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
SPOCD1	90853	hgsc.bcm.edu	hg19	1	32265460	32265460	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SPOCD1	NM_144569	exon6	c.G1733A	p.G578D	ATTGGGCCACTCT	.	101.0	44.0	108.0	0.0	.	109	.	.	.	none	.	.	PASS	Atlas-SNP
SFPQ	6421	hgsc.bcm.edu	hg19	1	35656516	35656516	+	Silent	SNP	A	A	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SFPQ	NM_005066	exon3	c.T1098C	p.F366F	TGTGGCAAAGCGA	.	192.0	93.0	183.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC8D	55144	hgsc.bcm.edu	hg19	1	90400895	90400895	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	LRRC8D	NM_018103	exon3	c.T2268G	p.H756Q	GCAGCATTTGCAT	.	212.0	94.0	184.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
INSRR	3645	hgsc.bcm.edu	hg19	1	156811515	156811515	+	Missense_Mutation	SNP	G	G	A	rs201172210	bycluster	TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	INSRR_ENST00000368195,NS,carcinoma,+2,2	INSRR	NM_014215	exon20	c.C3469T	p.R1157C	TCCAGCGCACGGG	.	174.0	43.0	182.0	0.0	.	309	.	.	.	weak	.	.	PASS	Atlas-SNP
CFHR4	10877	hgsc.bcm.edu	hg19	1	196887456	196887456	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	CFHR4	NM_001201550	exon10	c.G1657A	p.G553R	AAATTGGGATATA	.	450.0	189.0	456.0	1.0	.	141	.	.	.	none	.	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	hg19	2	73613036	73613036	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	ALMS1	NM_015120	exon1	c.G40C	p.E14Q	CTGGAGGAGGAGG	.	241.0	19.0	149.0	0.0	.	384	.	.	.	none	.	.	PASS	Atlas-SNP
SEMA4C	54910	hgsc.bcm.edu	hg19	2	97532110	97532110	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SEMA4C	NM_017789	exon3	c.G168A	p.L56L	CAGCGTCAGTGTC	.	170.0	71.0	230.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179474203	179474203	+	Silent	SNP	A	A	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	TTN	NM_001267550	exon273	c.T51834A	p.T17278T	TGTAATAGTTGGG	.	79.0	40.0	62.0	0.0	.	18412	.	.	.	none	.	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179611761	179611761	+	Silent	SNP	T	T	A	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	TTN	NM_133379	exon46	c.A15366T	p.G5122G	TGGTCCTCCAGTA	.	122.0	48.0	139.0	0.0	.	18412	.	.	.	none	.	.	PASS	Atlas-SNP
CREB1	1385	hgsc.bcm.edu	hg19	2	208420472	208420472	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	CREB1	NM_004379	exon2	c.A113G	p.Q38R	TAGCCCAGGTATA	.	125.0	15.0	126.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
ANKZF1	55139	hgsc.bcm.edu	hg19	2	220099756	220099756	+	Silent	SNP	A	A	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	ANKZF1	NM_001042410	exon10	c.A1413G	p.S471S	ACAGTCATCCCAG	.	96.0	51.0	100.0	0.0	.	45	.	.	.	none	.	.	PASS	Atlas-SNP
SPEG	10290	hgsc.bcm.edu	hg19	2	220336993	220336993	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SPEG	NM_005876	exon15	c.G3880A	p.V1294M	GTGGCTGTGACGG	.	116.0	53.0	89.0	0.0	.	272	.	.	.	none	.	.	PASS	Atlas-SNP
SCG2	7857	hgsc.bcm.edu	hg19	2	224463553	224463553	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SCG2	NM_003469	exon2	c.G448A	p.D150N	CATAATCATCACT	.	75.0	26.0	58.0	0.0	.	99	.	.	.	none	.	.	PASS	Atlas-SNP
C3orf20	84077	hgsc.bcm.edu	hg19	3	14803122	14803122	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	C3orf20	NM_032137	exon15	c.G2495A	p.S832N	AATTCAGGTAAAA	.	60.0	25.0	83.0	0.0	.	109	.	.	.	none	.	.	PASS	Atlas-SNP
C3orf20	84077	hgsc.bcm.edu	hg19	3	14803123	14803123	+	Splice_Site	SNP	G	G	C	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	C3orf20	NM_032137	exon15	c.2495+1G>C	.	ATTCAGGTAAAAC	.	58.0	25.0	83.0	0.0	.	109	.	.	.	none	.	.	PASS	Atlas-SNP
KBTBD8	84541	hgsc.bcm.edu	hg19	3	67053891	67053891	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	KBTBD8	NM_032505	exon3	c.T500C	p.L167P	AGGAACTCGGAGA	.	133.0	64.0	162.0	0.0	.	101	.	.	.	none	.	.	PASS	Atlas-SNP
PIK3CA	5290	hgsc.bcm.edu	hg19	3	178943786	178943786	+	Missense_Mutation	SNP	G	G	T	rs371049193	alternate_allele	TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	PIK3CA	NM_006218	exon17	c.G2453T	p.R818L	TTATTCGTATTAT	.	80.0	4.0	77.0	0.0	.	8460	.	.	.	alt	.	.	PASS	Atlas-SNP
DTHD1	401124	hgsc.bcm.edu	hg19	4	36345277	36345277	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	DTHD1	NM_001170700	exon9	c.T2177G	p.F726C	ACGAGTTTCTTTG	.	159.0	83.0	163.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
ATP10D	57205	hgsc.bcm.edu	hg19	4	47593159	47593159	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	ATP10D	NM_020453	exon23	c.A4042G	p.K1348E	GCTCTCAAGAAGT	.	143.0	81.0	136.0	0.0	.	168	.	.	.	none	.	.	PASS	Atlas-SNP
LPHN3	23284	hgsc.bcm.edu	hg19	4	62936619	62936619	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	LPHN3	NM_015236	exon23	c.G4403T	p.S1468I	TCACTAGTCTATA	.	77.0	34.0	64.0	0.0	.	800	.	.	.	none	.	.	PASS	Atlas-SNP
SH3RF1	57630	hgsc.bcm.edu	hg19	4	170037559	170037559	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SH3RF1	NM_020870	exon10	c.C2000A	p.P667Q	ATGCTTGGGGAAG	.	93.0	4.0	83.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
C6	729	hgsc.bcm.edu	hg19	5	41201803	41201803	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	C6,NS,carcinoma,0,1	C6	NM_001115131	exon3	c.G157T	p.D53Y	ACTTATCTACTAC	.	79.0	37.0	78.0	0.0	.	197	.	.	.	none	.	.	PASS	Atlas-SNP
HCN1	348980	hgsc.bcm.edu	hg19	5	45462104	45462104	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	HCN1	NM_021072	exon3	c.C855A	p.F285L	CATGTGGAATATC	.	208.0	97.0	231.0	0.0	.	298	.	.	.	none	.	.	PASS	Atlas-SNP
BDP1	55814	hgsc.bcm.edu	hg19	5	70793235	70793235	+	Silent	SNP	A	A	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	BDP1	NM_018429	exon13	c.A1938G	p.S646S	ACATTCAAAAACT	.	356.0	166.0	339.0	1.0	.	204	.	.	.	none	.	.	PASS	Atlas-SNP
AP3B1	8546	hgsc.bcm.edu	hg19	5	77511925	77511925	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	AP3B1	NM_003664	exon7	c.T740C	p.M247T	GTTAGCATGTGGA	.	80.0	29.0	78.0	0.0	.	94	.	.	.	none	.	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	hg19	5	90016841	90016841	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	GPR98	NM_032119	exon45	c.A9713G	p.Q3238R	GTGTGCAGTGGGA	.	88.0	45.0	88.0	0.0	.	605	.	.	.	none	.	.	PASS	Atlas-SNP
DIAPH1	1729	hgsc.bcm.edu	hg19	5	140909206	140909206	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	DIAPH1	NM_005219	exon20	c.G2640C	p.E880D	ATTCACCTCCAGG	.	84.0	35.0	90.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
SOX4	6659	hgsc.bcm.edu	hg19	6	21594835	21594835	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SOX4	NM_003107	exon1	c.G70T	p.A24S	TCGGGCGCCGGCC	.	91.0	4.0	92.0	0.0	.	11	.	.	.	none	.	.	PASS	Atlas-SNP
TEAD3	7005	hgsc.bcm.edu	hg19	6	35443200	35443200	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	TEAD3	NM_003214	exon12	c.G1107A	p.E369E	CATGTACTCGCAC	.	61.0	41.0	47.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
TBCC	6903	hgsc.bcm.edu	hg19	6	42713428	42713428	+	Silent	SNP	G	G	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	TBCC	NM_003192	exon1	c.C384A	p.R128R	CCCCCGGCGCCGC	.	103.0	48.0	103.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
MAP3K7	6885	hgsc.bcm.edu	hg19	6	91296573	91296573	+	Silent	SNP	G	G	C	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	MAP3K7	NM_145333	exon1	c.C30G	p.S10S	CGAGGAGGAGGAG	.	48.0	23.0	60.0	0.0	.	100	.	.	.	none	.	.	PASS	Atlas-SNP
AHI1	54806	hgsc.bcm.edu	hg19	6	135784363	135784363	+	Silent	SNP	A	A	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	AHI1	NM_001134832	exon7	c.T831C	p.H277H	ATCTTGATGAGAA	.	43.0	20.0	47.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
USP17L7	392197	hgsc.bcm.edu	hg19	8	11990259	11990259	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	.	NM_001256869	exon1	c.G1260A	p.L420L	CTCGTCCAACTCG	.	120.0	25.0	123.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
RNF139	11236	hgsc.bcm.edu	hg19	8	125499771	125499771	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	RNF139	NM_007218	exon2	c.G1881C	p.R627S	TGACAGGGAATTG	.	88.0	42.0	136.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
C9orf43	257169	hgsc.bcm.edu	hg19	9	116185621	116185621	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	C9orf43,NS,carcinoma,0,1	C9orf43	NM_152786	exon7	c.C499T	p.L167L	TCATTTCTGGGTC	.	68.0	28.0	82.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
SEC16A	9919	hgsc.bcm.edu	hg19	9	139368591	139368591	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SEC16A	NM_014866	exon3	c.C3477A	p.Y1159X	GTAGTAGTAGGCG	.	155.0	85.0	158.0	0.0	.	249	.	.	.	none	.	.	PASS	Atlas-SNP
PGBD3	267004	hgsc.bcm.edu	hg19	10	50723698	50723698	+	Silent	SNP	A	A	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	PGBD3	NM_170753	exon2	c.C1463C	p.S488S	CAGAACAAAAGAG	.	39.0	20.0	43.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
IFIT2	3433	hgsc.bcm.edu	hg19	10	91065753	91065753	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	IFIT2	NM_001547	exon2	c.C40T	p.R14W	AGCCTACGGCAAC	.	107.0	42.0	98.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
BTRC	8945	hgsc.bcm.edu	hg19	10	103190124	103190124	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	BTRC	NM_001256856	exon2	c.G71A	p.W24X	CTCTGTGGCTGGG	.	62.0	25.0	66.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
MADD	8567	hgsc.bcm.edu	hg19	11	47305994	47305994	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	MADD	NM_130474	exon12	c.C2035A	p.Q679K	CAGAATCAGAAGG	.	96.0	54.0	91.0	0.0	.	172	.	.	.	none	.	.	PASS	Atlas-SNP
MAP3K12	7786	hgsc.bcm.edu	hg19	12	53877202	53877202	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	MAP3K12	NM_001193511	exon10	c.A1544G	p.H515R	TTTCCATGCAGGA	.	150.0	44.0	92.0	0.0	.	160	.	.	.	none	.	.	PASS	Atlas-SNP
OTOGL	283310	hgsc.bcm.edu	hg19	12	80648329	80648329	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	OTOGL	NM_173591	exon14	c.T1393C	p.C465R	TGGAACTGCACTG	.	88.0	47.0	65.0	0.0	.	235	.	.	.	none	.	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	hg19	14	64634024	64634024	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SYNE2	NM_182914	exon91	c.T16679A	p.L5560H	TCCCACTTAGTGA	.	168.0	74.0	160.0	0.0	.	577	.	.	.	none	.	.	PASS	Atlas-SNP
SPTLC2	9517	hgsc.bcm.edu	hg19	14	78028818	78028818	+	Silent	SNP	C	C	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SPTLC2	NM_004863	exon6	c.G771C	p.L257L	ATCACTCAGAATC	.	80.0	41.0	79.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
SPG11	80208	hgsc.bcm.edu	hg19	15	44955757	44955757	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SPG11	NM_025137	exon1	c.T89C	p.L30S	GGCACCAACAGCA	.	56.0	29.0	60.0	0.0	.	207	.	.	.	none	.	.	PASS	Atlas-SNP
ST8SIA2	8128	hgsc.bcm.edu	hg19	15	92987941	92987941	+	Silent	SNP	G	G	A	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	ST8SIA2	NM_006011	exon5	c.G624A	p.S208S	CCCCTCGGTCATC	.	129.0	62.0	115.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
ACSM2A	123876	hgsc.bcm.edu	hg19	16	20476871	20476871	+	Missense_Mutation	SNP	G	G	T	rs199594429	by1000genomes;alternate_allele	TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	ACSM2A	NM_001010845	exon4	c.G210T	p.W70C	CCTGTGGTGGGTG	.	241.0	98.0	242.0	0.0	.	120	.	.	.	alt	G|1.000;A|0.000	.	PASS	Atlas-SNP
SMPD3	55512	hgsc.bcm.edu	hg19	16	68405808	68405808	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SMPD3	NM_018667	exon3	c.C277T	p.R93W	AGGGCCGGCGGGC	.	129.0	54.0	171.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
GLG1	2734	hgsc.bcm.edu	hg19	16	74505131	74505131	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	GLG1	NM_001145667	exon15	c.G2169A	p.Q723Q	TTTGTTCTGTATC	.	79.0	37.0	87.0	0.0	.	106	.	.	.	none	.	.	PASS	Atlas-SNP
KRT10	3858	hgsc.bcm.edu	hg19	17	38975316	38975316	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	KRT10	NM_000421	exon7	c.C1471T	p.H491Y	CGCCGTGGCCGCC	.	98.0	13.0	26.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
KRT10	3858	hgsc.bcm.edu	hg19	17	38975319	38975319	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	KRT10	NM_000421	exon7	c.G1468A	p.G490S	CGTGGCCGCCGCC	.	104.0	19.0	20.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
ACSF2	80221	hgsc.bcm.edu	hg19	17	48538115	48538115	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	ACSF2	NM_025149	exon2	c.T206G	p.L69R	AGCATCTTAACAG	.	161.0	106.0	92.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
CNDP2	55748	hgsc.bcm.edu	hg19	18	72180835	72180835	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	CNDP2	NM_018235	exon8	c.A784G	p.I262V	CCCGGCATTAACG	.	33.0	12.0	43.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF556	80032	hgsc.bcm.edu	hg19	19	2877876	2877876	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	ZNF556	NM_024967	exon4	c.G920C	p.R307T	ACGTGAGAATTCA	.	148.0	63.0	128.0	0.0	.	73	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM145	284339	hgsc.bcm.edu	hg19	19	42817621	42817621	+	Silent	SNP	C	C	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	TMEM145	NM_173633	exon1	c.C93T	p.Y31Y	CAAGTACGTGCGG	.	82.0	31.0	79.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
PPP1R13L	10848	hgsc.bcm.edu	hg19	19	45889399	45889399	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	PPP1R13L	NM_001142502	exon9	c.A1855G	p.K619E	GGGCCTTGCGCGG	.	30.0	16.0	41.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
CHD6	84181	hgsc.bcm.edu	hg19	20	40086018	40086018	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	CHD6	NM_032221	exon18	c.T2715A	p.Y905X	GAGGCGATACACC	.	126.0	39.0	94.0	0.0	.	312	.	.	.	none	.	.	PASS	Atlas-SNP
ADAMTS1	9510	hgsc.bcm.edu	hg19	21	28217050	28217050	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	ADAMTS1	NM_006988	exon1	c.G224A	p.R75H	CGGAGGCGCGTGG	.	68.0	27.0	69.0	0.0	.	131	.	.	.	none	.	.	PASS	Atlas-SNP
CECR6	27439	hgsc.bcm.edu	hg19	22	17600499	17600499	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	CECR6	NM_031890	exon1	c.C1519A	p.L507I	AGCCGAGGAAGAA	.	26.0	11.0	32.0	0.0	.	11	.	.	.	none	.	.	PASS	Atlas-SNP
AR	367	hgsc.bcm.edu	hg19	X	66765229	66765229	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	AR	NM_000044	exon1	c.G241C	p.E81Q	CAGCAAGAGACTA	.	119.0	9.0	125.0	0.0	.	249	.	.	.	none	.	.	PASS	Atlas-SNP
CACNA2D4	93589	hgsc.bcm.edu	hg19	12	2027591	2027592	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	CACNA2D4	NM_172364	exon1	c.49_50insC	p.T17fs	.	.	136.0	10.0	82.0	0.0	.	220	.	0.0735294	0	none	.	.	PASS	Atlas-INDEL
DZIP1	22873	hgsc.bcm.edu	hg19	13	96242581	96242581	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	DZIP1	NM_198968	exon17	c.1796delA	p.E599fs	.	.	80.0	40.0	106.0	0.0	.	195	.	0.5	0	none	.	.	PASS	Atlas-Indel,Pindel
UMPS	7372	hgsc.bcm.edu	hg19	3	124458913	124458913	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	UMPS	NM_000373	exon4	c.1024delG	p.A342fs	.	.	133.0	45.0	198.0	0.0	.	43	.	0.338346	0	none	.	.	PASS	Atlas-INDEL
FMN1	342184	hgsc.bcm.edu	hg19	15	33261121	33261122	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	FMN1_ENST00000334528,NS,carcinoma,0,2	FMN1	NM_001103184	exon4	c.2112_2113insC	p.P704fs	.	.	30.0	10.0	19.0	0.0	.	174	.	0.333333	0	none	.	.	PASS	Atlas-INDEL
TNFSF8	944	hgsc.bcm.edu	hg19	9	117666251	117666257	+	Frame_Shift_Del	DEL	TCAAGAG	TCAAGAG	-	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	TCAAGAG	TCAAGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	TNFSF8	NM_001244	exon4	c.660_666del	p.220_222del	.	.	64.0	27.0	73.0	0.0	.	34	.	0.421875	0	none	.	.	PASS	Atlas-Indel,Pindel
KIAA1704	55425	hgsc.bcm.edu	hg19	13	45594477	45594477	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	KIAA1704	NM_018559	exon7	c.717delA	p.E239fs	.	.	377.0	156.0	325.0	0.0	.	36	.	0.413793	0	none	.	.	PASS	Atlas-Indel,Pindel
LRIG3	121227	hgsc.bcm.edu	hg19	12	59282143	59282149	+	Frame_Shift_Del	DEL	ATCAGGG	ATCAGGG	-	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	ATCAGGG	ATCAGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	LRIG3	NM_153377	exon7	c.910_916del	p.304_306del	.	.	90.0	22.0	65.0	0.0	.	120	.	0.244444	0	none	.	.	PASS	Atlas-Indel,Pindel
UQCRC1	7384	hgsc.bcm.edu	hg19	3	48637112	48637118	+	Frame_Shift_Del	DEL	CAGATCT	CAGATCT	-	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	CAGATCT	CAGATCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	UQCRC1	NM_003365	exon12	c.1329_1335del	p.443_445del	.	.	38.0	12.0	43.0	0.0	.	42	.	0.315789	0	none	.	.	PASS	Atlas-Indel,Pindel
MAPKBP1	23005	hgsc.bcm.edu	hg19	15	42107832	42107839	+	Frame_Shift_Del	DEL	AAATCATC	AAATCATC	-	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	AAATCATC	AAATCATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	MAPKBP1	NM_001128608	exon13	c.1345_1352del	p.449_451del	.	.	60.0	26.0	67.0	0.0	.	120	.	0.433333	0	none	.	.	PASS	Atlas-Indel,Pindel
FLRT2	23768	hgsc.bcm.edu	hg19	14	86089469	86089469	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	FLRT2	NM_013231	exon2	c.1610delT	p.M537fs	.	.	106.0	41.0	98.0	0.0	.	168	.	0.386792	0	none	.	.	PASS	Atlas-Indel,Pindel
UMPS	7372	hgsc.bcm.edu	hg19	3	124458915	124458920	+	In_Frame_Del	DEL	CACGTG	CACGTG	-	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	CACGTG	CACGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	UMPS	NM_000373	exon4	c.1026_1031del	p.342_344del	.	.	135.0	45.0	202.0	0.0	.	43	.	0.333333	0	none	.	.	PASS	Atlas-INDEL
IRF2BPL	64207	hgsc.bcm.edu	hg19	14	77493645	77493656	+	In_Frame_Del	DEL	GCAGCGGCGGCG	GCAGCGGCGGCG	-	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	GCAGCGGCGGCG	GCAGCGGCGGCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	IRF2BPL	NM_024496	exon1	c.481_492del	p.161_164del	.	.	31.0	11.0	24.0	0.0	.	40	.	0.354839	0	none	.	.	PASS	Atlas-Indel,Pindel
SLCO1C1	53919	hgsc.bcm.edu	hg19	12	20854365	20854365	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SLCO1C1	NM_017435	exon3	c.242delT	p.V81fs	.	.	132.0	73.0	114.0	0.0	.	216	.	0.55303	0	none	.	.	PASS	Atlas-Indel,Pindel
PTK6	5753	hgsc.bcm.edu	hg19	20	62168498	62168499	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	PTK6	NM_001256358	exon1	c.170_171insG	p.V57fs	.	.	98.0	10.0	67.0	0.0	.	33	.	0.102041	0	none	.	.	PASS	Atlas-INDEL
FAM13B	51306	hgsc.bcm.edu	hg19	5	137295872	137295873	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	FAM13B	NM_001101800	exon12	c.1276_1277insA	p.L426fs	.	.	355.0	90.0	340.0	0.0	.	46	.	0.254	.	none	.	.	PASS	Pindel
CCDC83	220047	hgsc.bcm.edu	hg19	11	85630396	85630397	+	Frame_Shift_Ins	INS	-	-	TG	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	CCDC83	NM_173556	exon12	c.1178_1179insTG	p.Y393fs	.	.	187.0	53.0	194.0	0.0	.	48	.	0.283	.	none	.	.	PASS	Pindel
UMPS	7372	hgsc.bcm.edu	hg19	3	124458913	124458920	+	Frame_Shift_Del	DEL	CTCACGTG	CTCACGTG	-	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	CTCACGTG	CTCACGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	UMPS	NM_000373	exon4	c.1024_1031del	p.342_344del	.	.	143.0	41.0	207.0	0.0	.	43	.	0.287	.	none	.	.	PASS	Pindel
SLC4A3	6508	hgsc.bcm.edu	hg19	2	220493130	220493131	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	.	SLC4A3	NM_005070	exon3	c.55_56insG	p.R19fs	.	.	152.0	49.0	154.0	0.0	.	144	.	0.322	.	none	.	.	PASS	Pindel
