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
ABCA5	23461	hgsc.bcm.edu	36	17	64767510	64767510	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	64767510	64767510	ABCA5	17	C	C	A	30
ADAMTS2	9509	hgsc.bcm.edu	36	5	178473838	178473838	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	178473838	178473838	ADAMTS2	5	T	T	C	56
APOBEC3H	164668	hgsc.bcm.edu	36	22	37827334	37827334	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	37827334	37827334	APOBEC3H	22	C	C	T	19
BAI3	577	hgsc.bcm.edu	36	6	69760463	69760463	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	69760463	69760463	BAI3	6	C	C	A	20
BOC	91653	hgsc.bcm.edu	36	3	114485036	114485036	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	114485036	114485036	BOC	3	G	G	A	39
C10orf118	55088	hgsc.bcm.edu	36	10	115884793	115884793	+	Silent	SNP	T	T	G	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	115884793	115884793	C10orf118	10	T	T	G	53
C9orf72	203228	hgsc.bcm.edu	36	9	27548578	27548578	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	27548578	27548578	C9orf72	9	T	T	C	58
CDC42BPB	9578	hgsc.bcm.edu	36	14	102500693	102500693	+	Silent	SNP	C	C	T	rs45512495	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	102500693	102500693	CDC42BPB	14	C	C	T	27
CDH22	64405	hgsc.bcm.edu	36	20	44303188	44303188	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	44303188	44303188	CDH22	20	C	C	T	27
CHRNA1	1134	hgsc.bcm.edu	36	2	175326592	175326592	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	175326592	175326592	CHRNA1	2	G	G	A	45
CRTC3	64784	hgsc.bcm.edu	36	15	88948681	88948681	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	88948681	88948681	CRTC3	15	C	C	G	17
DLC1	10395	hgsc.bcm.edu	36	8	12992326	12992326	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	12992326	12992326	DLC1	8	G	G	A	37
DNAH5	1767	hgsc.bcm.edu	36	5	13807367	13807367	+	Silent	SNP	T	T	C	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	13807367	13807367	DNAH5	5	T	T	C	56
EFEMP1	2202	hgsc.bcm.edu	36	2	55958421	55958421	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	55958421	55958421	EFEMP1	2	C	C	G	21
ELAVL3	1995	hgsc.bcm.edu	36	19	11430363	11430363	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	11430363	11430363	ELAVL3	19	G	G	A	43
ENPP3	5169	hgsc.bcm.edu	36	6	132089035	132089035	+	Splice_Site_SNP	SNP	T	T	C	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Splice_Site_SNP	SNP	132089035	132089035	ENPP3	6	T	T	C	57
FAM163A	148753	hgsc.bcm.edu	36	1	178049624	178049624	+	Missense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	178049624	178049624	FAM163A	1	A	A	T	6
FAM186B	84070	hgsc.bcm.edu	36	12	48283334	48283334	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	48283334	48283334	FAM186B	12	T	T	C	62
GLT25D2	23127	hgsc.bcm.edu	36	1	182210943	182210943	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	182210943	182210943	GLT25D2	1	G	G	T	46
HERV-FRD	405754	hgsc.bcm.edu	36	6	11212995	11212995	+	Missense_Mutation	SNP	T	T	G	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	11212995	11212995	HERV-FRD	6	T	T	G	57
HIRA	7290	hgsc.bcm.edu	36	22	17753104	17753104	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	17753104	17753104	HIRA	22	C	C	G	21
HMCN1	83872	hgsc.bcm.edu	36	1	184306404	184306404	+	Silent	SNP	A	A	G	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	184306404	184306404	HMCN1	1	A	A	G	7
HSP90B1	7184	hgsc.bcm.edu	36	12	102848445	102848445	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	102848445	102848445	HSP90B1	12	G	G	C	43
IGSF10	285313	hgsc.bcm.edu	36	3	152646065	152646065	+	Missense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	152646065	152646065	IGSF10	3	A	A	T	9
KCTD1	284252	hgsc.bcm.edu	36	18	22293730	22293730	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	22293730	22293730	KCTD1	18	G	G	A	40
KIF2B	84643	hgsc.bcm.edu	36	17	49257167	49257167	+	Nonsense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Nonsense_Mutation	SNP	49257167	49257167	KIF2B	17	C	C	T	25
KTN1	3895	hgsc.bcm.edu	36	14	55189516	55189516	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	55189516	55189516	KTN1	14	A	A	G	1
MCHR2	84539	hgsc.bcm.edu	36	6	100497715	100497715	+	Nonsense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Nonsense_Mutation	SNP	100497715	100497715	MCHR2	6	G	G	A	37
MYH9	4627	hgsc.bcm.edu	36	22	35042574	35042574	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	35042574	35042574	MYH9	22	G	G	T	48
NOX3	50508	hgsc.bcm.edu	36	6	155802890	155802890	+	Missense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	155802890	155802890	NOX3	6	A	A	T	12
NRG2	9542	hgsc.bcm.edu	36	5	139225327	139225327	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	139225327	139225327	NRG2	5	G	G	T	41
PARS2	25973	hgsc.bcm.edu	36	1	54996505	54996505	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	54996505	54996505	PARS2	1	C	C	T	24
PRICKLE2	166336	hgsc.bcm.edu	36	3	64059776	64059776	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	64059776	64059776	PRICKLE2	3	G	G	A	45
RPTOR	57521	hgsc.bcm.edu	36	17	76342410	76342411	+	Frame_Shift_Ins	INS	-	-	G	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Frame_Shift_Ins	INS	76342410	76342411	RPTOR	17	-	-	G	55
SALL4	57167	hgsc.bcm.edu	36	20	49840295	49840295	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	49840295	49840295	SALL4	20	G	G	A	33
SART1	9092	hgsc.bcm.edu	36	11	65501815	65501815	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	65501815	65501815	SART1	11	A	A	G	8
SLC16A14	151473	hgsc.bcm.edu	36	2	230619270	230619270	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	230619270	230619270	SLC16A14	2	C	C	T	26
SLC4A4	8671	hgsc.bcm.edu	36	4	72639728	72639728	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	72639728	72639728	SLC4A4	4	C	C	A	22
SLC4A5	57835	hgsc.bcm.edu	36	2	74311894	74311894	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	74311894	74311894	SLC4A5	2	C	C	G	17
SPTB	6710	hgsc.bcm.edu	36	14	64332020	64332020	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	64332020	64332020	SPTB	14	C	C	G	18
TBC1D22A	25771	hgsc.bcm.edu	36	22	45811697	45811697	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	45811697	45811697	TBC1D22A	22	A	A	C	2
TEK	7010	hgsc.bcm.edu	36	9	27159607	27159607	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	27159607	27159607	TEK	9	T	T	A	62
TEKT3	64518	hgsc.bcm.edu	36	17	15175183	15175183	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	15175183	15175183	TEKT3	17	G	G	A	40
TMEM135	65084	hgsc.bcm.edu	36	11	86456441	86456441	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	86456441	86456441	TMEM135	11	G	G	C	45
TMEM8B	51754	hgsc.bcm.edu	36	9	35832574	35832574	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	35832574	35832574	TMEM8B	9	G	G	A	41
TNFAIP3	7128	hgsc.bcm.edu	36	6	138234115	138234115	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	138234115	138234115	TNFAIP3	6	A	A	C	9
TOMM40	10452	hgsc.bcm.edu	36	19	50089096	50089096	+	Silent	SNP	G	G	C	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	50089096	50089096	TOMM40	19	G	G	C	43
TP53	7157	hgsc.bcm.edu	36	17	7517577	7517577	+	Splice_Site_SNP	SNP	C	C	T	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Splice_Site_SNP	SNP	7517577	7517577	TP53	17	C	C	T	18
UBE4A	9354	hgsc.bcm.edu	36	11	117765790	117765790	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	117765790	117765790	UBE4A	11	C	C	A	25
ZNF555	148254	hgsc.bcm.edu	36	19	2804696	2804696	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	2804696	2804696	ZNF555	19	T	T	C	56
ZNF559	84527	hgsc.bcm.edu	36	19	9313608	9313608	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-09-1669-01	TCGA-09-1669-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	9313608	9313608	ZNF559	19	C	C	A	17