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	dataset	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context
AFF3	3899	hgsc.bcm.edu	36	2	99989528	99989528	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	99989528	99989528	AFF3	2	C	C	T	30
AKAP6	9472	hgsc.bcm.edu	36	14	32217296	32217296	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	32217296	32217296	AKAP6	14	C	C	T	25
AKAP8	10270	hgsc.bcm.edu	36	19	15330826	15330826	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	15330826	15330826	AKAP8	19	A	A	C	6
AKAP9	10142	hgsc.bcm.edu	36	7	91490114	91490115	+	In_Frame_Ins	INS	-	-	AAC	rs10644111	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	In_Frame_Ins	INS	91490114	91490115	AKAP9	7	-	-	AAC	13
ASXL3	80816	hgsc.bcm.edu	36	18	29579797	29579798	+	Frame_Shift_Ins	INS	-	-	G	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Frame_Shift_Ins	INS	29579797	29579798	ASXL3	18	-	-	G	51
BAI3	577	hgsc.bcm.edu	36	6	69760509	69760509	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	69760509	69760509	BAI3	6	G	G	T	33
BTN2A1	11120	hgsc.bcm.edu	36	6	26571485	26571486	+	Frame_Shift_Del	DEL	CC	CC	-	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	CC	CC	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Frame_Shift_Del	DEL	26571485	26571486	BTN2A1	6	CC	CC	-	26
C20orf85	128602	hgsc.bcm.edu	36	20	56169159	56169159	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	56169159	56169159	C20orf85	20	G	G	T	43
CHRNA7	1139	hgsc.bcm.edu	36	15	30237996	30237996	+	Silent	SNP	G	G	A	rs1042722	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	30237996	30237996	CHRNA7	15	G	G	A	38
COQ2	27235	hgsc.bcm.edu	36	4	84407796	84407796	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	84407796	84407796	COQ2	4	G	G	A	43
COX10	1352	hgsc.bcm.edu	36	17	13913676	13913677	+	Frame_Shift_Del	DEL	CA	CA	-	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	CA	CA	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Frame_Shift_Del	DEL	13913676	13913677	COX10	17	CA	CA	-	29
CPA5	93979	hgsc.bcm.edu	36	7	129790036	129790036	+	Missense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	129790036	129790036	CPA5	7	A	A	T	6
CSMD1	64478	hgsc.bcm.edu	36	8	3250958	3250958	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	3250958	3250958	CSMD1	8	T	T	A	62
DMD	1756	hgsc.bcm.edu	36	X	31049933	31049933	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	31049933	31049933	DMD	23	C	C	A	29
DOCK11	139818	hgsc.bcm.edu	36	X	117615509	117615525	+	Frame_Shift_Del	DEL	GCTACTTGAATCTGAAT	GCTACTTGAATCTGAAT	-	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	GCTACTTGAATCTGAAT	GCTACTTGAATCTGAAT	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Frame_Shift_Del	DEL	117615509	117615525	DOCK11	23	GCTACTTGAATCTGAAT	GCTACTTGAATCTGAAT	-	42
EGFR	1956	hgsc.bcm.edu	36	7	55191790	55191790	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	55191790	55191790	EGFR	7	C	C	T	29
ELAVL2	1993	hgsc.bcm.edu	36	9	23682568	23682568	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	23682568	23682568	ELAVL2	9	G	G	A	40
EPS8L3	79574	hgsc.bcm.edu	36	1	110101296	110101296	+	Nonsense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Nonsense_Mutation	SNP	110101296	110101296	EPS8L3	1	G	G	T	42
FAM170A	340069	hgsc.bcm.edu	36	5	118997841	118997841	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	118997841	118997841	FAM170A	5	G	G	C	48
RALGAPA1	253959	hgsc.bcm.edu	36	14	35144664	35144664	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	35144664	35144664	RALGAPA1	14	C	C	A	31
RALGAPA1	253959	hgsc.bcm.edu	36	14	35174434	35174434	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	35174434	35174434	RALGAPA1	14	T	T	C	52
GART	2618	hgsc.bcm.edu	36	21	33803992	33803992	+	Frame_Shift_Del	DEL	T	T	-	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Frame_Shift_Del	DEL	33803992	33803992	GART	21	T	T	-	56
GRM1	2911	hgsc.bcm.edu	36	6	146393031	146393031	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	146393031	146393031	GRM1	6	G	G	T	46
HCN1	348980	hgsc.bcm.edu	36	5	45681093	45681093	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	45681093	45681093	HCN1	5	C	C	A	19
HNF1B	6928	hgsc.bcm.edu	36	17	33144717	33144717	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	33144717	33144717	HNF1B	17	G	G	A	48
MACF1	23499	hgsc.bcm.edu	36	1	39595898	39595898	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	39595898	39595898	MACF1	1	G	G	A	37
NBPF12	440675	hgsc.bcm.edu	36	1	144929408	144929408	+	Missense_Mutation	SNP	T	T	C	rs4098124	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	144929408	144929408	NBPF12	1	T	T	C	61
NCOA3	8202	hgsc.bcm.edu	36	20	45711204	45711205	+	In_Frame_Ins	INS	-	-	CTG	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	In_Frame_Ins	INS	45711204	45711205	NCOA3	20	-	-	CTG	14
OR11G2	390439	hgsc.bcm.edu	36	14	19736015	19736016	+	Frame_Shift_Ins	INS	-	-	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Frame_Shift_Ins	INS	19736015	19736016	OR11G2	14	-	-	A	25
P2RY2	5029	hgsc.bcm.edu	36	11	72623100	72623100	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	72623100	72623100	P2RY2	11	C	C	T	27
PROM2	150696	hgsc.bcm.edu	36	2	95305423	95305423	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	95305423	95305423	PROM2	2	G	G	T	43
RYR3	6263	hgsc.bcm.edu	36	15	31924372	31924374	+	In_Frame_Del	DEL	AGA	AGA	-	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	AGA	AGA	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	In_Frame_Del	DEL	31924372	31924374	RYR3	15	AGA	AGA	-	15
SLC12A9	56996	hgsc.bcm.edu	36	7	100292535	100292537	+	In_Frame_Del	DEL	CGG	CGG	-	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	CGG	CGG	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	In_Frame_Del	DEL	100292535	100292537	SLC12A9	7	CGG	CGG	-	23
SLC5A12	159963	hgsc.bcm.edu	36	11	26661948	26661948	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	26661948	26661948	SLC5A12	11	C	C	T	23
SRCIN1	80725	hgsc.bcm.edu	36	17	33958934	33958934	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	33958934	33958934	SRCIN1	17	A	A	C	11
SNRPB	6628	hgsc.bcm.edu	36	20	2394385	2394385	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	2394385	2394385	SNRPB	20	G	G	A	45
SNX7	51375	hgsc.bcm.edu	36	1	98933689	98933689	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	98933689	98933689	SNX7	1	C	C	T	30
TMPRSS2	7113	hgsc.bcm.edu	36	21	41762266	41762266	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	41762266	41762266	TMPRSS2	21	T	T	A	49
TP53	7157	hgsc.bcm.edu	36	17	7519280	7519280	+	Splice_Site_SNP	SNP	C	C	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Splice_Site_SNP	SNP	7519280	7519280	TP53	17	C	C	T	20
TRIP12	9320	hgsc.bcm.edu	36	2	230377159	230377159	+	Missense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	230377159	230377159	TRIP12	2	A	A	T	8
TTN	7273	hgsc.bcm.edu	36	2	179354220	179354220	+	Nonsense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Nonsense_Mutation	SNP	179354220	179354220	TTN	2	G	G	T	48
ZFHX3	463	hgsc.bcm.edu	36	16	71549769	71549769	+	Nonsense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Nonsense_Mutation	SNP	71549769	71549769	ZFHX3	16	C	C	A	31
ZNF180	7733	hgsc.bcm.edu	36	19	49693201	49693201	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	49693201	49693201	ZNF180	19	G	G	A	47
ZNF354A	6940	hgsc.bcm.edu	36	5	178072848	178072848	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-04-1365-01	TCGA-04-1365-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_IV	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	178072848	178072848	ZNF354A	5	G	G	A	40