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
GFI1	2672	broad.mit.edu	37	1	92941764	92941764	+	Missense_Mutation	SNP	C	T	T			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr1:92941764C>T	uc001dou.3	-	7	1255	c.1091G>A	c.(1090-1092)GGT>GAT	p.G364D	GFI1_uc001dov.3_Missense_Mutation_p.G364D|GFI1_uc001dow.3_Missense_Mutation_p.G364D	NM_001127215	NP_001120687	Q99684	GFI1_HUMAN	growth factor independent 1	364					negative regulation of calcidiol 1-monooxygenase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription involved in G1/S phase of mitotic cell cycle|transcription, DNA-dependent|viral reproduction	nucleus	protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(1)	1		all_lung(203;0.00292)|Lung NSC(277;0.0115)|all_neural(321;0.185)|Glioma(108;0.203)		OV - Ovarian serous cystadenocarcinoma(397;9.04e-07)|Epithelial(280;1.17e-05)|all cancers(265;5.61e-05)|GBM - Glioblastoma multiforme(16;0.0191)		AGGCTTCTCACCTGTGGGGAT	0.582000													4	21	---	---	---		0	0	0.009096	0	0
MOV10	4343	broad.mit.edu	37	1	113234306	113234306	+	Nonsense_Mutation	SNP	G	T	T			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr1:113234306G>T	uc001eck.2	+	6	1126	c.856G>T	c.(856-858)GAG>TAG	p.E286*	MOV10_uc001ecl.2_Nonsense_Mutation_p.E286*|MOV10_uc001ecn.2_Nonsense_Mutation_p.E286*|MOV10_uc001ecm.2_Nonsense_Mutation_p.E226*|MOV10_uc009wgj.1_Nonsense_Mutation_p.E226*	NM_001130079	NP_001123551	Q9HCE1	MOV10_HUMAN	Mov10, Moloney leukemia virus 10, homolog	286					mRNA cleavage involved in gene silencing by miRNA|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body	ATP binding|helicase activity|protein binding|RNA binding			ovary(4)|skin(1)	5	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		CTATGACCTGGAGTTAAGTAT	0.557000													66	79	---	---	---		7.05995e-25	8.34358e-25	0.048971	1	0
GBF1	8729	broad.mit.edu	37	10	104139192	104139192	+	Splice_Site	SNP	G	A	A			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr10:104139192G>A	uc001kux.1	+	34	4882	c.4642_splice	c.e34+1	p.G1548_splice	GBF1_uc001kuy.1_Splice_Site_p.G1544_splice|GBF1_uc001kuz.1_Splice_Site_p.G1545_splice	NM_004193	NP_004184	Q92538	GBF1_HUMAN	golgi-specific brefeldin A resistant guanine						COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		TTACTGCAGGGTAAACCAGGA	0.582000													3	55	---	---	---		0	0	0.004672	0	0
LOC650368	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	T	T			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr11:3427845C>T	uc010qxs.1	+	9		c.838C>T			LOC650368_uc001lxx.2_RNA|LOC650368_uc001lxy.2_RNA	NR_024248				Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						CTTCAAGTGGCAGGAGCAGAA	0.587000													4	72	---	---	---		0	0	0.009096	0	0
Unknown	0	broad.mit.edu	37	15	25425564	25425564	+	5'Flank	SNP	C	T	T			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr15:25425564C>T	uc001yyy.1	+						uc001yza.1_5'Flank|uc001yys.1_RNA|SNORD115-7_uc001yyw.1_RNA|SNORD115-6_uc001yyx.1_5'Flank|SNORD115-7_uc001yyz.2_5'Flank					Homo sapiens clone Rt-7 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.																		TTCCTGGCATCCTGGTCTCCT	0.597000													38	60	---	---	---		0	0	0.064281	0	0
GOLGA6L10	647042	broad.mit.edu	37	15	82635117	82635117	+	RNA	SNP	T	C	C			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr15:82635117T>C	uc002bgx.2	-	5		c.463A>G						A6NI86	GG6LA_HUMAN	Homo sapiens cDNA FLJ40113 fis, clone TESTI2008621.												0						TTTTTCAATTTCTTGACCCGC	0.383000													3	15	---	---	---		0	0	0.009096	0	0
UBE2Q2P1	388165	broad.mit.edu	37	15	85085493	85085493	+	RNA	SNP	C	T	T			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr15:85085493C>T	uc002bkn.1	-	4		c.1476G>A				NR_003661				Homo sapiens cDNA FLJ43276 fis, clone KIDNE2011532, moderately similar to Homo sapiens melanoma-associated chondroitin sulfate proteoglycan 4.												0						TTTCATCTCACAGTGATCTAA	0.358000													3	11	---	---	---		0	0	0.004672	0	0
Unknown	0	broad.mit.edu	37	17	39296152	39296152	+	RNA	SNP	A	G	G			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr17:39296152A>G	uc010cxk.1	-	1		c.552T>C								Homo sapiens partial mRNA for keratin associated protein 4.6 (KRTAP4.6 gene).																		AGCACAAGGGACGGGGGCAGG	0.507000													2	9	---	---	---		0	0	0.004672	0	0
GNA15	2769	broad.mit.edu	37	19	3151776	3151776	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr19:3151776G>A	uc002lxf.2	+	4	815	c.557G>A	c.(556-558)CGC>CAC	p.R186H		NM_002068	NP_002059	P30679	GNA15_HUMAN	guanine nucleotide binding protein (G protein),	186	GTP (By similarity).				activation of phospholipase C activity by dopamine receptor signaling pathway|activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			skin(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.04e-05)|OV - Ovarian serous cystadenocarcinoma(105;5.08e-113)|Epithelial(107;6.19e-111)|all cancers(105;6.19e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00145)|STAD - Stomach adenocarcinoma(1328;0.184)		CTCCGCAGCCGCATGCCCACC	0.532000													4	166	---	---	---		0	0	0.009096	0	0
XRCC6	2547	broad.mit.edu	37	22	42052945	42052945	+	Missense_Mutation	SNP	A	G	G			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr22:42052945A>G	uc003bao.1	+	10	1400	c.1330A>G	c.(1330-1332)AGG>GGG	p.R444G	XRCC6_uc003bap.1_Missense_Mutation_p.R403G|XRCC6_uc011apc.1_Missense_Mutation_p.R394G|XRCC6_uc003baq.1_Missense_Mutation_p.R444G|XRCC6_uc003bar.1_Missense_Mutation_p.R444G|XRCC6_uc003bas.1_Missense_Mutation_p.R394G	NM_001469	NP_001460	P12956	XRCC6_HUMAN	ATP-dependent DNA helicase II, 70 kDa subunit	444	Ku.				DNA ligation|double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|provirus integration|telomere maintenance|transcription, DNA-dependent	DNA-dependent protein kinase-DNA ligase 4 complex|Ku70:Ku80 complex|membrane fraction|nuclear telomere cap complex|transcription factor complex	5'-deoxyribose-5-phosphate lyase activity|ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|transcription regulatory region DNA binding			skin(2)|ovary(1)|lung(1)|kidney(1)	5						TGATGATAAAAGGAAGATGCC	0.403000								Direct_reversal_of_damage|NHEJ					3	69	---	---	---		0	0	0.009096	0	0
LRP2BP	55805	broad.mit.edu	37	4	186295505	186295505	+	Silent	SNP	T	C	C			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr4:186295505T>C	uc003ixj.1	-	4	1253	c.441A>G	c.(439-441)AAA>AAG	p.K147K	LRP2BP_uc003ixk.1_Silent_p.K121K|LRP2BP_uc011ckr.1_Silent_p.K147K	NM_018409	NP_060879	Q9P2M1	LR2BP_HUMAN	LRP2 binding protein	147	Sel1-like 2.					cytoplasm	protein binding				0		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;2.14e-25)|Epithelial(43;1.55e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-11)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000766)|Colorectal(24;0.00116)|LUSC - Lung squamous cell carcinoma(40;0.00904)|COAD - Colon adenocarcinoma(29;0.0101)|READ - Rectum adenocarcinoma(43;0.161)		GTTTAACACCTTTTCCTTCAT	0.383000													3	132	---	---	---		0	0	0.004672	0	0
FOXP4	116113	broad.mit.edu	37	6	41557797	41557797	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr6:41557797G>A	uc003oql.2	+	11	1704	c.1246G>A	c.(1246-1248)GCA>ACA	p.A416T	FOXP4_uc003oqm.2_Missense_Mutation_p.A414T|FOXP4_uc003oqn.2_Missense_Mutation_p.A403T	NM_001012426	NP_001012426	Q8IVH2	FOXP4_HUMAN	forkhead box P4 isoform 1	416					embryonic foregut morphogenesis|heart development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			breast(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)					GACCTCGGCCGCAGCCCCTGT	0.672000													3	49	---	---	---		0	0	0.004672	0	0
BRAF	673	broad.mit.edu	37	7	140453134	140453134	+	Missense_Mutation	SNP	T	C	C	rs121913377		TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr7:140453134T>C	uc003vwc.3	-	15	1862	c.1801A>G	c.(1801-1803)AAA>GAA	p.K601E		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	601	Protein kinase.		K -> Q (in CFC syndrome).|K -> E (in colorectal cancer).		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.K601E(47)|p.V600_K601>E(8)|p.K601N(7)|p.K601del(4)|p.K601Q(3)|p.T599_R603>I(2)|p.V600_W604del(1)|p.K601K(1)|p.K601L(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.K601I(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)	CATCGAGATTTCACTGTAGCT	0.368000		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				43	66	---	---	---		0	0	0.045515	0	0
IDO1	3620	broad.mit.edu	37	8	39775722	39775722	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr8:39775722G>A	uc003xnm.2	+	3	413	c.299G>A	c.(298-300)CGT>CAT	p.R100H	IDO1_uc003xnn.2_RNA	NM_002164	NP_002155	P14902	I23O1_HUMAN	indoleamine 2,3-dioxygenase 1	100					female pregnancy|tryptophan catabolic process	cytosol	electron carrier activity|heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			central_nervous_system(2)	2					L-Tryptophan(DB00150)	GGAGATGTCCGTAAGGTTTGG	0.393000													4	111	---	---	---		0	0	0.009096	0	0
ATAD2	29028	broad.mit.edu	37	8	124361593	124361593	+	Missense_Mutation	SNP	T	C	C			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr8:124361593T>C	uc003yqh.3	-	14	1846	c.1738A>G	c.(1738-1740)ATA>GTA	p.I580V	ATAD2_uc011lii.1_Missense_Mutation_p.I371V|ATAD2_uc003yqi.3_RNA|ATAD2_uc003yqj.2_Missense_Mutation_p.I580V|MIR548D1_hsa-mir-548d-1|MI0003668_5'Flank	NM_014109	NP_054828	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	580					regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			GCAGGATCTATAGAATCTAGC	0.408000													4	156	---	---	---		0	0	0.009096	0	0
ZNF169	169841	broad.mit.edu	37	9	97063304	97063304	+	Silent	SNP	C	T	T			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr9:97063304C>T	uc004aum.1	+	5	1569	c.1464C>T	c.(1462-1464)TGC>TGT	p.C488C		NM_194320	NP_919301	Q14929	ZN169_HUMAN	zinc finger protein 169	488	C2H2-type 10.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)				CTTATCTGTGCCCCAAGTGTG	0.562000													34	45	---	---	---		0	0	0.086207	0	0
MAGEE1	57692	broad.mit.edu	37	X	75648746	75648746	+	Silent	SNP	G	A	A			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chrX:75648746G>A	uc004ecm.1	+	1	630	c.423G>A	c.(421-423)CCG>CCA	p.P141P		NM_020932	NP_065983	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	141	Pro-rich.					dendrite|nucleus|perinuclear region of cytoplasm|postsynaptic membrane				breast(3)|ovary(1)|pancreas(1)|skin(1)	6						CCTCCAGGCCGCCCACTTCCT	0.677000													3	50	---	---	---		0	0	0.004672	0	0
Unknown	0	broad.mit.edu	37	1	5248310	5248312	+	IGR	DEL	GAG	-	-			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr1:5248310_5248312delGAG								AJAP1 (404460 upstream) : NPHP4 (674558 downstream)																							ggaggaggaagaggaggaggagg	0.271													3	5	---	---	---	---					
Unknown	0	broad.mit.edu	37	10	42387774	42387774	+	IGR	DEL	C	-	-	rs141701904		TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr10:42387774delC								None (None upstream) : LOC441666 (439541 downstream)																							aatcattgaacggaattgaat	0.000													7	328	---	---	---	---					
Unknown	0	broad.mit.edu	37	10	42597165	42597165	+	IGR	DEL	G	-	-			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr10:42597165delG								None (None upstream) : LOC441666 (230150 downstream)																							ggaatcgaatggaatcatcat	0.020													8	889	---	---	---	---					
TPTE2	93492	broad.mit.edu	37	13	20041394	20041394	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr13:20041394delA	uc001umd.2	-	8	694	c.483delT	c.(481-483)TTTfs	p.F161fs	TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Intron|TPTE2_uc001ume.2_Intron|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_RNA	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	161	Helical; (Potential).					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		ACTTAATGTCAAAAAAAATGT	0.303													7	114	---	---	---	---					
Unknown	0	broad.mit.edu	37	15	20508055	20508056	+	IGR	INS	-	GCCCT	GCCCT	rs138742206	by1000genomes	TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr15:20508055_20508056insGCCCT								None (None upstream) : GOLGA6L6 (229038 downstream)																							ccctggccccggccctgccctg	0.243													4	3	---	---	---	---					
Unknown	0	broad.mit.edu	37	15	22500352	22500353	+	IGR	INS	-	G	G			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr15:22500352_22500353insG								OR4N3P (85967 upstream) : MIR1268 (12876 downstream)																							TGGCGGGACCAGGGTGGGACCA	0.510													5	2	---	---	---	---					
Unknown	0	broad.mit.edu	37	17	26603003	26603003	+	IGR	DEL	T	-	-			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr17:26603003delT								PPY2 (27689 upstream) : FLJ40504 (605 downstream)																							tttttttttctttttttttAA	0.328													2	4	---	---	---	---					
TSHZ3	57616	broad.mit.edu	37	19	31840398	31840400	+	5'Flank	DEL	GAG	-	-			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr19:31840398_31840400delGAG	uc002nsy.3	-							NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537						negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)					ggaggaggcagaggaggaggagg	0.512													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	21	10862646	10862646	+	IGR	DEL	T	-	-			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr21:10862646delT								None (None upstream) : TPTE (44097 downstream)																							GAGGATCCTGTTTTTGGTGGT	0.512													7	719	---	---	---	---					
Unknown	0	broad.mit.edu	37	21	47474920	47474920	+	IGR	DEL	C	-	-			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr21:47474920delC								COL6A1 (49957 upstream) : COL6A2 (43113 downstream)																							ccctgcacagccccctccctc	0.055													5	6	---	---	---	---					
CXCL5	6374	broad.mit.edu	37	4	74864215	74864217	+	In_Frame_Del	DEL	CAG	-	-	rs139966143		TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr4:74864215_74864217delCAG	uc003hhk.2	-	1	200_202	c.82_84delCTG	c.(82-84)CTGdel	p.L28del		NM_002994	NP_002985	P42830	CXCL5_HUMAN	chemokine (C-X-C motif) ligand 5 precursor	28					cell-cell signaling|chemotaxis|immune response|positive regulation of cell proliferation|signal transduction	extracellular space	chemokine activity				0	Breast(15;0.00136)		all cancers(17;0.00273)|Lung(101;0.196)			CTGGCTGCGTCAGCAGCAGCAGC	0.700													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	9	68426353	68426353	+	IGR	DEL	G	-	-			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr9:68426353delG								FAM27B (632164 upstream) : MIR1299 (575886 downstream)																							TCTTGAAGGCGGTGTTCCTCA	0.313													4	4	---	---	---	---					
