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	patient	dataset	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context
ZNF644	84146	broad.mit.edu	36	1	91178903	91178904	+	Missense_Mutation	DNP	GA	GA	TT	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	DNP	91178903	91178904	ZNF644	1	GA	GA	TT	45
HMCN1	83872	broad.mit.edu	36	1	184326562	184326562	+	Silent	SNP	T	T	C	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Silent	SNP	184326562	184326562	HMCN1	1	T	T	C	62
TP53BP2	7159	broad.mit.edu	36	1	222052709	222052709	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Silent	SNP	222052709	222052709	TP53BP2	1	G	G	A	43
VN1R5	317705	broad.mit.edu	36	1	245486694	245486694	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	245486694	245486694	VN1R5	1	C	C	T	24
NUDT5	11164	broad.mit.edu	36	10	12252907	12252907	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	12252907	12252907	NUDT5	10	C	C	A	30
RUFY2	55680	broad.mit.edu	36	10	69775776	69775776	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	69775776	69775776	RUFY2	10	C	C	G	32
LRRC55	219527	broad.mit.edu	36	11	56706465	56706465	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Silent	SNP	56706465	56706465	LRRC55	11	C	C	T	17
FOSL1	8061	broad.mit.edu	36	11	65421052	65421052	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	65421052	65421052	FOSL1	11	T	T	C	56
SSH3	54961	broad.mit.edu	36	11	66831958	66831958	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	66831958	66831958	SSH3	11	G	G	T	36
CNTN1	1272	broad.mit.edu	36	12	39623793	39623793	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	39623793	39623793	CNTN1	12	G	G	C	35
SILV	6490	broad.mit.edu	36	12	54646039	54646039	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	54646039	54646039	SILV	12	G	G	C	42
PEBP1	5037	broad.mit.edu	36	12	117060263	117060263	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	117060263	117060263	PEBP1	12	C	C	G	32
ATP12A	479	broad.mit.edu	36	13	24162510	24162510	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	24162510	24162510	ATP12A	13	C	C	A	18
DDHD1	80821	broad.mit.edu	36	14	52640269	52640269	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Silent	SNP	52640269	52640269	DDHD1	14	C	C	T	28
KIAA1409	57578	broad.mit.edu	36	14	93148948	93148948	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Silent	SNP	93148948	93148948	KIAA1409	14	C	C	T	19
FES	2242	broad.mit.edu	36	15	89229808	89229808	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	89229808	89229808	FES	15	G	G	C	41
TP53	7157	broad.mit.edu	36	17	7519131	7519131	+	Missense_Mutation	SNP	C	C	T	rs28934578	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	7519131	7519131	TP53	17	C	C	T	27
IKZF3	22806	broad.mit.edu	36	17	35175946	35175946	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	35175946	35175946	IKZF3	17	C	C	G	31
FADS6	283985	broad.mit.edu	36	17	70386174	70386175	+	Missense_Mutation	DNP	GT	GT	CG	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	DNP	70386174	70386175	FADS6	17	GT	GT	CG	40
TYK2	7297	broad.mit.edu	36	19	10324642	10324643	+	Missense_Mutation	DNP	AC	AC	GG	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	DNP	10324642	10324643	TYK2	19	AC	AC	GG	14
TMEM38A	79041	broad.mit.edu	36	19	16651828	16651828	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	16651828	16651828	TMEM38A	19	C	C	T	27
RELB	5971	broad.mit.edu	36	19	50217161	50217161	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	50217161	50217161	RELB	19	G	G	A	48
MATN3	4148	broad.mit.edu	36	2	20069530	20069530	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	20069530	20069530	MATN3	2	C	C	A	21
RASGRP3	25780	broad.mit.edu	36	2	33622158	33622158	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	33622158	33622158	RASGRP3	2	T	T	C	64
ITPRIPL1	150771	broad.mit.edu	36	2	96357578	96357578	+	Silent	SNP	C	C	G	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Silent	SNP	96357578	96357578	ITPRIPL1	2	C	C	G	29
ANKZF1	55139	broad.mit.edu	36	2	219806811	219806811	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	219806811	219806811	ANKZF1	2	G	G	T	43
MYH7B	57644	broad.mit.edu	36	20	33032158	33032158	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	33032158	33032158	MYH7B	20	A	A	G	16
TH1L	51497	broad.mit.edu	36	20	56999478	56999478	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	56999478	56999478	TH1L	20	G	G	A	40
SLC17A9	63910	broad.mit.edu	36	20	61067431	61067431	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	61067431	61067431	SLC17A9	20	G	G	A	40
MKL1	57591	broad.mit.edu	36	22	39155704	39155704	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Silent	SNP	39155704	39155704	MKL1	22	C	C	T	28
L3MBTL2	83746	broad.mit.edu	36	22	39942158	39942158	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	39942158	39942158	L3MBTL2	22	C	C	A	24
NKTR	4820	broad.mit.edu	36	3	42662461	42662462	+	Missense_Mutation	DNP	GA	GA	TC	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	DNP	42662461	42662462	NKTR	3	GA	GA	TC	33
SPCS1	28972	broad.mit.edu	36	3	52715333	52715333	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	52715333	52715333	SPCS1	3	C	C	A	25
GTF2E1	2960	broad.mit.edu	36	3	121972336	121972336	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	121972336	121972336	GTF2E1	3	C	C	T	19
SH3BP2	6452	broad.mit.edu	36	4	2792266	2792267	+	Missense_Mutation	DNP	CA	CA	AT	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	DNP	2792266	2792267	SH3BP2	4	CA	CA	AT	25
PDGFRA	5156	broad.mit.edu	36	4	54839404	54839404	+	Silent	SNP	C	C	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Silent	SNP	54839404	54839404	PDGFRA	4	C	C	A	32
SCLT1	132320	broad.mit.edu	36	4	130140282	130140282	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	130140282	130140282	SCLT1	4	G	G	C	48
CYFIP2	26999	broad.mit.edu	36	5	156671363	156671363	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	156671363	156671363	CYFIP2	5	G	G	T	36
BAK1	578	broad.mit.edu	36	6	33649943	33649943	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	33649943	33649943	BAK1	6	C	C	G	26
PKHD1	5314	broad.mit.edu	36	6	51990192	51990192	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	51990192	51990192	PKHD1	6	G	G	T	41
FHL5	9457	broad.mit.edu	36	6	97158346	97158346	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	97158346	97158346	FHL5	6	A	A	C	1
C6orf174	387104	broad.mit.edu	36	6	127839177	127839178	+	Missense_Mutation	DNP	AG	AG	TA	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	DNP	127839177	127839178	C6orf174	6	AG	AG	TA	3
TAAR2	9287	broad.mit.edu	36	6	132980498	132980498	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Silent	SNP	132980498	132980498	TAAR2	6	G	G	A	33
NAT1	9	broad.mit.edu	36	8	18124406	18124406	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Silent	SNP	18124406	18124406	NAT1	8	C	C	T	20
XKR4	114786	broad.mit.edu	36	8	56177895	56177895	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	56177895	56177895	XKR4	8	T	T	A	55
PQBP1	10084	broad.mit.edu	36	X	48643523	48643524	+	Splice_Site_SNP	DNP	GT	GT	CA	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Splice_Site_SNP	DNP	48643523	48643524	PQBP1	23	GT	GT	CA	44
BCORL1	63035	broad.mit.edu	36	X	128984616	128984616	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Missense_Mutation	SNP	128984616	128984616	BCORL1	23	G	G	A	38
MAGEA5	4104	broad.mit.edu	36	X	151034552	151034552	+	Silent	SNP	C	C	A	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Silent	SNP	151034552	151034552	MAGEA5	23	C	C	A	17
SRPK3	26576	broad.mit.edu	36	X	152702942	152702942	+	Splice_Site_SNP	SNP	G	G	C	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Splice_Site_SNP	SNP	152702942	152702942	SRPK3	23	G	G	C	34
SRPK3	26576	broad.mit.edu	36	X	152702944	152702944	+	Silent	SNP	A	A	T	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-61-2003-01	Broad	Silent	SNP	152702944	152702944	SRPK3	23	A	A	T	6
AHNAK2	113146	broad.mit.edu	36	14	104485644	104485680	+	Frame_Shift_Del	DEL	GGCCGGCTCCCTCCGGCACGGGGCCCTCTGGGAGTTT	-	GGCCGGCTCCCTCCGGCACGGGGCCCTCTGGGAGTTT	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	TCGA-61-2003-01	Broad	Frame_Shift_Del	DEL	104485644	104485680	AHNAK2	14	GGCCGGCTCCCTCCGGCACGGGGCCCTCTGGGAGTTT	-	GGCCGGCTCCCTCCGGCACGGGGCCCTCTGGGAGTTT	35
ABCB11	8647	broad.mit.edu	36	2	169541442	169541451	+	Splice_Site_Del	DEL	TTCTGGAGTG	-	TTCTGGAGTG	novel	Unknown	TCGA-61-2003-01	TCGA-61-2003-01							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	TCGA-61-2003-01	Broad	Splice_Site_Del	DEL	169541442	169541451	ABCB11	2	TTCTGGAGTG	-	TTCTGGAGTG	64
