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_WU	start_WU	stop_WU	reference_WU	variant_WU	type_WU	gene_name_WU	transcript_name_WU	transcript_species_WU	transcript_source_WU	transcript_version_WU	strand_WU	transcript_status_WU	trv_type_WU	c_position_WU	amino_acid_change_WU	ucsc_cons_WU	domain_WU	all_domains_WU	deletion_substructures_WU	transcript_error
ADAMTS7	0	genome.wustl.edu	37	15	79067099	79067099	+	Silent	SNP	G	G	C	rs142017909	byFrequency	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	15	79067099	79067099	G	C	SNP	ADAMTS7	NM_014272.3	human	genbank	58_37c	-1	reviewed	silent	c.1743	p.R581	0.974	HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat	"HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMPfam_Reprolysin,HMMPfam_Pep_M12B_propep,HMMPfam_ADAM_spacer1,superfamily_Metalloproteases (""zincins"") catalytic domain"	-	no_errors
AKD1	0	genome.wustl.edu	37	6	109906330	109906332	+	Splice_Site	DEL	CTT	CTT	-	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	CTT	CTT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	6	109906330	109906332	CTT	-	DEL	AKD1	ENST00000368948	human	ensembl	58_37c	-1	known	splice_site_del	c.2106+2_2106+1	e18+2	0.004:0.003:0.004	-	-	-	no_errors
ATM	0	genome.wustl.edu	37	11	108098605	108098605	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	11	108098605	108098605	G	T	SNP	ATM	NM_000051.3	human	genbank	58_37c	+1	reviewed	missense	c.175	p.A59S	1.000	NULL	HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,HMMPfam_FAT,HMMPfam_FATC,superfamily_Protein kinase-like (PK-like),superfamily_ARM repeat,PatternScan_PI3_4_KINASE_1,PatternScan_PI3_4_KINASE_2	-	no_errors
BTBD12	0	genome.wustl.edu	37	16	3656563	3656563	+	Missense_Mutation	SNP	C	C	A	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	16	3656563	3656563	C	A	SNP	BTBD12	NM_032444.2	human	genbank	58_37c	-1	provisional	missense	c.672	p.L224F	0.588	NULL	HMMSmart_SM00225,superfamily_POZ domain,HMMPfam_BTB	-	no_errors
C20orf117	0	genome.wustl.edu	37	20	35443694	35443694	+	Silent	SNP	C	C	A	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	20	35443694	35443694	C	A	SNP	C20orf117	NM_199181.2	human	genbank	58_37c	-1	validated	silent	c.1437	p.L479	0.938	NULL	NULL	-	no_errors
C6orf57	0	genome.wustl.edu	37	6	71298411	71298411	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	6	71298411	71298411	G	T	SNP	C6orf57	NM_145267.2	human	genbank	58_37c	+1	validated	missense	c.311	p.R104L	1.000	HMMPfam_DUF1674	HMMPfam_DUF1674	-	no_errors
CDH1	0	genome.wustl.edu	37	16	68857397	68857398	+	Frame_Shift_Ins	INS	-	-	T	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	16	68857397	68857398	-	T	INS	CDH1	NM_004360.3	human	genbank	58_37c	+1	reviewed	frame_shift_ins	c.2032_2033	p.T679fs	1.000:1.000	HMMPfam_Cadherin,superfamily_Cadherin-like	HMMPfam_Cadherin_C,HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_pro,superfamily_Cadherin-like	-	no_errors
ENSG00000210107	0	genome.wustl.edu	37	MT	4396	4396	+	RNA	SNP	T	T	C	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	MT	4396	4396	T	C	SNP	ENSG00000210107	ENST00000387372	human	ensembl	58_37c	-1	novel	rna	NULL	NULL	NULL	-	-	-	no_errors
ENSG00000250881	0	genome.wustl.edu	37	X	117578556	117578562	+	RNA	DEL	TTTCTTT	TTTCTTT	-	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	TTTCTTT	TTTCTTT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	X	117578556	117578562	TTTCTTT	-	DEL	ENSG00000250881	ENST00000504917	human	ensembl	58_37c	-1	novel	rna	NULL	NULL	0.019:0.011:0.012:0.013:0.016:0.027:0.006	-	-	-	no_errors
FAM153A	0	genome.wustl.edu	37	5	177171957	177171957	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	5	177171957	177171957	G	A	SNP	FAM153A	NM_173663.3	human	genbank	58_37c	-1	predicted	missense	c.40	p.R14W	0.012	NULL	NULL	-	no_errors
FGFR3	0	genome.wustl.edu	37	4	1809128	1809129	+	Splice_Site	DEL	GT	GT	-	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	GT	GT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	4	1809128	1809129	GT	-	DEL	FGFR3	ENST00000312875	human	ensembl	58_37c	+1	known	splice_site_del	c.243+1_243+1	e2+1	0.041:0.000	-	-	-	no_start_codon
FRG1B	0	genome.wustl.edu	37	20	29632643	29632643	+	Missense_Mutation	SNP	T	T	C	rs143379667	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	20	29632643	29632643	T	C	SNP	FRG1B	ENST00000278882	human	ensembl	58_37c	+1	known	missense	c.458	p.L153P	1.000	HMMPfam_FRG1	superfamily_Actin_crosslink,HMMPfam_FRG1	-	no_errors
GPNMB	0	genome.wustl.edu	37	7	23309653	23309653	+	Missense_Mutation	SNP	A	A	C	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	7	23309653	23309653	A	C	SNP	GPNMB	NM_001005340.1	human	genbank	58_37c	+1	reviewed	missense	c.1324	p.S442R	0.036	NULL	HMMPfam_PKD,HMMSmart_SM00089,superfamily_PKD domain	-	no_errors
GSR	0	genome.wustl.edu	37	8	30557645	30557645	+	Silent	SNP	G	G	A	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	8	30557645	30557645	G	A	SNP	GSR	NM_000637.2	human	genbank	58_37c	-1	validated	silent	c.648	p.S216	0.754	HMMPfam_Pyr_redox_2,superfamily_FAD/NAD(P)-binding domain	HMMPfam_Pyr_redox_dim,PatternScan_PYRIDINE_REDOX_1,HMMPfam_Pyr_redox_2,superfamily_FAD/NAD-linked reductases dimerisation (C-terminal) domain,superfamily_FAD/NAD(P)-binding domain	-	no_errors
HLA-DQB2	0	genome.wustl.edu	37	6	32725653	32725653	+	Silent	SNP	C	C	T	rs144961216	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	6	32725653	32725653	C	T	SNP	HLA-DQB2	ENST00000435145	human	ensembl	58_37c	-1	known	silent	c.654	p.Q218	0.998	superfamily_SSF48726	HMMPfam_MHC_II_beta,PatternScan_IG_MHC,HMMPfam_C1-set,HMMSmart_IGc1,superfamily_MHC_I/II-like_Ag-recog,superfamily_SSF48726	-	no_errors
KDM6B	0	genome.wustl.edu	37	17	7751859	7751861	+	In_Frame_Del	DEL	CAC	CAC	-	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	CAC	CAC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	17	7751859	7751861	CAC	-	DEL	KDM6B	NM_001080424.1	human	genbank	58_37c	+1	provisional	in_frame_del	c.2253_2255	p.T755in_frame_del	0.000:0.006:0.963	NULL	HMMSmart_SM00558,HMMPfam_JmjC	-	no_errors
LOC643677	0	genome.wustl.edu	37	13	103392396	103392396	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	13	103392396	103392396	G	T	SNP	LOC643677	XM_002344085.1	human	genbank	58_37c	-1	model	missense	c.10438	p.Q3480K	0.001	NULL	NULL	-	no_errors
LOC730257	0	genome.wustl.edu	37	1	144519342	144519343	+	RNA	INS	-	-	A	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	1	144519342	144519343	-	A	INS	LOC730257	XR_078229.1	human	genbank	58_37c	+1	model	rna	NULL	NULL	0.011:0.352	-	-	-	pseudogene
MST1P9	0	genome.wustl.edu	37	1	17087542	17087546	+	Splice_Site	DEL	GTGCT	GTGCT	-	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	GTGCT	GTGCT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	1	17087542	17087546	GTGCT	-	DEL	MST1P9	ENST00000389184	human	ensembl	58_37c	-1	known	splice_site_del	c.NULL	NULL	0.993:0.992:0.992:0.992:0.993	-	-	-	no_coding_region:pseudogene
NUP214	0	genome.wustl.edu	37	9	134027158	134027158	+	Silent	SNP	T	T	G	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	9	134027158	134027158	T	G	SNP	NUP214	NM_005085.2	human	genbank	58_37c	+1	reviewed	silent	c.2313	p.T771	0.000	NULL	HMMSmart_SM00320,superfamily_WD40 repeat-like	-	no_errors
OPN4	0	genome.wustl.edu	37	10	88421081	88421081	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	10	88421081	88421081	G	A	SNP	OPN4	NM_001030015.2	human	genbank	58_37c	+1	validated	missense	c.1042	p.V348I	0.995	HMMPfam_7tm_1,PatternScan_OPSIN,superfamily_SSF81321	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,PatternScan_OPSIN,superfamily_SSF81321	-	no_errors
TAS2R38	0	genome.wustl.edu	37	7	141672880	141672880	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	7	141672880	141672880	G	T	SNP	TAS2R38	NM_176817.4	human	genbank	58_37c	-1	reviewed	missense	c.610	p.P204T	0.000	HMMPfam_TAS2R,superfamily_SSF81321	HMMPfam_TAS2R,superfamily_SSF81321	-	no_errors
TBX5	0	genome.wustl.edu	37	12	114793417	114793417	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	12	114793417	114793417	C	T	SNP	TBX5	NM_000192.3	human	genbank	58_37c	-1	reviewed	missense	c.1477	p.V493M	0.986	NULL	HMMPfam_T-box,HMMSmart_SM00425,superfamily_p53-like transcription factors,PatternScan_TBOX_2,PatternScan_TBOX_1	-	no_errors
TNRC6C	0	genome.wustl.edu	37	17	76089144	76089144	+	Nonsense_Mutation	SNP	G	G	A	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	17	76089144	76089144	G	A	SNP	TNRC6C	NM_001142640.1	human	genbank	58_37c	+1	validated	nonsense	c.4092	p.W1364*	1.000	NULL	HMMPfam_UBA,HMMPfam_RRM_1,superfamily_UBA-like,HMMSmart_SM00165,HMMPfam_Ago_hook,superfamily_RNA-binding domain RBD	-	no_errors
TSC22D1	0	genome.wustl.edu	37	13	45010182	45010182	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	13	45010182	45010182	T	C	SNP	TSC22D1	NM_183422.2	human	genbank	58_37c	-1	validated	missense	c.2962	p.M988V	1.000	HMMPfam_TSC22,PatternScan_TSC22	HMMPfam_TSC22,PatternScan_TSC22	-	no_errors
