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
HNRNPF	3185	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	43882166	43882166	+	Silent	SNP	G	G	A			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CCAGGCCACTGTAAGTGGCCT	0.537	121	148
PAX2	5076	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	102541110	102541110	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	TGAGAAGAGGAAACGTGATGA	0.587	26	192
PWWP2B	170394	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	134219372	134219372	+	Silent	SNP	G	G	A			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CAGCGCCCTCGGTGTCCAGAG	0.701	35	60
OR51Q1	390061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	5444223	5444223	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	TATGACTCATCGCTTTGCCAA	0.517	29	50
STK38L	23012	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	27467498	27467498	+	Silent	SNP	C	C	T			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CACAGTTCTACATTTCAGAGA	0.383	10	49
SPG7	6687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	89620236	89620236	+	Silent	SNP	C	C	T	rs140356355		TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	TCACCCGCATCGCCTACTCCA	0.677	37	122
CTDNEP1	23399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7150176	7150176	+	Silent	SNP	T	T	C			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	GTTTGTCTATTACCACCTACA	0.512	159	174
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7578190	7578190	+	Missense_Mutation	SNP	T	T	C	rs121912666		TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	AGGCGGCTCATAGGGCACCAC	0.557	46	5
ZNF560	147741	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	9577986	9577986	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	ACATTTCTTACATTGATAGAG	0.398	59	81
IL12RB1	3594	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	18184406	18184406	+	Missense_Mutation	SNP	T	T	G			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CTGTGGGGGGTTTTCTGCAAT	0.512	7	33
KIR2DL3	3804	hgsc.bcm.edu;broad.mit.edu	37	19	55255285	55255285	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CCGGGCCCCACGGTTCTGGCA	0.567	37	30
MEGF6	1953	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	3428609	3428609	+	Missense_Mutation	SNP	C	C	A			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	TCATAGCCCGCGTGACACACG	0.667	76	74
CYB5RL	606495	hgsc.bcm.edu;ucsc.edu	37	1	54661191	54661191	+	Nonsense_Mutation	SNP	G	G	T			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CACAGGGTGAGCAGCCACTGC	0.612	52	69
IPO9	55705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	201841994	201841994	+	Missense_Mutation	SNP	A	A	G	rs141172151		TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CATGGCATCAATGCAGATGAC	0.527	22	87
OR2T12	127064	hgsc.bcm.edu;broad.mit.edu	37	1	248458438	248458438	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	TGCACCCAGGAGCCAGGACGA	0.612	68	83
C2orf53	0	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	27360157	27360157	+	Silent	SNP	G	G	A			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	GGACTGGGTCGGCCCGGGCCT	0.637	39	110
FAM126B	285172	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	201876188	201876188	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	ATCTTTATCAGCGATTTCCTA	0.303	7	10
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	ATAAGCATGACGACCTATGAT	0.393	15	45
CCDC108	255101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	219868765	219868765	+	Missense_Mutation	SNP	A	A	T			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	GACTCCTGGGACTCAGGCTGT	0.577	144	153
ITPR1	3708	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	4699950	4699950	+	Missense_Mutation	SNP	G	G	A	rs6766212		TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	GGAGGTGACAGCCTTGTCCCA	0.493	8	61
GOLGA4	2803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	37396655	37396655	+	Nonsense_Mutation	SNP	G	G	T			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	GAAAATTTTGGAAAGAGAAGA	0.383	28	55
DNASE1L3	1776	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	58190566	58190566	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CATCCTGATAGTCATGGTAGT	0.493	13	64
TP63	8626	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	189604292	189604292	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CCCTCAGCAGCGCAACGCCCT	0.502	27	63
TMPRSS11F	389208	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	68935722	68935722	+	Missense_Mutation	SNP	A	A	C			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	TTTGCTGTCAATAGCTGGAAT	0.313	34	93
MMAA	166785	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	146560298	146560298	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	GAATATGCCCATGCTGCTACC	0.423	71	110
CDH12	1010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	21752319	21752319	+	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	TTCTGCCTTCGCAGTGCTACA	0.398	39	11
FAT2	2196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	150947117	150947117	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	GGAAGACCTGTTGAAGAGGGG	0.537	56	101
LRRC16A	55604	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	25517626	25517626	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	TTCAGGATATAGCTGTTGCTA	0.313	27	47
FAM188B	84182	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	30898919	30898919	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CTTTCTGCCATCCTGTCCAGG	0.567	17	70
TG	7038	hgsc.bcm.edu;ucsc.edu	37	8	134145830	134145830	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	GAGCTGCTCCCCAATCGACAG	0.537	12	53
TG	7038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	134145854	134145854	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CTGAAGAAAGCCGACTGCTCC	0.547	11	43
ST3GAL1	6482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	134488257	134488257	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CCTCTTCCGCAGGGTCACCAT	0.552	35	76
TTF1	7270	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	135275446	135275446	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	TCCTTAAACCGTTCCAAGTCG	0.468	26	123
CUL4B	8450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	119694140	119694140	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	aggaggaTTCCTCAGCCATCT	0.488	10	35
MRPS27	23107	broad.mit.edu;ucsc.edu	37	5	71593520	71593520	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CATTAAAGATGCAAGATCAGC	0.294	5	14
ZAN	7455	broad.mit.edu;ucsc.edu	37	7	100363082	100363082	+	RNA	SNP	G	G	T			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	GTGCGTGGAGGCCTGTGAATG	0.612	13	37
GBA2	57704	broad.mit.edu;ucsc.edu	37	9	35741041	35741041	+	Silent	SNP	T	T	C			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	ACACAAAGACTCCTACAGGCA	0.567	20	68
TMEM132B	114795	broad.mit.edu;ucsc.edu	37	12	126135302	126135302	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	GTACCAGCACGCCACAGTGCG	0.587	8	67
FLRT1	23769	broad.mit.edu;ucsc.edu	37	11	63884997	63884997	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	GCCAGGGCTGCGCCTCCCCGA	0.652	5	26
STK32A	202374	broad.mit.edu;ucsc.edu	37	5	146657719	146657719	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	TTTGCGAGCCATTGGGAAAGG	0.358	5	12
ELP2	55250	broad.mit.edu;ucsc.edu	37	18	33738840	33738840	+	Nonsense_Mutation	SNP	G	G	T			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	CCCTGCATTGGGATTATCAAA	0.333	26	21
GSPT1	2935	broad.mit.edu;hgsc.bcm.edu	37	16	11981588	11981589	+	Frame_Shift_Ins	INS	-	-	T			TCGA-HT-A61B-01A-11D-A29Q-08	TCGA-HT-A61B-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97a07589-3dd1-4724-8458-343a8b54d8db	b32d8211-d6fb-4fbd-9727-536b1e77a69d	TGATTTGTGTCTAAGGCCCAAG	0.356	33	100
