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	chromosome_name	start	stop	reference	variant	type	gene_name	transcript_name	transcript_species	transcript_source	transcript_version	strand	transcript_status	trv_type	c_position	amino_acid_change	ucsc_cons	domain	all_domains	deletion_substructures	transcript_error
ANKRD13B	124930	broad.mit.edu	36	17	24961842	24961842	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	17	24961842	24961842	C	G	SNP	ANKRD13B	NM_152345	human	genbank	54_36p	1	validated	missense	c.836	p.S279C	1	NULL	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat,HMMPfam_UIM,HMMSmart_SM00726	-	no_errors
C4orf23	152992	broad.mit.edu	36	4	8528564	8528564	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	4	8528564	8528564	C	T	SNP	C4orf23	NM_152544	human	genbank	54_36p	1	predicted	missense	c.1034	p.P345L	1	NULL	HMMPfam_AdoMet_MTase	-	no_errors
COL11A2	1302	broad.mit.edu	36	6	33249789	33249789	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	6	33249789	33249789	G	A	SNP	COL11A2	NM_080680	human	genbank	54_36p	-1	reviewed	missense	c.2506	p.P836S	1	HMMPfam_Collagen	HMMPfam_COLFI,HMMSmart_SM00038,HMMSmart_SM00282,HMMSmart_SM00210,HMMPfam_Collagen,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2	-	no_errors
FARSA	2193	broad.mit.edu	36	19	12900613	12900613	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	19	12900613	12900613	G	T	SNP	FARSA	NM_004461	human	genbank	54_36p	-1	validated	missense	c.552	p.S184R	0.26	NULL	HMMPfam_tRNA-synt_2d,superfamily_Winged helix DNA-binding domain,superfamily_Class II aaRS and biotin synthetases	-	no_errors
GPR132	29933	broad.mit.edu	36	14	104589067	104589067	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	14	104589067	104589067	C	T	SNP	GPR132	NM_013345	human	genbank	54_36p	-1	reviewed	missense	c.452	p.R151Q	0.01	superfamily_Family A G protein-coupled receptor-like,HMMPfam_7tm_1	superfamily_Family A G protein-coupled receptor-like,HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1	-	no_errors
HSPG2	3339	broad.mit.edu	36	1	22095357	22095357	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	1	22095357	22095357	A	G	SNP	HSPG2	NM_005529	human	genbank	54_36p	-1	validated	missense	c.97	p.S33P	0.7	NULL	HMMPfam_Laminin_B,HMMPfam_SEA,HMMSmart_SM00200,HMMSmart_SM00282,HMMSmart_SM00179,HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,superfamily_LDL receptor-like module,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_1,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,HMMSmart_SM00281,superfamily_Immunoglobulin,superfamily_EGF/Laminin	-	no_errors
LRP1B	53353	broad.mit.edu	36	2	140918674	140918674	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	2	140918674	140918674	G	A	SNP	LRP1B	NM_018557	human	genbank	54_36p	-1	validated	missense	c.10102	p.L3368F	0.99	HMMPfam_Ldl_recept_a,HMMSmart_LDLa,superfamily_LDL_rcpt_classA_cys-rich	HMMPfam_Ldl_recept_b,HMMSmart_LY,PatternScan_ASX_HYDROXYL,HMMPfam_NHL,HMMSmart_EGF_CA,HMMPfam_Ldl_recept_a,HMMSmart_LDLa,PatternScan_LDLRA_1,superfamily_LDL_rcpt_classA_cys-rich,HMMPfam_EGF,HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,superfamily_SSF57196,superfamily_SSF63825	-	no_errors
MAP3K1	4214	broad.mit.edu	36	5	56217522	56217522	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	5	56217522	56217522	C	T	SNP	MAP3K1	NM_005921	human	genbank	54_36p	1	validated	missense	c.3989	p.S1330L	1	superfamily_Kinase_like,HMMSmart_S_TKc,HMMPfam_Pkinase	PatternScan_ZF_RING_1,HMMPfam_SWIM,superfamily_SSF57850,HMMSmart_RING,superfamily_Kinase_like,HMMSmart_S_TKc,HMMPfam_Pkinase,PatternScan_PROTEIN_KINASE_ATP,PatternScan_PROTEIN_KINASE_ST	-	no_errors
MED12L	116931	broad.mit.edu	36	3	152588602	152588602	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	3	152588602	152588602	G	T	SNP	MED12L	NM_053002	human	genbank	54_36p	1	validated	missense	c.5298	p.K1766N	1	NULL	HMMPfam_Med12	-	no_errors
MYH1	4619	broad.mit.edu	36	17	10339040	10339040	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	17	10339040	10339040	C	T	SNP	MYH1	NM_005963	human	genbank	54_36p	-1	reviewed	missense	c.5399	p.R1800H	1	HMMPfam_Myosin_tail_1	HMMPfam_IQ,HMMSmart_IQ,HMMPfam_Myosin_head,HMMSmart_MYSc,HMMPfam_Myosin_tail_1,HMMPfam_Myosin_N,superfamily_SSF52540	-	no_errors
PIGA	5277	broad.mit.edu	36	X	15259426	15259426	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	X	15259426	15259426	C	T	SNP	PIGA	NM_002641	human	genbank	54_36p	-1	reviewed	missense	c.548	p.C183Y	1	superfamily_UDP-Glycosyltransferase/glycogen phosphorylase	superfamily_UDP-Glycosyltransferase/glycogen phosphorylase,HMMPfam_PIGA,HMMPfam_Glycos_transf_1	-	no_errors
RERG	85004	broad.mit.edu	36	12	15153377	15153377	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	12	15153377	15153377	C	T	SNP	RERG	NM_032918	human	genbank	54_36p	-1	provisional	silent	c.534	p.R178	1	superfamily_P-loop containing nucleoside triphosphate hydrolases	superfamily_P-loop containing nucleoside triphosphate hydrolases,HMMSmart_SM00173,HMMSmart_SM00175,HMMPfam_Ras,HMMSmart_SM00174	-	no_errors
RTP3	83597	broad.mit.edu	36	3	46517046	46517046	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	3	46517046	46517046	C	T	SNP	RTP3	NM_031440	human	genbank	54_36p	1	provisional	silent	c.352	p.L118	0.94	NULL	NULL	-	no_errors
SUPT6H	6830	broad.mit.edu	36	17	24030025	24030025	+	Silent	SNP	T	T	G	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	17	24030025	24030025	T	G	SNP	SUPT6H	NM_003170	human	genbank	54_36p	1	validated	silent	c.1266	p.A422	1	NULL	HMMPfam_Tex_N,HMMSmart_SM00732,superfamily_Nucleic acid-binding proteins,HMMSmart_SM00316,HMMPfam_S1,superfamily_SH2 domain,HMMSmart_SM00252	-	no_errors
TP53	7157	broad.mit.edu	36	17	7518288	7518296	+	In_Frame_Del	DEL	TGTTACACA	TGTTACACA	-	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	TGTTACACA	TGTTACACA	TGTTACACA	-	TGTTACACA	TGTTACACA	Unknown	Valid	Somatic	Phase_I	Capture	Sanger_PCR_WGA			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	17	7518288	7518296	TGTTACACA	-	DEL	TP53	NM_000546	human	genbank	54_36p	-1	reviewed	in_frame_del	c.718_710	p.MCN237in_frame_del	1.000:1.000:1.000:1.000:0.999:1.000:1.000:1.000:1.000	PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53	PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD	(deletion:cds_exon[7518224,7518333])	no_errors
USP21	27005	broad.mit.edu	36	1	159397442	159397442	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	1	159397442	159397442	C	T	SNP	USP21	NM_001014443	human	genbank	54_36p	1	reviewed	missense	c.388	p.R130C	0.96	NULL	superfamily_Cysteine proteinases,HMMPfam_UCH,PatternScan_UCH_2_1,PatternScan_UCH_2_2	-	no_errors
WNT2	7472	broad.mit.edu	36	7	116742442	116742442	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	7	116742442	116742442	G	A	SNP	WNT2	NM_003391	human	genbank	54_36p	-1	reviewed	silent	c.507	p.R169	0.98	HMMPfam_wnt,HMMSmart_SM00097	HMMPfam_wnt,HMMSmart_SM00097,PatternScan_WNT1	-	no_errors
ZNF140	7699	broad.mit.edu	36	12	132169760	132169760	+	Splice_Site	SNP	A	A	C	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	12	132169760	132169760	A	C	SNP	ZNF140	NM_003440	human	genbank	54_36p	1	validated	splice_site	c.10-2	e2-2	0.99	-	-	-	no_errors
ZNF717	401074	broad.mit.edu	36	3	75869508	75869516	+	Intron	DEL	ACATTCATT	-	ACATTCATT	novel	Unknown	TCGA-61-2088-01A-01W-0722-08	TCGA-61-2088-11A-01W-0722-08	ACATTCATT	ACATTCATT					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	4c6653f9-1392-4ce5-8da0-ccbe33a02c21	bfa13152-b083-4497-90e1-580eda689b62	3	75869508	75869516	ACATTCATT	-	DEL	LOC401074	XM_001714392	human	genbank	54_36p	1	model	intronic	c.961-2926_961-2918	e4-2918	0.996:0.997:0.958:0.251:0.222:0.116:0.000:0.001:0.007	-	-	(deletion:intron[75804611,75872433])	no_errors
