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
UBIAD1	29914	hgsc.bcm.edu	hg19	1	11345827	11345827	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	UBIAD1,caecum,carcinoma,0,1	UBIAD1	NM_013319	exon2	c.T656C	p.I219T	ATGCCATCCCCCT	.	107.0	39.0	145.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
COL16A1	1307	hgsc.bcm.edu	hg19	1	32151315	32151315	+	Silent	SNP	A	A	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	COL16A1	NM_001856	exon29	c.T1941C	p.R647R	CACCACACGGACA	.	270.0	87.0	292.0	0.0	.	137	.	.	.	none	.	.	PASS	Atlas-SNP
SH3D21	79729	hgsc.bcm.edu	hg19	1	36773209	36773209	+	Splice_Site	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	SH3D21	NM_001162530	exon5	c.436+1G>A	.	CCCCAAGTGAGAC	.	126.0	37.0	144.0	0.0	.	73	.	.	.	none	.	.	PASS	Atlas-SNP
BSND	7809	hgsc.bcm.edu	hg19	1	55472846	55472846	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	BSND	NM_057176	exon3	c.G449T	p.G150V	AAGGTGGCCCTGG	.	121.0	40.0	162.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
PYGO2	90780	hgsc.bcm.edu	hg19	1	154931749	154931749	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	PYGO2,NS,carcinoma,0,1	PYGO2	NM_138300	exon3	c.C727T	p.P243S	GAAAGGGACTTGT	.	148.0	38.0	139.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
ARHGAP30	257106	hgsc.bcm.edu	hg19	1	161018086	161018086	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ARHGAP30	NM_001025598	exon12	c.T2725G	p.C909G	ATAGACAGCCGTC	.	47.0	17.0	65.0	0.0	.	105	.	.	.	none	.	.	PASS	Atlas-SNP
MTR	4548	hgsc.bcm.edu	hg19	1	236979823	236979823	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	MTR	NM_000254	exon8	c.G744A	p.V248V	CAGCGTGTCTCAT	.	71.0	19.0	85.0	0.0	.	127	.	.	.	none	.	.	PASS	Atlas-SNP
SMC6	79677	hgsc.bcm.edu	hg19	2	17865003	17865003	+	Nonsense_Mutation	SNP	A	A	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	SMC6	NM_001142286	exon24	c.T2706G	p.Y902X	ATCAAGATAGGTC	.	234.0	76.0	289.0	0.0	.	102	.	.	.	none	.	.	PASS	Atlas-SNP
NCOA1	8648	hgsc.bcm.edu	hg19	2	24930361	24930361	+	Silent	SNP	T	T	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	NCOA1	NM_147223	exon11	c.T2022G	p.G674G	AGGAGGTTCTTGT	.	108.0	35.0	145.0	0.0	.	210	.	.	.	none	.	.	PASS	Atlas-SNP
NAT8	9027	hgsc.bcm.edu	hg19	2	73868395	73868395	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	NAT8	NM_003960	exon2	c.A361G	p.M121V	CTACCATGCCCAC	.	105.0	38.0	101.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
ACTG2	72	hgsc.bcm.edu	hg19	2	74129580	74129580	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ACTG2	NM_001615	exon3	c.C220T	p.H74Y	ATTGAACACGGCA	.	76.0	45.0	92.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
RFX8	731220	hgsc.bcm.edu	hg19	2	102029382	102029382	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	RFX8	NM_001145664	exon8	c.T713C	p.M238T	CATTTCATCTCTG	.	62.0	23.0	62.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
FMNL2	114793	hgsc.bcm.edu	hg19	2	153415322	153415322	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	FMNL2	NM_052905	exon5	c.C428A	p.A143E	CATTTGCACAGTA	.	83.0	24.0	104.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179421832	179421832	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	TTN	NM_001267550	exon330	c.A88049G	p.N29350S	ACAGAGTTCTTTG	.	47.0	18.0	99.0	0.0	.	18412	.	.	.	none	.	.	PASS	Atlas-SNP
GLS	2744	hgsc.bcm.edu	hg19	2	191795233	191795233	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	GLS	NM_014905	exon13	c.T1496C	p.M499T	GTATGATGTGCTG	.	90.0	33.0	123.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
PTPRN	5798	hgsc.bcm.edu	hg19	2	220173977	220173977	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	PTPRN	NM_002846	exon1	c.C78T	p.S26S	GCGGCTGCTCAGC	.	95.0	42.0	94.0	0.0	.	138	.	.	.	none	.	.	PASS	Atlas-SNP
SERPINE2	5270	hgsc.bcm.edu	hg19	2	224856616	224856616	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	SERPINE2	NM_001136530	exon4	c.T625C	p.F209L	GTTGGAACCGTGA	.	105.0	32.0	117.0	0.0	.	103	.	.	.	none	.	.	PASS	Atlas-SNP
KIF1A	547	hgsc.bcm.edu	hg19	2	241696843	241696843	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	KIF1A	NM_001244008	exon27	c.G2751T	p.E917D	CTCATCCTCCTCC	.	81.0	14.0	70.0	0.0	.	152	.	.	.	none	.	.	PASS	Atlas-SNP
KLHL40	131377	hgsc.bcm.edu	hg19	3	42730387	42730387	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	.	NM_152393	exon4	c.A1448G	p.Y483C	GCGTCTATGACCC	.	129.0	25.0	135.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
FAM212A	389119	hgsc.bcm.edu	hg19	3	49841865	49841865	+	Silent	SNP	C	C	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	.	NM_203370	exon2	c.C309T	p.G103G	GTCAGGCAGCACA	.	79.0	17.0	61.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
TKT	7086	hgsc.bcm.edu	hg19	3	53264594	53264594	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	TKT	NM_001258028	exon9	c.G1010A	p.G337D	GCATGGCCCAGCT	.	118.0	67.0	98.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
GOLGB1	2804	hgsc.bcm.edu	hg19	3	121417110	121417110	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	GOLGB1	NM_001256486	exon13	c.C2260G	p.L754V	AGAGAAGCTGGTC	.	95.0	26.0	82.0	0.0	.	319	.	.	.	none	.	.	PASS	Atlas-SNP
STAG1	10274	hgsc.bcm.edu	hg19	3	136096520	136096520	+	Silent	SNP	A	A	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	STAG1	NM_005862	exon23	c.T2352C	p.N784N	TGGAGTATTAACA	.	63.0	27.0	55.0	0.0	.	135	.	.	.	none	.	.	PASS	Atlas-SNP
PARL	55486	hgsc.bcm.edu	hg19	3	183560125	183560125	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	PARL	NM_018622	exon6	c.C718G	p.L240V	GACCCAGAATGTT	.	80.0	20.0	72.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
ATOH1	474	hgsc.bcm.edu	hg19	4	94750807	94750807	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ATOH1	NM_005172	exon1	c.T730C	p.Y244H	GCCTCCTATGAAG	.	105.0	43.0	136.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
ANK2	287	hgsc.bcm.edu	hg19	4	114278777	114278777	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ANK2	NM_001148	exon38	c.T9003A	p.S3001R	GGAAAGTACCTTG	.	144.0	42.0	222.0	0.0	.	576	.	.	.	none	.	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	hg19	5	90446037	90446037	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	GPR98	NM_032119	exon88	c.A18623T	p.E6208V	TGGAGGAGGTGTC	.	85.0	25.0	126.0	0.0	.	605	.	.	.	none	.	.	PASS	Atlas-SNP
FSTL4	23105	hgsc.bcm.edu	hg19	5	132534854	132534854	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	FSTL4	NM_015082	exon16	c.A2462T	p.N821I	AGCGTGTTTTGTC	.	70.0	26.0	70.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
PITX1	5307	hgsc.bcm.edu	hg19	5	134367076	134367076	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	PITX1	NM_002653	exon2	c.A292G	p.S98G	GCTGGCTTGTGAA	.	91.0	25.0	127.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
DPYSL3	1809	hgsc.bcm.edu	hg19	5	146833138	146833138	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	DPYSL3	NM_001387	exon1	c.G13T	p.G5C	TCTTGCCTTGGTA	.	101.0	9.0	95.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
CLINT1	9685	hgsc.bcm.edu	hg19	5	157214655	157214655	+	Silent	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	CLINT1	NM_001195555	exon12	c.A1931G	p.X644X	ATCTCTTATTTGC	.	65.0	7.0	67.0	0.0	.	86	.	.	.	none	.	.	PASS	Atlas-SNP
PHIP	55023	hgsc.bcm.edu	hg19	6	79655791	79655791	+	Silent	SNP	C	C	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	PHIP	NM_017934	exon38	c.G4557A	p.E1519E	TGGTTGCTCAGTG	.	109.0	38.0	127.0	0.0	.	177	.	.	.	none	.	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	hg19	7	100679990	100679990	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	MUC17	NM_001040105	exon3	c.G5293A	p.E1765K	AGTTCTGAGGCTA	.	94.0	31.0	76.0	0.0	.	804	.	.	.	none	.	.	PASS	Atlas-SNP
CUX1	1523	hgsc.bcm.edu	hg19	7	101891788	101891788	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	CUX1	NM_001202543	exon24	c.G4017A	p.R1339R	CGGCCGGGCGGCG	.	36.0	18.0	41.0	0.0	.	253	.	.	.	none	.	.	PASS	Atlas-SNP
ATP6V1B2	526	hgsc.bcm.edu	hg19	8	20069635	20069635	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ATP6V1B2	NM_001693	exon8	c.T728A	p.F243Y	CCCGGTTCTTCAA	.	88.0	36.0	97.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
MYBL1	4603	hgsc.bcm.edu	hg19	8	67514696	67514696	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	MYBL1	NM_001080416	exon2	c.G83A	p.G28E	TTCAGTCCTTTTT	.	78.0	27.0	96.0	0.0	.	73	.	.	.	none	.	.	PASS	Atlas-SNP
NCOA2	10499	hgsc.bcm.edu	hg19	8	71056986	71056986	+	Silent	SNP	A	A	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	NCOA2	NM_006540	exon13	c.T2703C	p.P901P	TGGGAAAGGTCCA	.	155.0	45.0	181.0	0.0	.	147	.	.	.	none	.	.	PASS	Atlas-SNP
TP53INP1	94241	hgsc.bcm.edu	hg19	8	95952262	95952262	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	TP53INP1	NM_001135733	exon3	c.C299A	p.P100Q	GGGGGTGGGGTGA	.	133.0	51.0	153.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	hg19	8	101717893	101717893	+	Silent	SNP	A	A	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	PABPC1	NM_002568	exon12	c.T1611C	p.V537V	TACATGAACAGCA	.	252.0	86.0	244.0	0.0	.	76	.	.	.	none	.	.	PASS	Atlas-SNP
GNAQ	2776	hgsc.bcm.edu	hg19	9	80537112	80537112	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	GNAQ,NS,carcinoma,0,2	GNAQ	NM_002072	exon2	c.A286T	p.T96S	TGAGTGTGTCCAT	.	59.0	3.0	34.0	1.0	.	384	.	.	.	none	.	.	PASS	Atlas-SNP
OR13C2	392376	hgsc.bcm.edu	hg19	9	107367111	107367111	+	Missense_Mutation	SNP	C	C	A	rs75116810		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	OR13C2	NM_001004481	exon1	c.G798T	p.E266D	AAGTGTCTCTTTA	.	109.0	44.0	148.0	0.0	.	46	.	.	.	weak	.	.	PASS	Atlas-SNP
CDK5RAP2	55755	hgsc.bcm.edu	hg19	9	123287316	123287316	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	CDK5RAP2	NM_018249	exon11	c.C1040T	p.A347V	GCAAAGGCAGCAC	.	83.0	30.0	102.0	0.0	.	157	.	.	.	none	.	.	PASS	Atlas-SNP
STOX1	219736	hgsc.bcm.edu	hg19	10	70645490	70645490	+	Silent	SNP	C	C	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	STOX1	NM_152709	exon3	c.C1938A	p.A646A	AGGTGCCTCCTTT	.	64.0	46.0	78.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
FUT11	170384	hgsc.bcm.edu	hg19	10	75535419	75535419	+	Silent	SNP	C	C	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	FUT11	NM_173540	exon3	c.C1455A	p.I485I	TGAAATCTTCATG	.	80.0	51.0	116.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
PTEN	5728	hgsc.bcm.edu	hg19	10	89720837	89720837	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	PTEN	NM_000314	exon8	c.A988T	p.K330X	GCAAATAAAGACA	.	271.0	186.0	398.0	1.0	.	3652	.	.	.	none	.	.	PASS	Atlas-SNP
AMBRA1	55626	hgsc.bcm.edu	hg19	11	46563838	46563838	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	AMBRA1	NM_001267783	exon8	c.T1459C	p.F487L	TGTTGAAGGTCAG	.	40.0	15.0	54.0	0.0	.	201	.	.	.	none	.	.	PASS	Atlas-SNP
AMBRA1	55626	hgsc.bcm.edu	hg19	11	46569397	46569397	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	AMBRA1	NM_001267783	exon3	c.C164A	p.S55Y	AAGGTAGAGCGTG	.	53.0	16.0	65.0	0.0	.	201	.	.	.	none	.	.	PASS	Atlas-SNP
NXF1	10482	hgsc.bcm.edu	hg19	11	62561809	62561809	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	NXF1	NM_006362	exon19	c.C1681T	p.P561S	GGGTGGGCACCGG	.	127.0	6.0	123.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
PCF11	51585	hgsc.bcm.edu	hg19	11	82877708	82877708	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	PCF11	NM_015885	exon5	c.G1769A	p.S590N	GGCAAAGTTCCAA	.	277.0	83.0	291.0	0.0	.	220	.	.	.	none	.	.	PASS	Atlas-SNP
CREBZF	58487	hgsc.bcm.edu	hg19	11	85375427	85375427	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	CREBZF	NM_001039618	exon1	c.A493G	p.R165G	ACAGCCTTTGCAG	.	67.0	20.0	89.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
DDX10	1662	hgsc.bcm.edu	hg19	11	108562631	108562631	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	DDX10	NM_004398	exon8	c.G1004A	p.R335Q	TTTGCCGGCTACG	.	100.0	29.0	104.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
ARHGAP9	64333	hgsc.bcm.edu	hg19	12	57872506	57872506	+	Missense_Mutation	SNP	C	C	G	rs368912616	alternate_allele	TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ARHGAP9	NM_001080157	exon2	c.G351C	p.L117F	CTGAGACAACTCC	.	53.0	32.0	59.0	0.0	.	79	.	.	.	alt	.	.	PASS	Atlas-SNP
TRHDE	29953	hgsc.bcm.edu	hg19	12	72962372	72962372	+	Silent	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	TRHDE	NM_013381	exon10	c.T1932C	p.T644T	ATTAACTATTGTG	.	133.0	70.0	108.0	0.0	.	194	.	.	.	none	.	.	PASS	Atlas-SNP
CMA1	1215	hgsc.bcm.edu	hg19	14	24976587	24976587	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	CMA1	NM_001836	exon2	c.C184G	p.L62V	CCGTCAGCACAAA	.	94.0	24.0	146.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
CMA1	1215	hgsc.bcm.edu	hg19	14	24976588	24976588	+	Silent	SNP	C	C	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	CMA1	NM_001836	exon2	c.G183T	p.V61V	CGTCAGCACAAAG	.	98.0	26.0	148.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
ARG2	384	hgsc.bcm.edu	hg19	14	68113700	68113700	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ARG2	NM_001172	exon6	c.T680A	p.I227N	TTGGTATCCAGAA	.	59.0	25.0	60.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
SNURF	8926	hgsc.bcm.edu	hg19	15	25207341	25207341	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	SNURF	NM_005678	exon2	c.C95A	p.S32X	CTGCCTCACTGAG	.	94.0	36.0	131.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
C15orf62	643338	hgsc.bcm.edu	hg19	15	41062848	41062848	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	C15orf62	NM_001130448	exon1	c.T155C	p.I52T	AAGTCATCCGGGA	.	45.0	15.0	57.0	0.0	.	3	.	.	.	none	.	.	PASS	Atlas-SNP
GLCE	26035	hgsc.bcm.edu	hg19	15	69548297	69548297	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	GLCE	NM_015554	exon3	c.G152A	p.G51E	TGGATGGGTTTGA	.	155.0	49.0	178.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
CYP1A2	1544	hgsc.bcm.edu	hg19	15	75042653	75042653	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	CYP1A2	NM_000761	exon2	c.G574A	p.V192M	AATCAGGTGGTGG	.	51.0	24.0	68.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
GOLGA6C	653641	hgsc.bcm.edu	hg19	15	75562489	75562489	+	Silent	SNP	C	C	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	GOLGA6C	NM_001164404	exon18	c.C2031T	p.N677N	TGACAACCCCCCG	.	441.0	55.0	542.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
NR2F2	7026	hgsc.bcm.edu	hg19	15	96880778	96880778	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	NR2F2	NM_021005	exon3	c.C1172A	p.P391H	AAACCCCCATCGA	.	129.0	45.0	155.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
ZG16B	124220	hgsc.bcm.edu	hg19	16	2880794	2880794	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ZG16B	NM_145252	exon3	c.A260T	p.K87I	TGGTGAAAAGGTG	.	140.0	76.0	97.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
CES4A	283848	hgsc.bcm.edu	hg19	16	67038021	67038021	+	Missense_Mutation	SNP	T	T	A	rs3859072	byhapmap;alternate_allele	TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	CES4A	NM_173815	exon9	c.T974A	p.V325E	ATGGTGTGGTGAT	.	142.0	30.0	139.0	0.0	.	24	.	.	.	alt	T|1.000;|0.000	.	PASS	Atlas-SNP
OR1A1	8383	hgsc.bcm.edu	hg19	17	3119721	3119721	+	Silent	SNP	C	C	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	OR1A1,NS,carcinoma,0,1	OR1A1	NM_014565	exon1	c.C807T	p.D269D	AAAAGACGCAGTG	.	112.0	38.0	135.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
MYH1	4619	hgsc.bcm.edu	hg19	17	10404016	10404016	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	MYH1	NM_005963	exon28	c.G3792C	p.K1264N	CTTGGTCTTAATT	.	77.0	23.0	74.0	0.0	.	403	.	.	.	none	.	.	PASS	Atlas-SNP
GRB7	2886	hgsc.bcm.edu	hg19	17	37903002	37903002	+	Splice_Site	SNP	A	A	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	GRB7	NM_005310	exon15	c.1453-2A>C	.	TACCCCAGAGCGA	.	59.0	20.0	65.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
KRT28	162605	hgsc.bcm.edu	hg19	17	38955927	38955927	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	KRT28	NM_181535	exon1	c.C219T	p.G73G	AGCAAAGCCAATA	.	90.0	32.0	93.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
KRT33B	3884	hgsc.bcm.edu	hg19	17	39521769	39521769	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	KRT33B	NM_002279	exon4	c.C625A	p.L209I	CGTTGAGGCGGTC	.	136.0	6.0	159.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
KPNB1	3837	hgsc.bcm.edu	hg19	17	45735997	45735997	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	KPNB1	NM_002265	exon5	c.A607A	p.T203T	TCATTGGAGTTCA	.	49.0	20.0	62.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
HOXB13	10481	hgsc.bcm.edu	hg19	17	46805780	46805780	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	HOXB13	NM_006361	exon1	c.C176T	p.P59L	TTTGGCGGCTCCG	.	59.0	21.0	71.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
DLX3	1747	hgsc.bcm.edu	hg19	17	48072155	48072155	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	DLX3	NM_005220	exon1	c.A208G	p.N70D	TGAGATTGAATTG	.	73.0	28.0	109.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
USP32	84669	hgsc.bcm.edu	hg19	17	58262881	58262881	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	USP32	NM_032582	exon30	c.G3774T	p.K1258N	CTTACACTTGGAA	.	180.0	65.0	203.0	0.0	.	128	.	.	.	none	.	.	PASS	Atlas-SNP
MED13	9969	hgsc.bcm.edu	hg19	17	60039087	60039087	+	Silent	SNP	G	G	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	MED13,colon,carcinoma,0,1	MED13	NM_005121	exon22	c.C5118A	p.I1706I	GGGATAGATTTCT	.	82.0	19.0	109.0	0.0	.	181	.	.	.	none	.	.	PASS	Atlas-SNP
ACE	1636	hgsc.bcm.edu	hg19	17	61558530	61558530	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ACE	NM_000789	exon6	c.C926G	p.T309S	ATGTCACCAGTAC	.	128.0	42.0	148.0	0.0	.	187	.	.	.	none	.	.	PASS	Atlas-SNP
SOCS3	9021	hgsc.bcm.edu	hg19	17	76355088	76355088	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	SOCS3	NM_003955	exon2	c.A89G	p.E30G	TGGTACTCGCTCT	.	90.0	32.0	129.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
PIEZO2	63895	hgsc.bcm.edu	hg19	18	10680336	10680336	+	Silent	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.,2	.	NM_022068	exon48	c.A7473G	p.K2491K	GTCTTCTTTTTCA	.	64.0	28.0	73.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
PIEZO2	63895	hgsc.bcm.edu	hg19	18	10680342	10680342	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	.	NM_022068	exon48	c.T7467A	p.Y2489X	TTTTTCATAATTT	.	60.0	27.0	63.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
FUT5	2527	hgsc.bcm.edu	hg19	19	5867537	5867537	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	FUT5	NM_002034	exon2	c.G200A	p.S67N	GCCATGCTGTCCT	.	80.0	33.0	93.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
CRB3	92359	hgsc.bcm.edu	hg19	19	6466490	6466490	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	CRB3	NM_174881	exon4	c.T170C	p.I57T	AAGCCATCACTGC	.	34.0	7.0	39.0	0.0	.	8	.	.	.	none	.	.	PASS	Atlas-SNP
ZGLP1	100125288	hgsc.bcm.edu	hg19	19	10418909	10418909	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ZGLP1	NM_001103167	exon1	c.A449T	p.K150M	TGAAACTTCAGAG	.	30.0	12.0	29.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
GCDH	2639	hgsc.bcm.edu	hg19	19	13010540	13010540	+	Missense_Mutation	SNP	A	A	G	rs376334735		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	GCDH	NM_013976	exon12	c.A1270G	p.T424A	AAAAGAAGATGGA	.	136.0	36.0	174.0	0.0	.	76	.	.	.	weak	.	.	PASS	Atlas-SNP
CILP2	148113	hgsc.bcm.edu	hg19	19	19655554	19655554	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	CILP2,caecum,carcinoma,0,1	CILP2	NM_153221	exon8	c.C2200T	p.R734C	CCTGAGCGCCGCC	.	70.0	27.0	80.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF527	84503	hgsc.bcm.edu	hg19	19	37879856	37879856	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.,1	ZNF527	NM_032453	exon5	c.A905G	p.Y302C	AACCATATGCATG	.	85.0	5.0	63.0	2.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
PRKD2	25865	hgsc.bcm.edu	hg19	19	47181737	47181737	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	PRKD2	NM_016457	exon16	c.A2254C	p.N752H	CCTCGTTGAAAGG	.	100.0	34.0	109.0	0.0	.	94	.	.	.	none	.	.	PASS	Atlas-SNP
CRX	1406	hgsc.bcm.edu	hg19	19	48342911	48342911	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	CRX	NM_000554	exon4	c.C587T	p.A196V	CCTACGCCCCGGC	.	66.0	29.0	50.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
HRC	3270	hgsc.bcm.edu	hg19	19	49656860	49656860	+	Silent	SNP	C	C	T	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	HRC,NS,carcinoma,0,1	HRC	NM_002152	exon1	c.G1635A	p.E545E	TTCTTCCTCCTCC	.	25.0	3.0	38.0	1.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF71	58491	hgsc.bcm.edu	hg19	19	57133451	57133451	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ZNF71	NM_021216	exon3	c.G796A	p.G266R	CACACCGGGGAGA	.	186.0	66.0	180.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF419	79744	hgsc.bcm.edu	hg19	19	58004676	58004676	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ZNF419	NM_001098491	exon5	c.A754G	p.I252V	CACCAAATAGTTC	.	92.0	33.0	105.0	0.0	.	134	.	.	.	none	.	.	PASS	Atlas-SNP
STAU1	6780	hgsc.bcm.edu	hg19	20	47732330	47732330	+	Silent	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	STAU1	NM_017453	exon13	c.A1707G	p.G569G	CATTGGTCCGTTT	.	51.0	15.0	54.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
BRWD1	54014	hgsc.bcm.edu	hg19	21	40670471	40670471	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	BRWD1	NM_001007246	exon5	c.T236G	p.L79W	ATTTGCAAAAGAT	.	323.0	91.0	301.0	0.0	.	325	.	.	.	none	.	.	PASS	Atlas-SNP
MN1	4330	hgsc.bcm.edu	hg19	22	28193970	28193970	+	Silent	SNP	T	T	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	MN1	NM_002430	exon1	c.A2562G	p.P854P	GCCCTCTGGCGGG	.	28.0	12.0	38.0	0.0	.	122	.	.	.	none	.	.	PASS	Atlas-SNP
ATF4	468	hgsc.bcm.edu	hg19	22	39918544	39918544	+	Silent	SNP	C	C	A	rs189922789	bycluster;by1000genomes;alternate_allele	TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ATF4	NM_001675	exon2	c.C993A	p.I331I	GGAGATCCAGTAC	.	122.0	64.0	210.0	0.0	.	27	.	.	.	alt	C|1.000;G|0.000	.	PASS	Atlas-SNP
RGAG1	57529	hgsc.bcm.edu	hg19	X	109694814	109694814	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	RGAG1	NM_020769	exon3	c.G969A	p.P323P	CACACCGCTACTG	.	69.0	5.0	148.0	0.0	.	168	.	.	.	none	.	.	PASS	Atlas-SNP
IL32	9235	hgsc.bcm.edu	hg19	16	3119166	3119166	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	IL32	NM_004221	exon7	c.376delG	p.V126fs	.	.	317.0	117.0	267.0	0.0	.	32	.	0.369085	0	none	.	.	PASS	Atlas-Indel,Pindel
HOXD4	3233	hgsc.bcm.edu	hg19	2	177016768	177016783	+	Frame_Shift_Del	DEL	GGATGAAGAAGGTGCA	GGATGAAGAAGGTGCA	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	GGATGAAGAAGGTGCA	GGATGAAGAAGGTGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	HOXD4	NM_014621	exon1	c.406_421del	p.136_141del	.	.	66.0	14.0	127.0	0.0	.	32	.	0.212121	0	none	.	.	PASS	Atlas-Indel,Pindel
TUBGCP3	10426	hgsc.bcm.edu	hg19	13	113212595	113212596	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	TUBGCP3,NS,carcinoma,0,1	TUBGCP3	NM_006322	exon5	c.463_464insC	p.G155fs	.	.	79.0	30.0	97.0	0.0	.	74	.	0.379747	0	none	.	.	PASS	Atlas-Indel,Pindel
RNF185	91445	hgsc.bcm.edu	hg19	22	31583132	31583132	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	RNF185	NM_152267	exon2	c.51delA	p.A17fs	.	.	102.0	47.0	184.0	0.0	.	14	.	0.460784	0	none	.	.	PASS	Atlas-Indel,Pindel
SOX12	6666	hgsc.bcm.edu	hg19	20	306671	306679	+	In_Frame_Del	DEL	ACCCCGAGC	ACCCCGAGC	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	ACCCCGAGC	ACCCCGAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	SOX12	NM_006943	exon1	c.102_110del	p.34_37del	.	.	71.0	15.0	95.0	0.0	.	8	.	0.211268	0	none	.	.	PASS	Atlas-Indel,Pindel
EFCAB13	124989	hgsc.bcm.edu	hg19	17	45452288	45452311	+	In_Frame_Del	DEL	AAAAACAGGTTTCGTCTACGGAAA	AAAAACAGGTTTCGTCTACGGAAA	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	AAAAACAGGTTTCGTCTACGGAAA	AAAAACAGGTTTCGTCTACGGAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	.	NM_152347	exon12	c.1327_1350del	p.443_450del	.	.	168.0	23.0	248.0	0.0	.	.	.	0.136905	0	none	.	.	PASS	Atlas-Indel,Pindel
KLK3	354	hgsc.bcm.edu	hg19	19	51361852	51361853	+	Splice_Site	INS	-	-	TTT	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	KLK3	NM_001030047	exon4	c.630+1->TTT	.	.	.	59.0	18.0	77.0	0.0	.	76	.	0.305085	0	none	.	.	PASS	Atlas-Indel,Pindel
MUC16	94025	hgsc.bcm.edu	hg19	19	9074427	9074427	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	MUC16	NM_024690	exon3	c.13020delC	p.V4340fs	.	.	78.0	36.0	78.0	0.0	.	4315	.	0.461538	0	none	.	.	PASS	Atlas-Indel,Pindel
MRC2	9902	hgsc.bcm.edu	hg19	17	60743875	60743875	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	MRC2	NM_006039	exon4	c.753delT	p.F251fs	.	.	47.0	15.0	78.0	0.0	.	126	.	0.319149	0	none	.	.	PASS	Atlas-INDEL
GDF15	9518	hgsc.bcm.edu	hg19	19	18497000	18497001	+	Frame_Shift_Del	DEL	AT	AT	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	GDF15	NM_004864	wholegene	.	.	.	.	48.0	11.0	66.0	0.0	.	31	.	0.229167	0	none	.	.	PASS	Atlas-INDEL
ANKRD50	57182	hgsc.bcm.edu	hg19	4	125590179	125590187	+	In_Frame_Del	DEL	TCAGAACCT	TCAGAACCT	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	TCAGAACCT	TCAGAACCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	ANKRD50	NM_020337	exon4	c.4246_4254del	p.1416_1418del	.	.	66.0	15.0	78.0	0.0	.	136	.	0.227273	0	none	.	.	PASS	Atlas-Indel,Pindel
SETD1A	9739	hgsc.bcm.edu	hg19	16	30976438	30976439	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	SETD1A	NM_014712	exon7	c.1375_1376insC	p.S459fs	.	.	66.0	14.0	51.0	0.0	.	143	.	0.212121	0	none	.	.	PASS	Atlas-Indel,Pindel
HTR1B	3351	hgsc.bcm.edu	hg19	6	78172132	78172132	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	HTR1B	NM_000863	exon1	c.990delC	p.F330fs	.	.	75.0	32.0	93.0	0.0	.	55	.	0.426667	0	none	.	.	PASS	Atlas-Indel,Pindel
GOT2	2806	hgsc.bcm.edu	hg19	16	58742096	58742096	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	GOT2	NM_002080	exon10	c.1273delA	p.I425fs	.	.	53.0	28.0	47.0	0.0	.	42	.	0.528302	0	none	.	.	PASS	Atlas-Indel,Pindel
GOLGA6B	55889	hgsc.bcm.edu	hg19	15	72947139	72947139	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	GOLGA6B	NM_018652	exon1	c.60delT	p.N20fs	.	.	621.0	33.0	703.0	0.0	.	30	.	0.053	.	none	.	.	PASS	Pindel
GDF15	9518	hgsc.bcm.edu	hg19	19	18496998	18497015	+	Frame_Shift_Del	DEL	AACCTGCACAGCCATGCC	AACCTGCACAGCCATGCC	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	AACCTGCACAGCCATGCC	AACCTGCACAGCCATGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	GDF15	NM_004864	wholegene	.	.	.	.	48.0	11.0	62.0	0.0	.	31	.	0.229	.	none	.	.	PASS	Pindel
PTEN	5728	hgsc.bcm.edu	hg19	10	89720833	89720833	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	.	PTEN	NM_000314	exon8	c.983delC	p.A328fs	.	.	270.0	97.0	416.0	0.0	.	3652	.	0.359	.	none	.	.	PASS	Pindel
