	.	.	PASS	Atlas-SNP
SLC5A12	159963	hgsc.bcm.edu	hg19	11	26725402	26725402	+	Silent	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	SLC5A12	NM_178498	exon5	c.T618C	p.H206H	CCCAGCATGAGTT	.	225.0	91.0	287.0	0.0	.	134	.	.	.	none	.	.	PASS	Atlas-SNP
TCP11L1	55346	hgsc.bcm.edu	hg19	11	33083137	33083137	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	TCP11L1	NM_001145541	exon7	c.G837C	p.K279N	TCAGAAGTATAAA	.	55.0	22.0	59.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
NDUFS3	4722	hgsc.bcm.edu	hg19	11	47605943	47605943	+	Silent	SNP	G	G	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	NDUFS3	NM_004551	exon7	c.G705A	p.L235L	TGACCTGAACAGC	.	205.0	85.0	305.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
ATP5L	10632	hgsc.bcm.edu	hg19	11	118272388	118272388	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	ATP5L	NM_006476	exon1	c.A8G	p.Q3R	TGGCCCAATTTGT	.	49.0	20.0	60.0	0.0	.	11	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM45B	120224	hgsc.bcm.edu	hg19	11	129724698	129724698	+	Silent	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	TMEM45B	NM_138788	exon3	c.A372G	p.A124A	TGTGGCAGTATTC	.	103.0	39.0	151.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
IFFO1	25900	hgsc.bcm.edu	hg19	12	6649694	6649694	+	Silent	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	IFFO1	NM_001193457	exon10	c.T1671C	p.A557A	GTCCTCAGCCTCG	.	89.0	83.0	137.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
TAS2R50	259296	hgsc.bcm.edu	hg19	12	11139402	11139402	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	TAS2R50,NS,carcinoma,0,1	TAS2R50	NM_176890	exon1	c.G58T	p.G20X	AGTTTCCGAGAAC	.	68.0	4.0	75.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
ARID2	196528	hgsc.bcm.edu	hg19	12	46285793	46285793	+	Splice_Site	SNP	G	G	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	ARID2	NM_152641	exon18	c.5062-1G>A	.	CAAAAAGGATAAG	.	59.0	54.0	64.0	0.0	.	311	.	.	.	none	.	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	hg19	12	53685605	53685605	+	Silent	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	ESPL1	NM_012291	exon26	c.A5652G	p.T1884T	CCTGACAGTACCA	.	140.0	126.0	189.0	0.0	.	158	.	.	.	none	.	.	PASS	Atlas-SNP
RAB2B	84932	hgsc.bcm.edu	hg19	14	21931921	21931921	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	RAB2B	NM_032846	exon6	c.T368C	p.L123P	GACTCTAGGTCAC	.	85.0	37.0	113.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
PCK2	5106	hgsc.bcm.edu	hg19	14	24568928	24568928	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	PCK2_ENST00000396973,NS,carcinoma,0,2	PCK2	NM_001018073	exon6	c.A1014C	p.E338D	CAGTGAAGGTGAG	.	118.0	29.0	183.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
NID2	22795	hgsc.bcm.edu	hg19	14	52494036	52494036	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	NID2	NM_007361	exon12	c.G2557A	p.E853K	CATCCTCACAGGG	.	37.0	15.0	55.0	0.0	.	201	.	.	.	none	.	.	PASS	Atlas-SNP
PPM1A	5494	hgsc.bcm.edu	hg19	14	60750192	60750192	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	PPM1A	NM_177952	exon2	c.A990T	p.R330S	ATCCAGACTTGAA	.	232.0	94.0	329.0	1.0	.	72	.	.	.	none	.	.	PASS	Atlas-SNP
UNC79	57578	hgsc.bcm.edu	hg19	14	94079328	94079328	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	UNC79,colon,carcinoma,0,2	UNC79	NM_020818	exon27	c.G3409T	p.V1137F	CTGTACGTCTTAC	.	93.0	4.0	79.0	0.0	.	366	.	.	.	none	.	.	PASS	Atlas-SNP
UBR1	197131	hgsc.bcm.edu	hg19	15	43299483	43299483	+	Splice_Site	SNP	C	C	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	UBR1	NM_174916	exon31	c.3210-1G>T	.	GGGGTGCTACCAA	.	19.0	8.0	41.0	0.0	.	124	.	.	.	none	.	.	PASS	Atlas-SNP
PARP6	56965	hgsc.bcm.edu	hg19	15	72556908	72556908	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	PARP6	NM_020214	exon7	c.T383C	p.L128P	AACTGAAGACCCA	.	112.0	5.0	121.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
IDH2	3418	hgsc.bcm.edu	hg19	15	90634783	90634783	+	Splice_Site	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	IDH2	NM_002168	exon3	c.207+2T>C	.	GGCACTACCTTCT	.	95.0	12.0	127.0	0.0	.	1372	.	.	.	none	.	.	PASS	Atlas-SNP
RAB40C	57799	hgsc.bcm.edu	hg19	16	677608	677608	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	RAB40C	NM_021168	exon6	c.T832C	p.C278R	AGTAACTGCAAGA	.	104.0	59.0	111.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
HS3ST2	9956	hgsc.bcm.edu	hg19	16	22926750	22926750	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	HS3ST2,brain,glioma,0,1	HS3ST2	NM_006043	exon2	c.G971A	p.R324Q	TGCCTCGATGCTT	.	328.0	17.0	264.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	hg19	16	48249161	48249161	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	ABCC11	NM_033151	exon7	c.T1046C	p.I349T	AGCTTAATGCAAG	.	139.0	42.0	136.0	0.0	.	177	.	.	.	none	.	.	PASS	Atlas-SNP
INPP5K	51763	hgsc.bcm.edu	hg19	17	1400005	1400005	+	Silent	SNP	G	G	C	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	INPP5K	NM_016532	exon9	c.C1056G	p.T352T	GTCCGAGGTTGAA	.	124.0	68.0	135.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
LHX1	3975	hgsc.bcm.edu	hg19	17	35297717	35297717	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	LHX1	NM_005568	exon2	c.G301T	p.G101C	TCCACTGGCGAGG	.	68.0	16.0	60.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
ACLY	47	hgsc.bcm.edu	hg19	17	40048661	40048661	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	ACLY	NM_001096	exon16	c.G1641T	p.E547D	CAGGATCTCTTTG	.	180.0	68.0	112.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
HDAC5	10014	hgsc.bcm.edu	hg19	17	42158172	42158172	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	HDAC5	NM_001015053	exon21	c.G2689T	p.D897Y	CGTTGTCATAGCG	.	119.0	44.0	98.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
AFG3L2	10939	hgsc.bcm.edu	hg19	18	12358734	12358734	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	AFG3L2	NM_006796	exon8	c.A961G	p.M321V	ATTCCATGATCTC	.	67.0	27.0	74.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
APC2	10297	hgsc.bcm.edu	hg19	19	1468067	1468067	+	Silent	SNP	C	C	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	APC2	NM_005883	exon15	c.C4767T	p.P1589P	CGAGCCCGAGCCC	.	20.0	9.0	20.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
SUGP1	57794	hgsc.bcm.edu	hg19	19	19420931	19420931	+	Silent	SNP	C	C	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	SUGP1	NM_172231	exon3	c.G285A	p.K95K	CTGCAACTTCAGA	.	84.0	36.0	103.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
IGFLR1	79713	hgsc.bcm.edu	hg19	19	36232080	36232080	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	IGFLR1	NM_024660	exon2	c.T2C	p.M1T	GGCCCCATCTGGG	.	16.0	6.0	41.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
ADCK4	79934	hgsc.bcm.edu	hg19	19	41220537	41220537	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	ADCK4	NM_001142555	exon2	c.A1G	p.M1V	GCCACATTGCCTG	.	52.0	20.0	65.0	0.0	.	92	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF347	84671	hgsc.bcm.edu	hg19	19	53643807	53643807	+	Silent	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	ZNF347	NM_001172675	exon5	c.T2277C	p.I759I	AGTATGAATTCCC	.	265.0	24.0	226.0	0.0	.	87	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF347	84671	hgsc.bcm.edu	hg19	19	53643811	53643811	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	ZNF347	NM_001172675	exon5	c.G2273C	p.G758A	TGAATTCCCCGAT	.	267.0	28.0	226.0	0.0	.	87	.	.	.	none	.	.	PASS	Atlas-SNP
RBBP9	10741	hgsc.bcm.edu	hg19	20	18471080	18471080	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	RBBP9	NM_006606	exon4	c.C293T	p.A98V	GTGTACGCAGACA	.	111.0	39.0	135.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
ENTPD6	955	hgsc.bcm.edu	hg19	20	25201971	25201971	+	Splice_Site	SNP	T	T	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	ENTPD6	NM_001247	exon11	c.1045+2T>A	.	AGCAGGTACGGGG	.	41.0	21.0	52.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
SGK2	10110	hgsc.bcm.edu	hg19	20	42208647	42208647	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	SGK2	NM_016276	exon11	c.A1065G	p.I355M	CCCCATAAACTGG	.	107.0	51.0	131.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
LIMK2	3985	hgsc.bcm.edu	hg19	22	31655910	31655910	+	Missense_Mutation	SNP	T	T	C	rs377628882		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	LIMK2	NM_005569	exon5	c.T398C	p.M133T	CACCCATGTTTGA	.	38.0	32.0	95.0	0.0	.	101	.	.	.	weak	.	.	PASS	Atlas-SNP
BAIAP2L2	80115	hgsc.bcm.edu	hg19	22	38482355	38482355	+	Missense_Mutation	SNP	C	C	G	rs113792005	bycluster	TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.,1	BAIAP2L2	NM_025045	exon12	c.G1361C	p.R454P	GGGGTGCGGGAGC	.	2.0	2.0	0.0	0.0	.	39	.	.	.	weak	.	.	PASS	Atlas-SNP
ATL3	25923	hgsc.bcm.edu	hg19	11	63403801	63403802	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	ATL3	NM_015459	exon9	c.856_857insT	p.A286fs	.	.	110.0	44.0	135.0	0.0	.	31	.	0.4	0	none	.	.	PASS	Atlas-INDEL
RP1	6101	hgsc.bcm.edu	hg19	8	55540098	55540099	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	RP1	NM_006269	exon4	c.3656_3657insT	p.S1219fs	.	.	123.0	58.0	139.0	0.0	.	429	.	0.471545	0	none	.	.	PASS	Atlas-INDEL
CEP135	9662	hgsc.bcm.edu	hg19	4	56847415	56847423	+	In_Frame_Del	DEL	TAAGAAAGG	TAAGAAAGG	-	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	TAAGAAAGG	TAAGAAAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	CEP135	NM_025009	exon13	c.1648_1656del	p.550_552del	.	.	56.0	19.0	103.0	0.0	.	115	.	0.339286	0	none	.	.	PASS	Atlas-INDEL
PLA2G6	8398	hgsc.bcm.edu	hg19	22	38536176	38536176	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	PLA2G6	NM_001004426	exon5	c.611delT	p.L204fs	.	.	37.0	30.0	83.0	0.0	.	54	.	0.810811	0	none	.	.	PASS	Atlas-INDEL
SPPL2C	162540	hgsc.bcm.edu	hg19	17	43922606	43922611	+	In_Frame_Del	DEL	GGCCAA	GGCCAA	-	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	GGCCAA	GGCCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	.	NM_175882	exon1	c.333_338del	p.111_113del	.	.	95.0	10.0	105.0	0.0	.	.	.	0.105263	0	none	.	.	PASS	Atlas-INDEL
COMMD8	54951	hgsc.bcm.edu	hg19	4	47462160	47462160	+	Splice_Site	DEL	C	C	-	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	COMMD8	NM_017845	exon3	c.222+2G>-	.	.	.	72.0	33.0	129.0	0.0	.	15	.	0.458333	0	none	.	.	PASS	Atlas-INDEL
C10orf71	118461	hgsc.bcm.edu	hg19	10	50530974	50530974	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	C10orf71	NM_001135196	exon3	c.383delT	p.V128fs	.	.	122.0	44.0	165.0	0.0	.	179	.	0.360656	0	none	.	.	PASS	Atlas-INDEL
HNRNPC	3183	hgsc.bcm.edu	hg19	14	21679712	21679713	+	Frame_Shift_Del	DEL	AT	AT	-	novel		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	.	HNRNPC	NM_031314	exon8	c.690_691del	p.230_231del	.	.	31.0	16.0	22.0	0.0	.	31	.	0.516129	0	none	.	.	PASS	Atlas-INDEL
