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
LYZ	4069	broad.mit.edu	37	12	69743921	69743921	+	Missense_Mutation	SNP	A	T	T			TCGA-EL-A3D1-01A-11D-A19J-08	TCGA-EL-A3D1-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	d173b533-5eae-46e3-b624-9fa47623fb54	941d8f35-a642-4478-b457-e05547d484bc	g.chr12:69743921A>T	uc001suw.2	+	2	225	c.170A>T	c.(169-171)AAC>ATC	p.N57I		NM_000239	NP_000230	P61626	LYSC_HUMAN	lysozyme precursor	57					cell wall macromolecule catabolic process|cytolysis|defense response to bacterium|inflammatory response	extracellular space	lysozyme activity|protein binding				0	all_epithelial(5;2.98e-35)|Lung NSC(4;9.93e-33)|all_lung(4;5.66e-31)|Breast(13;2.56e-06)|Esophageal squamous(21;0.187)		Epithelial(6;8.26e-19)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00503)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)			AGTGGTTACAACACACGAGCT	0.398000													30	60	---	---	---	---	0	0	0.00209593	0	0
Unknown	0	broad.mit.edu	37	15	102292813	102292813	+	Missense_Mutation	SNP	T	G	G			TCGA-EL-A3D1-01A-11D-A19J-08	TCGA-EL-A3D1-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	d173b533-5eae-46e3-b624-9fa47623fb54	941d8f35-a642-4478-b457-e05547d484bc	g.chr15:102292813T>G	uc010usj.1	+	4	460	c.401T>G	c.(400-402)GTG>GGG	p.V134G	uc002bxo.2_RNA|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|uc002byr.2_5'Flank					RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																		TGCACTCGCGTGGGAACGAGA	0.607000													2	9	---	---	---	---	0	0	6.4e-05	0	0
SLC6A10P	386757	broad.mit.edu	37	16	32890622	32890622	+	Missense_Mutation	SNP	T	G	G			TCGA-EL-A3D1-01A-11D-A19J-08	TCGA-EL-A3D1-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	d173b533-5eae-46e3-b624-9fa47623fb54	941d8f35-a642-4478-b457-e05547d484bc	g.chr16:32890622T>G	uc002edh.1	-	5	440	c.264A>C	c.(262-264)AAA>AAC	p.K88N	SLC6A10P_uc002edi.1_RNA					RecName: Full=Transporter;												0						CGTTGGTGTTTTTGTAGACCA	0.512000													3	15	---	---	---	---	0	0	6.4e-05	0	0
Unknown	0	broad.mit.edu	37	17	45128742	45128742	+	5'Flank	SNP	T	G	G	rs34655963	by1000genomes	TCGA-EL-A3D1-01A-11D-A19J-08	TCGA-EL-A3D1-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	d173b533-5eae-46e3-b624-9fa47623fb54	941d8f35-a642-4478-b457-e05547d484bc	g.chr17:45128742T>G	uc010wkl.1	-						uc010wkm.1_RNA					Homo sapiens cDNA FLJ38031 fis, clone CTONG2013348.																		TAATGATTTTTATTATACTTT	0.318000													5	98	---	---	---	---	0	0	0.000602214	0	0
MKNK2	2872	broad.mit.edu	37	19	2039764	2039764	+	Missense_Mutation	SNP	C	T	T	rs142610986	byFrequency	TCGA-EL-A3D1-01A-11D-A19J-08	TCGA-EL-A3D1-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	d173b533-5eae-46e3-b624-9fa47623fb54	941d8f35-a642-4478-b457-e05547d484bc	g.chr19:2039764C>T	uc002lus.2	-	14	1491	c.1246G>A	c.(1246-1248)GAG>AAG	p.E416K	MKNK2_uc002luq.1_Intron|MKNK2_uc010xgu.1_Missense_Mutation_p.E255K|MKNK2_uc010xgv.1_Missense_Mutation_p.E285K|MKNK2_uc002lur.2_Intron|MKNK2_uc002lut.1_3'UTR	NM_199054	NP_951009	Q9HBH9	MKNK2_HUMAN	MAP kinase-interacting serine/threonine kinase 2	416					cell surface receptor linked signaling pathway|intracellular protein kinase cascade|regulation of translation		ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(1)|breast(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGGCCTCCTCCTCAGCCAGG	0.682000													4	18	---	---	---	---	0	0	0.00024832	0	0
IL7R	3575	broad.mit.edu	37	5	35876286	35876286	+	Missense_Mutation	SNP	A	G	G			TCGA-EL-A3D1-01A-11D-A19J-08	TCGA-EL-A3D1-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	d173b533-5eae-46e3-b624-9fa47623fb54	941d8f35-a642-4478-b457-e05547d484bc	g.chr5:35876286A>G	uc003jjs.2	+	8	1167	c.1078A>G	c.(1078-1080)AGC>GGC	p.S360G	IL7R_uc011cop.1_RNA	NM_002185	NP_002176	P16871	IL7RA_HUMAN	interleukin 7 receptor precursor	360	Cytoplasmic (Potential).				immune response|regulation of DNA recombination	extracellular region|integral to membrane	antigen binding|interleukin-7 receptor activity			ovary(3)|breast(1)|skin(1)	5	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			CACTCCAGAAAGCTTTGGAAG	0.527000													14	21	---	---	---	---	0	0	0.000308642	0	0
GUSBL2	375513	broad.mit.edu	37	6	58256521	58256521	+	Nonsense_Mutation	SNP	A	T	T			TCGA-EL-A3D1-01A-11D-A19J-08	TCGA-EL-A3D1-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	d173b533-5eae-46e3-b624-9fa47623fb54	941d8f35-a642-4478-b457-e05547d484bc	g.chr6:58256521A>T	uc011dxq.1	-	3	259	c.158T>A	c.(157-159)TTG>TAG	p.L53*	GUSBL2_uc011dxp.1_RNA					SubName: Full=Putative uncharacterized protein ENSP00000348869; Flags: Fragment;												0						ACACACTTCCAACTTGAACTG	0.552000													3	8	---	---	---	---	0	0	6.4e-05	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-EL-A3D1-01A-11D-A19J-08	TCGA-EL-A3D1-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	d173b533-5eae-46e3-b624-9fa47623fb54	941d8f35-a642-4478-b457-e05547d484bc	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				32	50	---	---	---	---	0	0	0.00209593	0	0
KIAA1009	22832	broad.mit.edu	37	6	84936070	84936070	+	Frame_Shift_Del	DEL	T	-	-			TCGA-EL-A3D1-01A-11D-A19J-08	TCGA-EL-A3D1-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	d173b533-5eae-46e3-b624-9fa47623fb54	941d8f35-a642-4478-b457-e05547d484bc	g.chr6:84936070delT	uc010kbp.2	-	2	139	c.42delA	c.(40-42)GAAfs	p.E14fs	KIAA1009_uc003pkj.3_Intron|KIAA1009_uc003pkk.2_Frame_Shift_Del_p.E14fs	NM_014895	NP_055710	Q5TB80	QN1_HUMAN	KIAA1009 protein	14					cell division|mitosis	centrosome|nucleus|plasma membrane|spindle	protein binding			ovary(1)	1		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		TCATAAACTGTTCAAACTCTT	0.328													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	7	57274473	57274476	+	IGR	DEL	TCTT	-	-	rs150621884		TCGA-EL-A3D1-01A-11D-A19J-08	TCGA-EL-A3D1-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	d173b533-5eae-46e3-b624-9fa47623fb54	941d8f35-a642-4478-b457-e05547d484bc	g.chr7:57274473_57274476delTCTT								ZNF479 (66902 upstream) : ZNF716 (235407 downstream)																							ttccttcctctctttctttctccc	0.064													3	4	---	---	---	---					
GIGYF1	64599	broad.mit.edu	37	7	100280993	100280994	+	Frame_Shift_Del	DEL	GC	-	-			TCGA-EL-A3D1-01A-11D-A19J-08	TCGA-EL-A3D1-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	d173b533-5eae-46e3-b624-9fa47623fb54	941d8f35-a642-4478-b457-e05547d484bc	g.chr7:100280993_100280994delGC	uc003uwg.1	-	18	3135_3136	c.2126_2127delGC	c.(2125-2127)CGCfs	p.R709fs		NM_022574	NP_072096	O75420	PERQ1_HUMAN	PERQ amino acid rich, with GYF domain 1	709										large_intestine(1)|central_nervous_system(1)	2	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					GCTGCTGGCGGCGCTTCTCCTC	0.649													45	67	---	---	---	---					
Unknown	0	broad.mit.edu	37	9	66960593	66960594	+	IGR	INS	-	T	T			TCGA-EL-A3D1-01A-11D-A19J-08	TCGA-EL-A3D1-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	d173b533-5eae-46e3-b624-9fa47623fb54	941d8f35-a642-4478-b457-e05547d484bc	g.chr9:66960593_66960594insT								LOC442421 (457566 upstream) : AQP7P1 (293673 downstream)																							ATACAGGTTTCCACCCCCCCCC	0.406													2	4	---	---	---	---					
