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
CROCCL1	84809	broad.mit.edu	37	1	16946434	16946434	+	RNA	SNP	C	T	T	rs367060		TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr1:16946434C>T	uc010ocf.1	-	3		c.464G>A			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						CTCAGCCTTCCGCCGGGCCAG	0.672000													9	30					0	0	0.010729	0	0
Unknown	0	broad.mit.edu	37	15	102292785	102292785	+	Missense_Mutation	SNP	C	G	G	rs143389223		TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr15:102292785C>G	uc010usj.1	+	4	432	c.373C>G	c.(373-375)CAG>GAG	p.Q125E	uc002bxp.3_5'Flank|uc002bxt.2_5'Flank|uc002bxz.3_5'Flank|uc002byd.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank					RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																		TGCTGCTTCTCAGAGCTGCTG	0.602000													4	32					0	0	0.003080	0	0
NETO2	81831	broad.mit.edu	37	16	47117466	47117466	+	Missense_Mutation	SNP	A	C	C			TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr16:47117466A>C	uc002eer.1	-	9	1629	c.1244T>G	c.(1243-1245)TTG>TGG	p.L415W	NETO2_uc002eeq.1_Missense_Mutation_p.L150W|NETO2_uc010vgf.1_Missense_Mutation_p.L272W	NM_018092	NP_060562	Q8NC67	NETO2_HUMAN	neuropilin- and tolloid-like protein 2	415	Cytoplasmic (Potential).					integral to membrane	receptor activity				0		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)				TTCTTCCGACAAGTCTGCCAG	0.517000										HNSCC(25;0.065)			3	145					0	0	0.009096	0	0
ZFHX3	463	broad.mit.edu	37	16	72829160	72829160	+	Missense_Mutation	SNP	A	C	C			TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr16:72829160A>C	uc002fck.2	-	9	8094	c.7421T>G	c.(7420-7422)CTG>CGG	p.L2474R	ZFHX3_uc002fcl.2_Missense_Mutation_p.L1560R	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	2474					muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)				CAGGGACACCAGCTGGGGGAG	0.617000													4	84					0	0	0.014758	0	0
ALDH1L1	10840	broad.mit.edu	37	3	125824683	125824683	+	Missense_Mutation	SNP	G	T	T			TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr3:125824683G>T	uc003eim.1	-	22	2729	c.2539C>A	c.(2539-2541)CTG>ATG	p.L847M	ALDH1L1_uc010hse.1_RNA|ALDH1L1_uc011bki.1_Missense_Mutation_p.L746M|ALDH1L1_uc003ein.1_Missense_Mutation_p.L382M	NM_012190	NP_036322	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	847	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process|biosynthetic process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	CTGACATACAGGGCCTTGTTG	0.552000													5	181					0.00116845	0.00749752	0.001168	1	0
DNAH8	1769	broad.mit.edu	37	6	38980292	38980292	+	Nonsense_Mutation	SNP	G	A	A			TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr6:38980292G>A	uc003ooe.1	+	89	13542	c.12942G>A	c.(12940-12942)TGG>TGA	p.W4314*		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						GAGTGTCTTGGGATTCGTCCA	0.413000													4	159					0	0	0.009096	0	0
SYNE1	23345	broad.mit.edu	37	6	152737750	152737750	+	Missense_Mutation	SNP	C	A	A			TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr6:152737750C>A	uc010kiw.2	-	41	6424	c.5822G>T	c.(5821-5823)AGC>ATC	p.S1941I	SYNE1_uc003qot.3_Missense_Mutation_p.S1948I|SYNE1_uc003qou.3_Missense_Mutation_p.S1941I|SYNE1_uc010kjb.1_Missense_Mutation_p.S1924I	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1941	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTGCTCAGAGCTCCCGATTTT	0.498000										HNSCC(10;0.0054)			4	112					2.56e-06	1.9712e-05	0.009096	1	0
MUC17	140453	broad.mit.edu	37	7	100675605	100675605	+	Missense_Mutation	SNP	A	G	G			TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr7:100675605A>G	uc003uxp.1	+	3	961	c.908A>G	c.(907-909)AAC>AGC	p.N303S	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	303	Extracellular (Potential).|Ser-rich.|3.|59 X approximate tandem repeats.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					GCTGCCACCAACATTCCTGTG	0.493000													11	355					0	0	0.013537	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	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				22	42					0	0	0.014323	0	0
Unknown	0	broad.mit.edu	37	1	78240626	78240627	+	IGR	INS	-	T	T			TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr1:78240626_78240627insT								USP33 (15089 upstream) : FAM73A (4682 downstream)																							CAttcttaacctttttttttta	0.267													2	4	---	---	---	---					
ABCC4	10257	broad.mit.edu	37	13	95727771	95727773	+	In_Frame_Del	DEL	AGA	-	-			TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr13:95727771_95727773delAGA	uc001vmd.3	-	22	2838_2840	c.2719_2721delTCT	c.(2719-2721)TCTdel	p.S907del	ABCC4_uc010afk.2_In_Frame_Del_p.S860del	NM_005845	NP_005836	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C, member 4	907	ABC transmembrane type-1 2.				platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)	GCCCCTGGAGAGAAGATGATAAG	0.512													37	117	---	---	---	---					
Unknown	0	broad.mit.edu	37	19	3131446	3131446	+	IGR	DEL	C	-	-	rs66993077		TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr19:3131446delC								GNA11 (9994 upstream) : GNA15 (4745 downstream)																							aaaaaaaaaacaaaaaaaaaa	0.348													3	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	11060846	11060847	+	IGR	INS	-	TG	TG	rs149638295	by1000genomes	TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr2:11060846_11060847insTG								KCNF1 (6496 upstream) : C2orf50 (212332 downstream)																							gtgcgtgtgcctgtgtgtgtgt	0.386													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	127069021	127069022	+	IGR	INS	-	T	T	rs140927368	by1000genomes	TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr2:127069021_127069022insT								None (None upstream) : GYPC (344662 downstream)																							TAGGAATTTCCTGGTCAAGTCT	0.386													3	3	---	---	---	---					
Unknown	0	broad.mit.edu	37	4	95290943	95290943	+	IGR	DEL	C	-	-			TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr4:95290943delC								HPGDS (26916 upstream) : PDLIM5 (82095 downstream)																							CATCTTGGATCCTATGGAGGC	0.443													2	4	---	---	---	---					
LOC441089	441089	broad.mit.edu	37	5	79646840	79646840	+	RNA	DEL	T	-	-	rs34240292		TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chr5:79646840delT	uc010jaj.1	-	1		c.946delA				NR_003665				Homo sapiens CRSP8 pseudogene (LOC441089), non-coding RNA.												0						GCGTGGGGGCTTACTGCCGGC	0.632													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	Y	13601466	13601467	+	IGR	INS	-	T	T	rs112972965		TCGA-EM-A2P0-01A-11D-A202-08	TCGA-EM-A2P0-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9c54088d-e00c-470f-af79-71c1dae9b4d6	1de7e8e6-34d9-405f-91f0-94ca4b582450	g.chrY:13601466_13601467insT								None (None upstream) : None (None downstream)																							AGAGCAGGCTCTTGCCCACATC	0.490													4	7	---	---	---	---					
