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
TRIM51	84767	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	55653246	55653246	+	Silent	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	TCTGTTTGCCGTGCTCCAACT	0.507	10	11
LRRC32	2615	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	76371628	76371628	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	GAGGTCAGGTGCTCAAGAAAG	0.587	9	17
LTA4H	4048	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	96410892	96410892	+	Splice_Site	SNP	C	C	G			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	TGTGCAATGACCTAAAGAAAA	0.299	29	23
TDG	6996	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	104374741	104374741	+	Splice_Site	SNP	G	G	T			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	AACCATTTTTGTAAGTGGTTA	0.318	33	14
PCNX	22990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	71444691	71444691	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	CGACCTAAATCTTCTAGCGTA	0.468	23	24
DYNC1H1	1778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	102474561	102474561	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	GGTGCCTGGGGCTGCTTTGAC	0.587	22	15
OTUD7A	161725	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	31776380	31776380	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	GATGAACTTGCGCTCCCCCTG	0.672	7	14
HIRIP3	8479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	30006466	30006466	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	TCCGGGTCGCTACAAGGGGTG	0.552	11	129
SPNS3	201305	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	4356345	4356345	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	CATGACCGGCGTCATTGGGGT	0.572	38	20
TP53	7157	hgsc.bcm.edu;broad.mit.edu	37	17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	rs28934576	by1000genomes	TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	GGCACAAACACGCACCTCAAA	0.542	5	3
LRRC59	55379	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	48465454	48465454	+	Missense_Mutation	SNP	G	G	A	rs140038553		TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	TGCCTCTCCCGCTCCTGATCT	0.527	97	50
ST8SIA5	29906	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	44260408	44260408	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	CAGCAGCACCGACGCGTTCTC	0.607	4	5
ZNF536	9745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	31040264	31040264	+	Silent	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	ACCCCTTGGCGGGCCTGCCAA	0.632	12	15
RERE	473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	8415150	8415150	+	Missense_Mutation	SNP	T	T	G			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	AAATAACTTATAACTGCTTGT	0.438	18	16
EPHA8	2046	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	22924293	22924293	+	Silent	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	TGAGCGAGGCGTCCATCATGG	0.662	77	60
NCMAP	400746	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	24932146	24932146	+	Missense_Mutation	SNP	G	G	A	rs113438005		TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	CAAGCCAACCGCCCCTTCTGC	0.592	14	45
RUNX3	864	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	25228881	25228881	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	GTAGGGGGACGGGTTGGCCTG	0.692	11	38
IPO9	55705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	201824023	201824023	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	GCCTATTGTTTGGAACACCCT	0.448	13	79
BPIFB4	149954	hgsc.bcm.edu;ucsc.edu	37	20	31695618	31695618	+	Missense_Mutation	SNP	G	G	A	rs138732736	byFrequency	TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	AGACATTGACGTGTTGGAGGT	0.493	7	11
DYSF	8291	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	71887771	71887771	+	Missense_Mutation	SNP	G	G	A	rs147056383	by1000genomes	TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	GCTGGAGCCCGTATTTGGAAA	0.507	5	32
COL4A4	1286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	227876966	227876966	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	GACCCAGGGACGCCATCCACA	0.567	16	34
SAG	6295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	234235841	234235841	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	AAATCCCCAAGAAGTAAGAGT	0.552	79	57
TTLL3	26140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	9870897	9870897	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	CGCTGACTTCGTGTTCGGGGA	0.617	33	23
ZNF654	55279	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	88189554	88189554	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	AGTCTGCCAGTTTCTACTAGC	0.358	6	17
SLC2A9	56606	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	9987317	9987317	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	ATGATGAAGCGTCCCACGATG	0.517	12	34
MUC7	4589	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	71347534	71347534	+	Missense_Mutation	SNP	G	G	A	rs145866670		TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	AAAATTTCTCGATTTCTTTTA	0.358	14	24
FRAS1	80144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	79387412	79387412	+	Silent	SNP	C	C	T			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	ATGGCACCATCGAGCGAACCA	0.547	33	69
SLC6A19	340024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	1217005	1217005	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	TCCGACCCCGCGGCCTACGCG	0.622	62	157
ADAMTS16	170690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	5222929	5222929	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	GTGGTGCCATCGTATTGGAAG	0.368	19	26
PCDHA1	56147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	140166983	140166983	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	CACCGTCATCGCCCTCATCAC	0.527	14	53
GABRA6	2559	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	161113291	161113291	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	CTCAGAAAACGTCAGTCGGAT	0.488	29	38
OR2V2	285659	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	180582042	180582042	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	CGTGGTTATGGCGGTCTTCAC	0.537	41	106
SOX4	6659	hgsc.bcm.edu;broad.mit.edu	37	6	21594838	21594838	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	CTCGGGCGCCGGCCTCGAGCT	0.731	4	20
MICB	4277	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	31473467	31473467	+	Silent	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	TTCTCGCTGAGGGACATCTGG	0.557	29	22
PKD1L1	168507	hgsc.bcm.edu;broad.mit.edu	37	7	47851503	47851503	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	GAGACTCCCCGTAGGGAGGAT	0.582	7	22
RP1L1	94137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	10470654	10470654	+	Silent	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	ACAGGCTGCCGTCCTCATTCA	0.662	57	52
ATF4P4	100127952	broad.mit.edu;ucsc.edu	37	11	113659993	113659993	+	RNA	SNP	A	A	C	rs906846	by1000genomes	TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	GGCAGCATGTAGGTTGCAGGG	0.657	3	26
HRG	3273	broad.mit.edu;ucsc.edu	37	3	186383868	186383868	+	Silent	SNP	G	G	A			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	TGCAGTATTCGTGTGCCGTGA	0.468	12	42
BEST2	54831	broad.mit.edu;ucsc.edu	37	19	12866569	12866569	+	Silent	SNP	C	C	T			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	TCTTCTACGCCGGCTGGCTCA	0.582	3	32
NF1	4763	broad.mit.edu;hgsc.bcm.edu	37	17	29527568	29527569	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-HT-A4DS-01A-11D-A26M-08	TCGA-HT-A4DS-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82900479-957f-424c-b32f-b1ecf4b1fd05	846758c1-5fd9-4c3a-bf82-66a60311bb64	GGGAAGATAACTCTGTCATTTT	0.381	17	8
