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	Trna_tot	Trna_ref	Trna_var	Trna_alt1	Trna_alt2
PLA2G2D	26279	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	20440719	20440719	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	PLA2G2D-90	NM_012400	exon4	c.G326A	p.C109Y	CAGGCACACAGCT	.	61	15	76	0	.	2	2	0	0	0
AGL	178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	100327977	100327977	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	AGL-92	NM_000644	exon4	c.C458G	p.S153X	AAGAATCAGGTAA	.	102	23	111	0	.	0	0	0	0	0
RPRD2	23248	hgsc.bcm.edu	37	1	150415711	150415711	+	Silent	SNP	T	T	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	RPRD2-23	NM_015203	exon5	c.T519C	p.S173S	AGCATCTACAAAT	.	9	2	8	0	.	2	2	0	0	0
NTRK1	4914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	156843561	156843561	+	Silent	SNP	C	C	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	NTRK1-1393	NM_001012331	exon8	c.C987T	p.F329F	CATCTTCACTGAG	.	25	8	41	0	.	0	0	0	0	0
GORAB	92344	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	170501324	170501324	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	GORAB-90	NM_152281	exon1	c.C35T	p.A12V	CGGCTGCGAGATT	.	95	16	113	0	.	1	0	1	0	0
RGS21	431704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	192321246	192321246	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	RGS21-92	NM_001039152	exon4	c.C158A	p.A53D	GGCTTGCCTGTGA	.	51	11	57	0	.	0	0	0	0	0
CDC73	79577	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	193099338	193099338	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	CDC73-1009	NM_024529	exon3	c.G272A	p.R91Q	CTGATCGAAAAGA	.	61	7	68	0	.	26	22	4	0	0
LBR	3930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	225599084	225599084	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	LBR-228	NM_194442	exon9	c.T1143A	p.F381L	GAGATCAAAAGTA	.	153	28	147	0	.	74	45	28	0	1
ITGB1	3688	hgsc.bcm.edu	37	10	33212557	33212557	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	ITGB1-1084	NM_002211	exon7	c.C898G	p.Q300E	GACATTGTCCATC	.	36	2	46	0	.	136	136	0	0	0
EXOC6	54536	hgsc.bcm.edu	37	10	94700514	94700514	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	EXOC6-91	NM_019053	exon13	c.G1243C	p.D415H	CTTTTTGACCTTT	.	48	3	53	0	.	6	6	0	0	0
OR10Q1	219960	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	57996225	57996225	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	OR10Q1-70	NM_001004471	exon1	c.G123A	p.M41I	GAGGATCATCAAG	.	106	28	129	0	.	0	0	0	0	0
PDGFD	80310	hgsc.bcm.edu	37	11	103797648	103797648	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	PDGFD-723	NM_025208	exon6	c.T979A	p.Y327N	CATGATACTTTTT	.	17	2	36	0	.	0	0	0	0	0
PFDN5	5204	hgsc.bcm.edu	37	12	53689653	53689653	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	PFDN5-227	NM_002624	exon2	c.C103G	p.Q35E	ATTGCTCAGCTCA	.	47	3	63	0	.	571	571	0	0	0
ZNF385A	25946	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	54764720	54764720	+	Silent	SNP	T	T	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	ZNF385A-23	NM_001130967	exon6	c.A825G	p.Q275Q	TTTCAGTTGGACC	.	122	34	217	0	.	2	1	1	0	0
PHLDA1	22822	hgsc.bcm.edu	37	12	76424937	76424937	+	Silent	SNP	T	T	C	rs76176478	bycluster	TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	PHLDA1-90	NM_007350	exon1	c.A585G	p.Q195Q	CTGCTGTTGCTGC	.	33	3	51	1	.	8204	91	8106	1	6
C12orf74	338809	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	93100691	93100691	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	C12orf74-90	NM_001037671	exon2	c.C284G	p.S95C	AGGATTCTTCACA	.	87	23	138	0	.	0	0	0	0	0
HS3ST6	64711	hgsc.bcm.edu	37	16	1962102	1962102	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	.	NM_001009606	exon2	c.A425G	p.D142G	TTCGTGTCCGGGG	.	18	3	41	0	.	2	2	0	0	0
KCNJ18	100134444	broad.mit.edu;bcgsc.ca	37	17	21319100	21319100	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	.	NM_001194958	exon3	c.G446A	p.R149H	GGCTGCGCTGTGT	.	68	5	94	0	.	0	0	0	0	0
SUZ12	23512	hgsc.bcm.edu	37	17	30323881	30323881	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	SUZ12-658	NM_015355	exon15	c.A1859G	p.H620R	ATCTCCATGTCAT	.	37	3	37	0	.	16	16	0	0	0
COASY	80347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	40717244	40717244	+	Splice_Site	SNP	G	G	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	COASY-115	NM_001042529	exon7	c.1303-1G>T	.	TCCCCAGAAGCAG	.	219	45	307	0	.	2	0	2	0	0
AOC2	314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	40997487	40997487	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	AOC2-92	NM_009590	exon1	c.G844C	p.V282L	TTGGAAGTGGTTA	.	102	23	116	0	.	0	0	0	0	0
MAPT	4137	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	44101444	44101444	+	Silent	SNP	C	C	G	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	MAPT-91	NM_001123066	exon15	c.C2238G	p.V746V	CAATGTCTCCTCC	.	155	10	186	0	.	0	0	0	0	0
TYMS	7298	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	662242	662242	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	TYMS-227	NM_001071	exon3	c.A376G	p.R126G	TCCACCAGAGAAG	.	416	65	528	1	.	56	45	11	0	0
NDC80	10403	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	2616466	2616466	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	NDC80-91	NM_006101	exon17	c.G1822C	p.D608H	AAAGTTGATAGAG	.	60	17	58	0	.	35	35	0	0	0
NDC80	10403	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	2616517	2616517	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	NDC80-91	NM_006101	exon17	c.G1873C	p.E625Q	ATTAAAGAGATTA	.	37	10	38	0	.	43	32	11	0	0
SEMA6B	10501	hgsc.bcm.edu	37	19	4544313	4544313	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	SEMA6B-91	NM_032108	exon17	c.A1967G	p.E656G	CTGCGCTCGCCCA	.	2	2	4	1	.	0	0	0	0	0
FBXW9	84261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	12800616	12800616	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	FBXW9-227	NM_032301	exon7	c.C1105T	p.H369Y	AGACGTGCAGCAG	.	98	22	180	0	.	24	11	13	0	0
KLHL26	55295	broad.mit.edu	37	19	18778682	18778682	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	KLHL26-91	NM_018316	exon3	c.G475A	p.A159T	AAGGCGGCCATGA	.	48	3	82	0	.	9	9	0	0	0
CCDC85A	114800	broad.mit.edu	37	2	56420491	56420491	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	CCDC85A-73	NM_001080433	exon2	c.G1156A	p.G386R	AGCGGCGGAGGCA	.	13	3	16	0	.	0	0	0	0	0
TMEM150A	129303	ucsc.edu	37	2	85828227	85828227	+	Silent	SNP	G	G	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	TMEM150A-90	NM_001031738	exon4	c.C117A	p.S39S	GTTGTAGGACCTG	.	36	4	54	0	.	1	1	0	0	0
SIRPG	55423	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	1615980	1615980	+	Silent	SNP	C	C	A	rs147655438	alternate_allele	TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	SIRPG-23	NM_018556	exon4	c.G1014T	p.A338A	GCTGACCGCCAGC	.	90	24	131	0	C|1.000;T|0.000	2	2	0	0	0
HELZ2	85441	broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	62203482	62203482	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	.	NM_001037335	exon2	c.C257T	p.S86F	AACTTGGAGAGTC	.	19	4	31	0	.	4	4	0	0	0
PRPF6	24148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	62642850	62642850	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	PRPF6-70	NM_012469	exon11	c.G1518C	p.W506C	GCAGTGGATCCAG	.	24	3	47	0	.	0	0	0	0	0
FTCD	10841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	21	47571511	47571511	+	Silent	SNP	G	G	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	FTCD-92	NM_206965	exon5	c.C597A	p.I199I	GAGCGCGATGCGG	.	97	27	157	0	.	0	0	0	0	0
DGCR2	9993	broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	19028613	19028613	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	DGCR2-90	NM_005137	exon9	c.G1354A	p.E452K	AGGCCTCGTAGGG	.	46	7	64	0	.	39	26	13	0	0
DLEC1	9940	hgsc.bcm.edu	37	3	38149133	38149133	+	Missense_Mutation	SNP	G	G	A	rs141938666		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	DLEC1-161	NM_007337	exon20	c.G2923A	p.V975M	AGCCAGGTGGAGG	.	39	10	46	0	G|0.997;A|0.003	0	0	0	0	0
HYAL1	3373	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	50340364	50340364	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	HYAL1-278	NM_033159	exon2	c.C24G	p.I8M	GGCGCAGATGGGA	.	46	6	60	0	.	3	3	0	0	0
SERPINI2	5276	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	167170764	167170764	+	Silent	SNP	G	G	A	rs140665807		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	SERPINI2-228	NM_001012303	exon7	c.C954T	p.T318T	TATCTCGGTTATG	.	48	17	37	0	G|1.000;A|0.000	0	0	0	0	0
DCK	1633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	71892401	71892401	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	DCK-116	NM_000788	exon6	c.C685A	p.Q229K	TATCTTCAAGAGG	.	39	13	70	0	.	23	16	7	0	0
PDE5A	8654	hgsc.bcm.edu	37	4	120486567	120486567	+	Splice_Site	SNP	T	T	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	PDE5A-90	NM_033430	exon6	c.778-2A>G	.	AAGTCCTAAAAAA	.	29	2	61	0	.	0	0	0	0	0
FAT4	79633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	126371574	126371574	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	FAT4-108	NM_024582	exon9	c.G9403A	p.G3135S	GAAGAAGGCATTT	.	37	15	89	0	.	0	0	0	0	0
PCDHA6	56142	broad.mit.edu;bcgsc.ca	37	5	140209735	140209735	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	PCDHA6-92	NM_018909	exon1	c.G2059A	p.A687T	GGCGCCGCGGGCC	.	83	6	142	0	.	0	0	0	0	0
HIST1H4C	8364	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	26104205	26104205	+	Silent	SNP	C	C	G	rs139978722	byfrequency;alternate_allele	TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	HIST1H4C-68	NM_003542	exon1	c.C30G	p.G10G	AAAAGGCTTGGGG	.	88	21	115	0	C|0.999;T|0.001	1	1	0	0	0
ZKSCAN8	7745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	28116192	28116192	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	.	NM_006298	exon2	c.G7A	p.E3K	ATGGCTGAAGAAT	.	35	12	67	0	.	2	1	1	0	0
CFB	629	bcgsc.ca	37	6	31919751	31919751	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	CFB-91	NM_001710	exon18	c.C2239G	p.Q747E	CTCTTTCAAGTGC	.	319	7	419	0	.	19	19	0	0	0
TFEB	7942	ucsc.edu	37	6	41658862	41658862	+	Silent	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	TFEB-659	NM_001167827	exon2	c.C132T	p.V44V	ATGCATGACAGCC	.	11	2	16	0	.	8	8	0	0	0
CRISP3	10321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	49696475	49696475	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	CRISP3-92	NM_001190986	exon8	c.G775A	p.A259T	AGGAGGCCTTGCA	.	120	38	150	0	.	41	17	24	0	0
COL9A1	1297	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	70990561	70990561	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	COL9A1-94	NM_001851	exon10	c.C929T	p.P310L	TTTCCCGGTTCAC	.	28	9	33	0	.	0	0	0	0	0
IMPG1	3617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	76660465	76660465	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	IMPG1-93	NM_001563	exon13	c.C1638G	p.F546L	CTCCAAGAAATGA	.	63	15	87	0	.	0	0	0	0	0
IMPG1	3617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	76660529	76660529	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	IMPG1-93	NM_001563	exon13	c.C1574T	p.S525F	GTGTCAGACAGAT	.	40	9	54	0	.	0	0	0	0	0
IMPG1	3617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	76660533	76660533	+	Silent	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	IMPG1-93	NM_001563	exon13	c.C1570T	p.L524L	CAGACAGATCCAT	.	39	10	52	0	.	0	0	0	0	0
IMPG1	3617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	76660636	76660636	+	Silent	SNP	G	G	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	IMPG1-93	NM_001563	exon13	c.C1467T	p.I489I	TTGGCTGATTGCA	.	78	20	104	0	.	0	0	0	0	0
LAMA4	3910	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	112454683	112454683	+	Silent	SNP	G	G	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	LAMA4-140	NM_001105206	exon27	c.C3564G	p.L1188L	TGCTCTGAGGGCC	.	119	29	154	0	.	0	0	0	0	0
MSRA	4482	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	8	9912062	9912062	+	Silent	SNP	C	C	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	MSRA-90	NM_012331	exon1	c.C36T	p.L12L	GCTCCTCCTCCTC	.	43	16	67	0	.	8	8	0	0	0
MSRA	4482	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	8	9912103	9912103	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	MSRA-90	NM_012331	exon1	c.C77T	p.S26L	GCAACTCGGCCTC	.	51	15	69	0	.	10	9	1	0	0
FAM74A3	728495	broad.mit.edu;ucsc.edu	37	9	40716117	40716117	+	RNA	SNP	G	G	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	FAM74A3-23	.	.	.	.	CTGCAAGAAGACG	.	52	6	87	0	.	0	0	0	0	0
ZNF189	7743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	104170234	104170234	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	ZNF189-229	NM_003452	exon3	c.G184C	p.E62Q	AAGGATGAGGAGC	.	17	5	29	0	.	3	2	1	0	0
KIAA0368	23392	hgsc.bcm.edu	37	9	114148697	114148697	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	KIAA0368-68	NM_001080398	exon33	c.A4021G	p.K1341E	GGTTCTTAACCAA	.	23	2	41	0	.	13	13	0	0	0
CXorf21	80231	bcgsc.ca	37	X	30578342	30578342	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	CXorf21-131	NM_025159	exon3	c.C131A	p.S44Y	ACAGAGGAATAGG	.	210	8	282	0	.	0	0	0	0	0
MSN	4478	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	64936758	64936758	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	MSN-1086	NM_002444	exon2	c.G91C	p.D31H	CTATTTGACCAGG	.	77	13	105	0	.	0	0	0	0	0
OGT	8473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	70782731	70782731	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	OGT-113	NM_181672	exon16	c.C2012T	p.A671V	GTGGTGCGCTTTT	.	132	31	123	0	.	13	12	0	0	1
STAG2	10735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	123197834	123197834	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	STAG2-134	NM_001042749	exon20	c.C1958A	p.S653X	ATATTTCAAGAAG	.	61	15	55	0	.	4	4	0	0	0
LYPD3	27076	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	43967294	43967300	+	Frame_Shift_Del	DEL	GTTGCCG	GTTGCCG	-	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	GTTGCCG	GTTGCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	LYPD3-91	NM_014400	exon4	c.522_528del	p.174_176del	.	.	98	20	171	0	.	0	0	0	0	0
TSC1	7248	broad.mit.edu;bcgsc.ca	37	9	135796822	135796826	+	Frame_Shift_Del	DEL	GGCTA	GGCTA	-	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	GGCTA	GGCTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	TSC1-1906	NM_000368	exon8	c.664_665del	p.222_222del	ATCATTGGCTAGA	.	31	8	68	0	.	0	0	0	0	0
RAB11FIP1	80223	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	8	37730588	37730589	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	RAB11FIP1-92	NM_001002814	exon4	c.1732_1733insC	p.S578fs	.	.	77	26	115	0	.	0	0	0	0	0
SNRPE	6635	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	203832834	203832835	+	Missense_Mutation	DNP	GG	GG	AA	novel		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	.	SNRPE		exon3	c.G126A	p.R42Q	TATGCGGATAGAA	.	247.0	87.0	239.0	1.0	.	0	0	0	0	0