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	ref_context	gc_content	t_alt_count	t_ref_count
MTA2	9219	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	62363998	62363998	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	AGTGACTTCCAGGGTAGCTAA	0.542	20	63
KRAS	3845	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	25398306	25398306	+	Missense_Mutation	SNP	T	T	C	rs121918682		TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	ACCACAAGTTTATATTCAGTC	0.358	20	31
PDE1B	5153	hgsc.bcm.edu;broad.mit.edu	37	12	54968886	54968886	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	AACCAGGATTGACAAGCCCAA	0.537	11	104
EEA1	8411	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	93244954	93244954	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	TTCTCGCTCACGTTCCAAGGT	0.383	35	41
FRY	10129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	32747575	32747575	+	Silent	SNP	A	A	C			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	TCCACGCTGTAGAAGGTTTTG	0.468	20	102
EFNB2	1948	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	107147326	107147326	+	Silent	SNP	T	T	A			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	TCCTGGTTGATCCAGCAGAAC	0.383	90	111
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	rs28934576	by1000genomes	TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	GGCACAAACACGCACCTCAAA	0.542	13	34
MTOR	2475	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	11184570	11184570	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	GTTTTTCCGAAGAGATGTTGG	0.443	32	7
VHLL	391104	hgsc.bcm.edu;broad.mit.edu	37	1	156268966	156268966	+	Silent	SNP	C	C	T			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	CCCCGTTCCCCGCTCTCCAGG	0.597	10	141
TIAM1	7074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	21	32617956	32617956	+	Missense_Mutation	SNP	C	C	G			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	CCGTCGCTCTCGTAGAAAAAT	0.527	10	49
NEB	4703	hgsc.bcm.edu;broad.mit.edu	37	2	152409920	152409920	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	ACATCATCACGTAGATCATAA	0.408	45	39
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	ATAAGCATGACGACCTATGAT	0.393	38	47
SLC6A6	6533	hgsc.bcm.edu;broad.mit.edu	37	3	14520692	14520692	+	Splice_Site	SNP	T	T	C			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	GTTCTCTGTGTTGTGAGTTCC	0.517	37	70
GADL1	339896	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	30885753	30885753	+	Silent	SNP	A	A	G			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	GTATCATTTTACCTCTAAGGG	0.433	80	106
HERC3	8916	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	89583639	89583639	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	TACCAGTTTAATAAATGATGA	0.333	45	68
ADH1A	124	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	100205754	100205754	+	Silent	SNP	G	G	A			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	CATCCTGCAGGGTCCCCTGAG	0.517	21	38
SLC26A8	116369	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	35922951	35922951	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	GACTAACCCCCGTGAATCCAC	0.527	59	92
DNPH1	10591	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	43193850	43193850	+	Silent	SNP	C	C	T			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	AGCCTACACCCAAGGATGGCT	0.607	12	34
EPHA7	2045	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	93964475	93964475	+	Missense_Mutation	SNP	T	T	C			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	CGGTACTGGATGGCTTCGGGT	0.373	40	44
MAP3K5	4217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	136935398	136935398	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	ATGCAATGCTATTTCTTCATG	0.363	65	100
CYCS	54205	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	25163609	25163609	+	Missense_Mutation	SNP	C	C	A	rs11548807		TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	TATCCAGGGGCCTGACCTGTC	0.443	21	68
GPR124	25960	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	37698790	37698790	+	Missense_Mutation	SNP	G	G	T			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	GTTCCACCAGGCTCAGGGGCA	0.706	6	6
SPATA31E1	286234	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	90502800	90502800	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	CTTCCAGGCCGCCACATGGAC	0.642	29	47
PHEX	5251	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	22095667	22095667	+	Silent	SNP	T	T	A			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	GGCCCGTGCTTGAATCTAATA	0.473	140	259
COL4A6	1288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	107406179	107406179	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	GGGATGCCATCGATCCCTGGT	0.592	116	174
TENM1	10178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	123680892	123680892	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	ACTTATATAACAGTTGCTTTG	0.393	38	78
PLXNA3	55558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	153695648	153695648	+	Missense_Mutation	SNP	G	G	T			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	CCCCAGCCTCGGGCGCAAGGC	0.617	32	114
THOP1	7064	broad.mit.edu;ucsc.edu	37	19	2810741	2810741	+	Missense_Mutation	SNP	G	G	T			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	TCTGCCAGGAGATCCTCGGGG	0.662	3	7
LPAL2	80350	broad.mit.edu;ucsc.edu	37	6	160906846	160906846	+	RNA	SNP	C	C	T	rs138121216	by1000genomes	TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	CAAAGACGTACGCATTTGGGT	0.463	98	189
KAT6B	23522	broad.mit.edu;hgsc.bcm.edu	37	10	76788415	76788415	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CS-5396-01A-02D-1468-08	TCGA-CS-5396-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	653af577-5555-4b77-bfec-3bd341cf58b5	bd28a937-72d5-4ee5-a2c4-c90271d33b1a	ACCCCGCCAGAAACACCCATG	0.493	31	70
