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
PTEN	5728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	89711899	89711899	+	Missense_Mutation	SNP	C	C	T	rs121913293		TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	CAGTCAGAGGCGCTATGTGTA	0.348	73	51
NUP160	23279	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	47809761	47809761	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	AAAGACTGGCGTTAAGGGAAG	0.398	30	45
PTPN11	5781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	112888199	112888199	+	Missense_Mutation	SNP	C	C	A	rs121918454		TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	GAGAAATTTGCCACTTTGGCT	0.418	74	120
SIPA1L1	26037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	72138006	72138006	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	ACTCGGACCCGCCAGGAATAC	0.473	29	51
NPAP1	23742	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	24921561	24921561	+	Missense_Mutation	SNP	G	G	A	rs151186438	byFrequency	TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	CCTTAGCAGCGGAGAAGCATC	0.597	20	27
ATP8B4	79895	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	50288937	50288937	+	Missense_Mutation	SNP	G	G	A	rs116334504	by1000genomes	TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	AGTGCATGGCGGACTTTTAGG	0.398	22	48
TMEM170A	124491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	75481522	75481522	+	Silent	SNP	T	T	G			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	CAGTGCCCAGTGTGAGGGCTT	0.408	65	113
LAMA1	284217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	6961754	6961754	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	AACACTCCGGATGGGCTGGAC	0.517	14	27
AC010336.1	0	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	7964897	7964897	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	GAGGAGCTCCGCGAGGTGCCG	0.657	10	22
ZNF229	7772	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	44933647	44933647	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	TTGCCACACTCGCTGCAGGTG	0.537	31	59
HIF3A	64344	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	46800337	46800337	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	GCGAGCCATGGCGCTGGGGCT	0.716	13	26
SZT2	23334	hgsc.bcm.edu;ucsc.edu	37	1	43888908	43888908	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	GTCACCCCCCGTGCTGGGGCC	0.617	18	26
USP24	23358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	55638164	55638164	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	TTTCAGTACCCCACTTGTGAA	0.368	22	73
CD1A	909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	158226760	158226760	+	Silent	SNP	C	C	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	GGTATCTCCGCGCAACCCTGG	0.632	66	95
OBSCN	84033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	228431148	228431148	+	Missense_Mutation	SNP	T	T	C			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	TCCTTCCGCCTGCACATCACA	0.547	11	16
ANKEF1	63926	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	10030224	10030224	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	TCCGTAGAACGTGAGGCTTTC	0.512	44	99
PCSK2	5126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	17410117	17410117	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	TTCTGCTGCCGCCAACAACAA	0.473	110	308
MAP3K19	80122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	135745373	135745373	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	TCAGGTTTTCGCGTTTTACTA	0.378	50	69
COL6A3	1293	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	238249727	238249727	+	Missense_Mutation	SNP	G	G	A	rs114806654	by1000genomes	TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	GCTCCCTGCCGCTCTCCTGTC	0.512	106	179
SEMA3F	6405	hgsc.bcm.edu;broad.mit.edu	37	3	50225347	50225347	+	Silent	SNP	C	C	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	CACCCCCAGGCGCAGGCCCCC	0.667	11	15
PDE6B	5158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	647918	647918	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	CAGCCGTACTCGGGCCCACGC	0.647	31	69
EDNRA	1909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	148407184	148407184	+	Silent	SNP	G	G	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	GCCCCAACGCGCTGATAGCCA	0.423	70	91
TRIP13	9319	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	908507	908507	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	GCCTGCAGGGCGGGCACCGAG	0.562	49	69
ATP10B	23120	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	160025790	160025790	+	Missense_Mutation	SNP	C	C	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	AGAGTTCTGGCCACTCTTGTA	0.502	195	286
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	51613287	51613287	+	Missense_Mutation	SNP	C	C	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	GTGCCAAACACAATATTGTCA	0.493	46	45
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	51892973	51892973	+	Missense_Mutation	SNP	C	C	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	TGAATGCTGACCCCATTGATA	0.498	124	213
COL19A1	1310	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	70866054	70866054	+	Silent	SNP	G	G	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	GTGTCCCAGGGCTGAAAAGCA	0.473	39	50
CALN1	83698	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	71252834	71252834	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	ATAGCAAAGGCGCATATGAGG	0.567	27	80
ADAM7	8756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	24346749	24346749	+	Missense_Mutation	SNP	T	T	G			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	CCAACATGCATGCTCAACATT	0.398	49	72
FER1L6	654463	hgsc.bcm.edu;broad.mit.edu	37	8	125094698	125094698	+	Splice_Site	SNP	A	A	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	CCAGTATGAGATGTAAGTTCT	0.512	63	110
TRPM6	140803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	77377508	77377508	+	Missense_Mutation	SNP	G	G	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	AGGCAAGACAGTTTCTGCTGA	0.507	104	160
OR13C5	138799	hgsc.bcm.edu;broad.mit.edu	37	9	107361264	107361264	+	Missense_Mutation	SNP	A	A	C			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	CCCAGCTGCCATGGGTACATA	0.473	24	338
SVEP1	79987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	113217968	113217968	+	Missense_Mutation	SNP	G	G	C			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	ATCGATGTCTGTTTCACACTT	0.418	20	33
RGN	9104	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	46943843	46943843	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	CGTGGCTCTTCGCCAGTCGGG	0.493	18	5
TENM1	10178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	123654451	123654451	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	TTAATTGCGGCGGGAAACCAC	0.473	114	25
CARD14	79092	broad.mit.edu;ucsc.edu	37	17	78171904	78171904	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	CCAGACCTTCCGCAGCTGGAA	0.592	27	103
SUPT16H	11198	broad.mit.edu;ucsc.edu	37	14	21821703	21821703	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	TTCTTCACTACCCAATGACTC	0.373	52	107
DDR2	4921	broad.mit.edu;ucsc.edu	37	1	162741843	162741843	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	GCCAGTCCAGCCCAGTGGCCC	0.577	11	15
SLC30A6	55676	broad.mit.edu;hgsc.bcm.edu	37	2	32422896	32422896	+	Splice_Site	DEL	G	G	-			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	TTGAAATTAAGTGAGTATTTT	0.373	47	91
PLCG1	5335	broad.mit.edu;hgsc.bcm.edu	37	20	39802386	39802387	+	In_Frame_Ins	INS	-	-	GAAGAA			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	TGGTGTATGAGGAAGACATGTT	0.515	47	228
