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	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
WASH7P	653635	broad.mit.edu	37	1	14976	14976	+	RNA	SNP	G	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr1:14976G>A	uc009vis.2	-	3		c.369C>T			WASH7P_uc009vit.2_RNA|WASH7P_uc001aae.3_RNA|WASH7P_uc009viu.2_RNA|WASH7P_uc001aab.3_RNA|WASH7P_uc001aah.3_RNA|WASH7P_uc009vir.2_RNA|WASH7P_uc009viq.2_Intron|WASH7P_uc001aac.3_RNA|WASH7P_uc009viv.2_RNA|WASH7P_uc009viw.2_RNA					Homo sapiens cDNA FLJ31670 fis, clone NT2RI2004984.												0						CTACCCTTGCGCCTCATGACC	0.582000													4	15	---	---	---	---	0	0	0.184627	0	0
KANK4	163782	broad.mit.edu	37	1	62728839	62728839	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr1:62728839G>A	uc001dah.3	-	7	2841	c.2464C>T	c.(2464-2466)CAC>TAC	p.H822Y	KANK4_uc001dai.3_Missense_Mutation_p.H194Y|KANK4_uc001daf.3_5'UTR|KANK4_uc001dag.3_Missense_Mutation_p.H178Y	NM_181712	NP_859063	Q5T7N3	KANK4_HUMAN	ankyrin repeat domain 38	822										ovary(3)|skin(2)|lung(1)	6						TTCCCGTTGTGATCGGCCAAG	0.582000													4	11	---	---	---	---	0	0	0.387290	0	0
PTCHD3	374308	broad.mit.edu	37	10	27687711	27687711	+	Missense_Mutation	SNP	C	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr10:27687711C>A	uc001itu.2	-	4	1934	c.1816G>T	c.(1816-1818)GTC>TTC	p.V606F		NM_001034842	NP_001030014	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	606	Helical; (Potential).				spermatid development	integral to membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|skin(1)	4						TATATAAAGACTACAAAATAC	0.378000													31	47	---	---	---	---	1.13719e-10	1.24814e-10	0.729181	1	0
LOC642826	642826	broad.mit.edu	37	10	47207813	47207813	+	RNA	SNP	T	C	C			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr10:47207813T>C	uc001jei.2	-	12		c.1586A>G			uc009xnf.2_Missense_Mutation_p.H132R					Homo sapiens cDNA, FLJ99065.												0						TTTACTTACATGGTTTGTACA	0.294000													4	52	---	---	---	---	0	0	0.150653	0	0
GYS2	2998	broad.mit.edu	37	12	21727126	21727126	+	Silent	SNP	C	T	T			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr12:21727126C>T	uc001rfb.2	-	4	885	c.630G>A	c.(628-630)GGG>GGA	p.G210G		NM_021957	NP_068776	P54840	GYS2_HUMAN	glycogen synthase 2	210					glucose metabolic process|glycogen biosynthetic process|response to glucose stimulus	cortical actin cytoskeleton|cytosol|ectoplasm|insoluble fraction|soluble fraction	glycogen (starch) synthase activity|protein homodimerization activity			lung(1)|skin(1)	2						AGAGATACCTCCCAAGTAGTG	0.438000													4	47	---	---	---	---	0	0	0.150653	0	0
PDZRN4	29951	broad.mit.edu	37	12	41966299	41966299	+	Missense_Mutation	SNP	C	A	A	rs139930178	byFrequency	TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr12:41966299C>A	uc010skn.1	+	10	1189	c.1121C>A	c.(1120-1122)GCA>GAA	p.A374E	PDZRN4_uc001rmq.3_Missense_Mutation_p.A315E|PDZRN4_uc009zjz.2_Missense_Mutation_p.A313E|PDZRN4_uc001rmr.2_Missense_Mutation_p.A200E	NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2	573							ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				CAGGAGAATGCAGCCGAGGAC	0.502000													4	24	---	---	---	---	0.00024832	0.00025987	0.150653	1	0
TBC1D3P2	440452	broad.mit.edu	37	17	60342311	60342311	+	RNA	SNP	G	T	T			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr17:60342311G>T	uc010woz.1	-	14		c.1818C>A				NR_027486				Homo sapiens cDNA FLJ60189 complete cds, highly similar to TBC1 domain family member 3.												0						AAAACGAGGAGGCGAAGCTTG	0.458000													9	106	---	---	---	---	4.96729e-08	5.3221e-08	0.575678	1	0
WBP11P1	441818	broad.mit.edu	37	18	30092097	30092097	+	RNA	SNP	C	T	T	rs718721	by1000genomes	TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr18:30092097C>T	uc010dmc.2	+	1		c.472C>T				NR_003558				Homo sapiens cDNA clone IMAGE:5265376, partial cds.												0						TATTCTATGACTCTATGAAAA	0.348000													3	16	---	---	---	---	0	0	0.150653	0	0
NCR1	9437	broad.mit.edu	37	19	55423572	55423572	+	Missense_Mutation	SNP	C	T	T			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr19:55423572C>T	uc002qib.2	+	6	757	c.719C>T	c.(718-720)ACG>ATG	p.T240M	NCR1_uc002qic.2_Missense_Mutation_p.T239M|NCR1_uc002qie.2_Intron|NCR1_uc002qid.2_Missense_Mutation_p.T145M|NCR1_uc002qif.2_Intron|NCR1_uc010esj.2_Missense_Mutation_p.T133M	NM_004829	NP_004820	O76036	NCTR1_HUMAN	natural cytotoxicity triggering receptor 1	240	Extracellular (Potential).				cellular defense response|natural killer cell activation|regulation of natural killer cell mediated cytotoxicity	integral to plasma membrane|SWI/SNF complex	receptor activity|receptor signaling protein activity			large_intestine(1)|ovary(1)	2				GBM - Glioblastoma multiforme(193;0.0449)		ACCACAGAGACGGGACTCCAG	0.512000													86	136	---	---	---	---	0	0	0.870114	0	0
LOC401010	401010	broad.mit.edu	37	2	132201582	132201582	+	Silent	SNP	A	G	G	rs1806886	by1000genomes	TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr2:132201582A>G	uc002tst.2	-	1	886	c.420T>C	c.(418-420)CGT>CGC	p.R140R		NR_002826				SubName: Full=cDNA FLJ12694 fis, clone NT2RP1000358, highly similar to Homo sapiens mRNA; cDNA DKFZp564C186 (from clone DKFZp564C186);												0						TAAGCAGCATACGGCACTGCT	0.602000													5	68	---	---	---	---	0	0	0.184627	0	0
SP140	11262	broad.mit.edu	37	2	231113619	231113619	+	Silent	SNP	T	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr2:231113619T>A	uc002vql.2	+	9	1027	c.912T>A	c.(910-912)ACT>ACA	p.T304T	SP140_uc010zma.1_RNA|SP140_uc002vqk.2_Silent_p.T304T|SP140_uc002vqn.2_Silent_p.T251T|SP140_uc002vqm.2_Silent_p.T278T|SP140_uc010fxl.2_Silent_p.T304T	NM_007237	NP_009168	Q13342	LY10_HUMAN	SP140 nuclear body protein isoform 1	304					defense response	cytoplasm|nuclear envelope|nucleolus|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		ATCTAAAAACTCCCCAAGTCA	0.423000													6	10	---	---	---	---	0	0	0.217242	0	0
EXOC2	55770	broad.mit.edu	37	6	637797	637797	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr6:637797G>A	uc003mtd.2	-	2	156	c.22C>T	c.(22-24)CCC>TCC	p.P8S	EXOC2_uc003mte.2_Missense_Mutation_p.P8S|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Sec5 protein	8	IPT/TIG.				exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		GTCACAAGGGGGGGTTGTCGT	0.473000													84	106	---	---	---	---	0	0	0.870114	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr7:140453136A>T	uc003vwc.3	-	15	1860	c.1799T>A	c.(1798-1800)GTG>GAG	p.V600E		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	600	Protein kinase.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).		activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.V600E(16892)|p.V600?(325)|p.V600K(176)|p.V600R(36)|p.V600M(25)|p.V600A(23)|p.V600D(21)|p.V600G(11)|p.V600_K601>E(8)|p.T599_V600insTT(3)|p.T599_R603>I(2)|p.T599_V600>IAL(2)|p.V600L(2)|p.T599_V600insT(2)|p.V600_W604del(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insV(1)|p.T599_V600insDFGLAT(1)	KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGAGATTTCACTGTAGCTAG	0.368000	V600E(UACC257_SKIN)|V600D(K029AX_SKIN)|V600E(HS695T_SKIN)|V600E(COLO679_SKIN)|V600E(BT474_BREAST)|V600E(IGR39_SKIN)|V600E(A101D_SKIN)|V600E(COLO783_SKIN)|V600E(IGR37_SKIN)|V600E(A375_SKIN)|V600E(WM793_SKIN)|V600E(COLO818_SKIN)|V600E(HS294T_SKIN)|V600E(SKMEL28_SKIN)|V600E(DU4475_BREAST)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(IGR1_SKIN)|V600E(SKHEP1_LIVER)|V600E(WM983B_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(RVH421_SKIN)|V600D(WM2664_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(SKMEL24_SKIN)|V600D(WM115_SKIN)|V600E(MALME3M_SKIN)|V600E(A673_BONE)|V600E(C32_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO800_SKIN)|V600E(COLO741_SKIN)|V600E(HS939T_SKIN)|V600E(COLO205_LARGE_INTESTINE)|V600E(K029AX_SKIN)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(SH4_SKIN)|V600E(WM88_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO849_SKIN)|V600E(MELHO_SKIN)|V600E(BHT101_THYROID)|V600E(G361_SKIN)|V600E(UACC62_SKIN)|V600E(BCPAP_THYROID)|V600E(8505C_THYROID)|V600E(SW1417_LARGE_INTESTINE)|V600E(COLO829_SKIN)|V600E(RKO_LARGE_INTESTINE)|V600E(A2058_SKIN)|V600E(RPMI7951_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(SKMEL5_SKIN)|V600E(ES2_OVARY)|V600E(LOXIMVI_SKIN)	61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				26	42	---	---	---	---	0	0	0.667858	0	0
TRPM6	140803	broad.mit.edu	37	9	77377018	77377018	+	Silent	SNP	T	A	A	rs150409948	byFrequency	TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr9:77377018T>A	uc004ajl.1	-	26	4807	c.4569A>T	c.(4567-4569)ACA>ACT	p.T1523T	TRPM6_uc004ajk.1_Silent_p.T1518T|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron|TRPM6_uc004ajj.1_Silent_p.T479T	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	1523	Cytoplasmic (Potential).				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						TCCAAAAGGATGTGTTTGGCT	0.473000													4	44	---	---	---	---	0	0	0.150653	0	0
CTNNAL1	8727	broad.mit.edu	37	9	111706098	111706098	+	Splice_Site	SNP	T	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr9:111706098T>A	uc004bdo.1	-	17	1984	c.1942_splice	c.e17-1	p.L648_splice	CTNNAL1_uc010mts.1_Splice_Site_p.L300_splice|CTNNAL1_uc010mtt.1_Intron|CTNNAL1_uc004bdp.1_Splice_Site_p.L648_splice|CTNNAL1_uc004bdq.1_Splice_Site_p.L134_splice	NM_003798	NP_003789	Q9UBT7	CTNL1_HUMAN	catenin, alpha-like 1						cell adhesion|Rho protein signal transduction	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			ovary(1)	1				STAD - Stomach adenocarcinoma(157;0.0768)		GTCTTTCAGCTGAAATGTAAT	0.358000													28	91	---	---	---	---	0	0	0.717897	0	0
CTNNAL1	8727	broad.mit.edu	37	9	111718076	111718076	+	Silent	SNP	C	T	T			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr9:111718076C>T	uc004bdo.1	-	12	1665	c.1623G>A	c.(1621-1623)AAG>AAA	p.K541K	CTNNAL1_uc010mts.1_Silent_p.K193K|CTNNAL1_uc010mtt.1_Silent_p.K541K|CTNNAL1_uc004bdp.1_Silent_p.K541K|CTNNAL1_uc004bdq.1_Silent_p.K27K	NM_003798	NP_003789	Q9UBT7	CTNL1_HUMAN	catenin, alpha-like 1	541					cell adhesion|Rho protein signal transduction	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			ovary(1)	1				STAD - Stomach adenocarcinoma(157;0.0768)		TTACCATTGGCTTTGGAAGTG	0.274000													15	39	---	---	---	---	0	0	0.608945	0	0
Unknown	0	broad.mit.edu	37	MT	1888	1888	+	5'Flank	SNP	G	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrM:1888G>A	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		TTTGCAAGGAGAGCCAAAGCT	0.398000													6	41	---	---	---	---	0	0	0.278610	0	0
Unknown	0	broad.mit.edu	37	MT	1977	1977	+	5'Flank	SNP	T	C	C			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrM:1977T>C	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		AGTGGGAAGATTTATAGGTAG	0.448000													5	50	---	---	---	---	0	0	0.278610	0	0
Unknown	0	broad.mit.edu	37	MT	4216	4216	+	RNA	SNP	T	C	C			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrM:4216T>C	uc004cos.3	+	2		c.2509T>C			uc011mfh.1_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP47.																		TACTTATATGATATGTCTCCA	0.388000													4	27	---	---	---	---	0	0	0.217242	0	0
Unknown	0	broad.mit.edu	37	MT	7028	7028	+	Missense_Mutation	SNP	C	T	T			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrM:7028C>T	uc011mfh.1	+	1	1175	c.127C>T	c.(127-129)CCA>TCA	p.P43S	uc004cou.3_5'Flank|uc011mfi.1_5'Flank					Homo sapiens cDNA: FLJ22894 fis, clone KAT04907.																		TACGTTGTAGCTCACTTCCAC	0.448000													6	26	---	---	---	---	0	0	0.335167	0	0
Unknown	0	broad.mit.edu	37	MT	8697	8697	+	RNA	SNP	G	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrM:8697G>A	uc011mfi.1	+	1		c.35G>A			uc004cov.3_5'Flank					Homo sapiens mRNA for OK/SW-CL.16, complete cds.																		TCAAAACAAATGATAGCCATA	0.403000													8	54	---	---	---	---	0	0	0.278610	0	0
Unknown	0	broad.mit.edu	37	MT	11251	11251	+	RNA	SNP	A	G	G			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrM:11251A>G	uc004cov.3	+	1		c.674A>G			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		CTCATCGCACTAATTTACACT	0.473000													7	54	---	---	---	---	0	0	0.248553	0	0
Unknown	0	broad.mit.edu	37	MT	11719	11719	+	RNA	SNP	G	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrM:11719G>A	uc004cov.3	+	1		c.1142G>A			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		ATCGCCCACGGACTCACATCC	0.483000													8	43	---	---	---	---	0	0	0.307466	0	0
Unknown	0	broad.mit.edu	37	MT	11812	11812	+	RNA	SNP	A	G	G			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrM:11812A>G	uc004cov.3	+	1		c.1235A>G			uc004cow.1_5'Flank|uc004cox.3_5'Flank|uc004coy.2_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		CTTCAAACTCTACTCCCACTA	0.473000													4	32	---	---	---	---	0	0	0.150653	0	0
Unknown	0	broad.mit.edu	37	MT	13368	13368	+	RNA	SNP	G	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrM:13368G>A	uc004cox.3	+	1		c.1032G>A			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		ATGTGCTCCGGGTCCATCATC	0.448000													6	48	---	---	---	---	0	0	0.217242	0	0
Unknown	0	broad.mit.edu	37	MT	14233	14233	+	RNA	SNP	A	G	G			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrM:14233A>G	uc004cox.3	+	1		c.1897A>G			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CAACGCCCATAATCATACAAA	0.408000													9	56	---	---	---	---	0	0	0.335167	0	0
Unknown	0	broad.mit.edu	37	MT	14905	14905	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrM:14905G>A	uc004coy.2	+	1	145	c.70G>A	c.(70-72)GCA>ACA	p.A24T	uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		TTCCTAGCCATACACTACTCA	0.532000													4	47	---	---	---	---	0	0	0.150653	0	0
USP9X	8239	broad.mit.edu	37	X	41073950	41073950	+	Silent	SNP	A	G	G			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrX:41073950A>G	uc004dfb.2	+	34	5952	c.5319A>G	c.(5317-5319)AAA>AAG	p.K1773K	USP9X_uc004dfc.2_Silent_p.K1773K	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	1773					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						ATTGTGAAAAATGCAATAAAA	0.323000													36	170	---	---	---	---	0	0	0.812448	0	0
FAIM3	9214	broad.mit.edu	37	1	207097707	207097708	+	5'Flank	INS	-	GT	GT			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr1:207097707_207097708insGT	uc001hey.2	-						FAIM3_uc010prz.1_5'Flank|FAIM3_uc010psa.1_5'Flank|FAIM3_uc010psb.1_5'Flank	NM_005449	NP_005440	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3 isoform a						anti-apoptosis|cellular defense response	integral to membrane				central_nervous_system(1)	1	Breast(84;0.201)					tgctctgtctagtgtgtgtggt	0.000													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	10	134206019	134206020	+	IGR	INS	-	G	G	rs142843997		TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr10:134206019_134206020insG								LRRC27 (11009 upstream) : PWWP2B (4682 downstream)																							atgatggtgatgtgataatggt	0.000													7	16	---	---	---	---					
Unknown	0	broad.mit.edu	37	11	55838769	55838769	+	IGR	DEL	T	-	-			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr11:55838769delT								OR5AS1 (39902 upstream) : OR8I2 (22015 downstream)																							CCATGTATTATTTCCTCAGCT	0.423													2	4	---	---	---	---					
LOC144438	144438	broad.mit.edu	37	12	49086750	49086750	+	5'Flank	DEL	A	-	-			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr12:49086750delA	uc001rsd.3	-							NR_024266				Homo sapiens cDNA FLJ11223 fis, clone PLACE1008209.												0						TTCTTAGTCCAAAAAAAAAAA	0.323													2	4	---	---	---	---					
KRT1	3848	broad.mit.edu	37	12	53069236	53069256	+	In_Frame_Del	DEL	TAGCTGCTACCTCCGGAGCCA	-	-	rs66529359		TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr12:53069236_53069256delTAGCTGCTACCTCCGGAGCCA	uc001sau.1	-	9	1715_1735	c.1656_1676delTGGCTCCGGAGGTAGCAGCTA	c.(1654-1677)TATGGCTCCGGAGGTAGCAGCTAC>TAC	p.552_559YGSGGSSY>Y	KRT1_uc001sav.1_Splice_Site_p.G556_splice	NM_006121	NP_006112	P04264	K2C1_HUMAN	keratin 1	552_559	Gly/Ser-rich.|Tail.				complement activation, lectin pathway|epidermis development|fibrinolysis|regulation of angiogenesis|response to oxidative stress	plasma membrane	protein binding|receptor activity|structural constituent of cytoskeleton|sugar binding			ovary(1)|skin(1)	2						tccggagccgtagctgctacctccggagccatagctgccac	0.000													4	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	12	124719517	124719522	+	IGR	DEL	CATAAT	-	-	rs112028864		TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr12:124719517_124719522delCATAAT								ZNF664 (219550 upstream) : FAM101A (54188 downstream)																							ccattaccaccataatcatcatcacc	0.092													3	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	15	78675656	78675656	+	IGR	DEL	T	-	-	rs112849950		TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr15:78675656delT								CRABP1 (35084 upstream) : IREB2 (54862 downstream)																							ATAAGGAGAAttttttttttt	0.209													3	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	19	3332504	3332506	+	IGR	DEL	CCC	-	-			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr19:3332504_3332506delCCC								CELF5 (35433 upstream) : NFIC (27110 downstream)																							ttccttccttccctccttccttc	0.000													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	19	53418429	53418430	+	IGR	INS	-	CTTCT	CTTCT	rs58621028		TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr19:53418429_53418430insCTTCT								ZNF320 (17483 upstream) : ZNF321 (11958 downstream)																							GAACATCCCCAGGAAGGAAGTT	0.450													8	150	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	91764886	91764893	+	IGR	DEL	TATGTGTG	-	-	rs4005074		TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr2:91764886_91764893delTATGTGTG								None (None upstream) : LOC654342 (40299 downstream)																							gatgtacgtatatgtgtgtgtgtgtgtg	0.000													3	6	---	---	---	---					
MUC4	4585	broad.mit.edu	37	3	195512373	195512374	+	In_Frame_Ins	INS	-	GAT	GAT	rs140335395	by1000genomes	TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr3:195512373_195512374insGAT	uc011bto.1	-	2	6537_6538	c.6077_6078insATC	c.(6076-6078)TCC>TCATCC	p.2026_2026S>SS	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	798	Ser-rich.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGTCACCAGTGGATGCTGAGGA	0.579													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	5	96816803	96816804	+	IGR	INS	-	AC	AC	rs143046862	by1000genomes	TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr5:96816803_96816804insAC								RIOK2 (297798 upstream) : None (None downstream)																							TACCTGTATGTacacacacaca	0.149													3	3	---	---	---	---					
Unknown	0	broad.mit.edu	37	7	63627059	63627060	+	IGR	INS	-	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr7:63627059_63627060insA								ZNF727 (88134 upstream) : ZNF735 (40521 downstream)																							atgaaggaaggaaggaaggaaa	0.045													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	7	131319257	131319260	+	IGR	DEL	TTCT	-	-			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr7:131319257_131319260delTTCT								PODXL (77881 upstream) : PLXNA4 (488832 downstream)																							ccttctttccttctttctttcttt	0.000													2	4	---	---	---	---					
SVOPL	136306	broad.mit.edu	37	7	138305790	138305790	+	Splice_Site	DEL	C	-	-			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr7:138305790delC	uc011kqh.1	-	13	1353	c.1353_splice	c.e13+1	p.Q451_splice	SVOPL_uc003vue.2_Splice_Site_p.Q299_splice	NM_001139456	NP_001132928	Q8N434	SVOPL_HUMAN	SVOP-like isoform 1							integral to membrane	transmembrane transporter activity				0						CTTGGCTGTACCTGGGATATA	0.567													13	23	---	---	---	---					
Unknown	0	broad.mit.edu	37	7	152445928	152445928	+	IGR	DEL	A	-	-			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr7:152445928delA								XRCC2 (72678 upstream) : ACTR3B (10923 downstream)																							gctctgtctcaaaaaaaaaaa	0.229													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	X	109010367	109010370	+	IGR	DEL	AGGA	-	-			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrX:109010367_109010370delAGGA								ACSL4 (33746 upstream) : TMEM164 (235493 downstream)																							ggagggagggaggaaggaaggaag	0.000													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	X	152871884	152871904	+	IGR	DEL	GTAAAGGGATTTTGTTCACCA	-	-	rs139494223		TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrX:152871884_152871904delGTAAAGGGATTTTGTTCACCA								FAM58A (7252 upstream) : DUSP9 (35993 downstream)																							ttaaaattaggtaaagggatttTGTTCACCAGTAAAGGGAT	0.271													4	4	---	---	---	---					
