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	Genome_Change	Annotation_Transcript	Transcript_Strand	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	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
RPS3	6188	broad.mit.edu	36	11	74793524	74793524	+	Silent	SNP	G	C	C			TCGA-32-1980-01	TCGA-32-1980-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:74793524G>C	uc001owh.1	+	c.699G>C	c.(697-699)CCG>CCC	p.P233P	RPS3_uc001owi.1_Silent_p.P233P|RPS3_uc001owk.1_Silent_p.P107P	NM_001005	NP_000996	P23396	RS3_HUMAN	ribosomal protein S3	233				P -> L (in Ref. 1; CAA39248).	activation of caspase activity|endocrine pancreas development|induction of apoptosis|negative regulation of DNA repair|negative regulation of NF-kappaB transcription factor activity|response to DNA damage stimulus|translational elongation|translational initiation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleus|ruffle membrane	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|endonuclease activity|iron-sulfur cluster binding|mRNA binding|NF-kappaB binding|protein kinase binding|structural constituent of ribosome				0														0.222222	6.854837	8.824012	6	21	GG		KEEP	---	---	---	---	capture			Silent	SNP	74793524	74793524	14123	11	G	C	C	38	38	RPS3	C	3	3
DDX11	1663	broad.mit.edu	36	12	31133692	31133692	+	Splice_Site_SNP	SNP	G	T	T			TCGA-32-1980-01	TCGA-32-1980-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:31133692G>T	uc001rjt.1	+	c.880_splice	c.e8+1	p.E294_splice	DDX11_uc001rjr.1_Splice_Site_SNP_p.E294_splice|DDX11_uc001rjs.1_Splice_Site_SNP_p.E294_splice|DDX11_uc001rju.1_5'UTR|DDX11_uc001rjv.1_Splice_Site_SNP_p.E294_splice|DDX11_uc001rjw.1_Splice_Site_SNP_p.E268_splice|DDX11_uc001rjx.1_5'UTR|DDX11_uc009zjn.1_Intron	NM_152438	NP_689651			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)										Multiple Myeloma(12;0.14)			0.178571	7.289094	9.992247	5	23	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	31133692	31133692	4514	12	G	T	T	44	44	DDX11	T	5	3
ARHGAP9	64333	broad.mit.edu	36	12	56152584	56152584	+	Missense_Mutation	SNP	T	G	G			TCGA-32-1980-01	TCGA-32-1980-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:56152584T>G	uc001sod.1	-	c.2449A>C	c.(2449-2451)ACC>CCC	p.T817P	ARHGAP9_uc001sny.1_Non-coding_Transcript|ARHGAP9_uc001snz.1_Missense_Mutation_p.T543P|ARHGAP9_uc001soa.1_Missense_Mutation_p.T416P|ARHGAP9_uc001sob.1_3'UTR|ARHGAP9_uc001soc.1_Missense_Mutation_p.T727P	NM_032496	NP_115885	Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9 isoform 1	746	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			lung(1)	1														0.368421	7.912402	8.278799	7	12	TT		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(3;3.37e-34)		Missense_Mutation	SNP	56152584	56152584	903	12	T	G	G	59	59	ARHGAP9	G	4	4
PLXNA2	5362	broad.mit.edu	36	1	206338934	206338934	+	Missense_Mutation	SNP	G	C	C			TCGA-32-1980-01	TCGA-32-1980-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:206338934G>C	uc001hgz.1	-	c.1611C>G	c.(1609-1611)TGC>TGG	p.C537W		NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2	537	Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)	2														0.25	7.136199	8.117143	4	12	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(81;0.199)	Missense_Mutation	SNP	206338934	206338934	12546	1	G	C	C	34	34	PLXNA2	C	3	3
EPHA10	284656	broad.mit.edu	36	1	37999723	37999723	+	Missense_Mutation	SNP	A	C	C			TCGA-32-1980-01	TCGA-32-1980-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:37999723A>C	uc009vvi.1	-	c.791T>G	c.(790-792)GTG>GGG	p.V264G	EPHA10_uc001cbw.2_Missense_Mutation_p.V264G	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	264	Extracellular (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity			breast(3)|stomach(1)	4	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)								328				0.238095	7.286449	8.688764	5	16	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37999723	37999723	5359	1	A	C	C	6	6	EPHA10	C	4	4
TTN	7273	broad.mit.edu	36	2	179348409	179348409	+	Missense_Mutation	SNP	C	G	G			TCGA-32-1980-01	TCGA-32-1980-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179348409C>G	uc002umr.1	-	c.6427G>C	c.(6427-6429)GCT>CCT	p.A2143P	TTN_uc002ums.1_Missense_Mutation_p.A2097P|TTN_uc010frc.1_Missense_Mutation_p.A2097P|TTN_uc010frd.1_Missense_Mutation_p.A2097P|TTN_uc002unb.1_Missense_Mutation_p.A2143P	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2143										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.2	8.216112	9.471695	3	12	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179348409	179348409	17290	2	C	G	G	25	25	TTN	G	3	3
SDHA	6389	broad.mit.edu	36	5	309514	309514	+	Silent	SNP	G	C	C	rs1042446	by-frequency	TCGA-32-1980-01	TCGA-32-1980-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:309514G>C	uc003jao.2	+	c.1974G>C	c.(1972-1974)CCG>CCC	p.P658P	SDHA_uc003jap.2_Silent_p.P577P|SDHA_uc003jaq.2_Silent_p.P433P|SDHA_uc003jar.2_Silent_p.P252P	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,	658					nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0					Succinic acid(DB00139)									0.12766	9.719096	16.069597	6	41	GG		KEEP	---	---	---	---	capture	Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Silent	SNP	309514	309514	14448	5	G	C	C	38	38	SDHA	C	3	3
RADIL	55698	broad.mit.edu	36	7	4840776	4840776	+	Silent	SNP	G	C	C			TCGA-32-1980-01	TCGA-32-1980-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:4840776G>C	uc003snj.1	-	c.1404C>G	c.(1402-1404)CGC>CGG	p.R468R	RADIL_uc003sng.1_Non-coding_Transcript|RADIL_uc003sni.1_5'Flank	NM_018059	NP_060529	Q96JH8	RADIL_HUMAN	Rap GTPase interactor	468					cell adhesion|multicellular organismal development|signal transduction		protein binding			central_nervous_system(2)|pancreas(2)|breast(1)	5		Ovarian(82;0.0175)												0.3	7.019943	7.378064	3	7	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)	Silent	SNP	4840776	4840776	13457	7	G	C	C	38	38	RADIL	C	3	3
ZNF782	158431	broad.mit.edu	36	9	98621151	98621151	+	Silent	SNP	G	C	C			TCGA-32-1980-01	TCGA-32-1980-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:98621151G>C	uc004awp.1	-	c.975C>G	c.(973-975)CTC>CTG	p.L325L		NM_001001662	NP_001001662	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	325	C2H2-type 2; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0527)												0.119403	13.248534	22.777819	8	59	GG		KEEP	---	---	---	---	capture			Silent	SNP	98621151	98621151	18753	9	G	C	C	41	41	ZNF782	C	3	3
ZNF711	7552	broad.mit.edu	36	X	84406002	84406002	+	Missense_Mutation	SNP	T	G	G			TCGA-32-1980-01	TCGA-32-1980-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:84406002T>G	uc004eeq.1	+	c.688T>G	c.(688-690)TCA>GCA	p.S230A	ZNF711_uc004eeo.1_Missense_Mutation_p.S230A|ZNF711_uc004eep.1_Missense_Mutation_p.S230A	NM_021998	NP_068838	Q9Y462	ZN711_HUMAN	zinc finger protein 711	230					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|transcription regulator activity|zinc ion binding			ovary(3)	3														0.666667	6.55425	6.624757	2	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	84406002	84406002	18712	23	T	G	G	62	62	ZNF711	G	4	4
