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	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	dbSNP_AF	Algorithm
TCEB3	6924	hgsc.bcm.edu	hg19	1	24078287	24078287	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	TCEB3	NM_003198	exon4	c.G1270A	p.D424N	ATGGAGGATGAAT	.	95.0	83.0	173.0	0.0	.	61	.	.	Atlas-SNP
PDZK1IP1	10158	hgsc.bcm.edu	hg19	1	47649702	47649702	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	PDZK1IP1	NM_005764	exon4	c.G286T	p.E96X	CATTCTCATGCTC	.	65.0	24.0	61.0	0.0	.	9	.	.	Atlas-SNP
DMRTA2	63950	hgsc.bcm.edu	hg19	1	50885040	50885040	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	DMRTA2	NM_032110	exon3	c.C926A	p.S309X	GGACCCGAGCCTC	.	32.0	13.0	18.0	0.0	.	17	.	.	Atlas-SNP
DEPDC1	55635	hgsc.bcm.edu	hg19	1	68947881	68947881	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	DEPDC1	NM_001114120	exon8	c.A1610T	p.N537I	CCAACATTTGGTT	.	145.0	63.0	78.0	0.0	.	102	.	.	Atlas-SNP
SOX13	9580	hgsc.bcm.edu	hg19	1	204095155	204095155	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	SOX13	NM_005686	exon14	c.G1762A	p.D588N	GGCACAGATGACA	.	210.0	68.0	135.0	0.0	.	38	.	.	Atlas-SNP
PLEKHA6	22874	hgsc.bcm.edu	hg19	1	204198158	204198158	+	Silent	SNP	G	G	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	PLEKHA6	NM_014935	exon19	c.C2658T	p.G886G	ATGCCCGCCAGGC	.	128.0	43.0	75.0	0.0	.	115	.	.	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	hg19	1	240256986	240256986	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	FMN2	NM_020066	exon1	c.C1577T	p.A526V	CTGGGGCCCCCGC	.	40.0	10.0	15.0	0.0	.	451	.	.	Atlas-SNP
BIRC6	57448	hgsc.bcm.edu	hg19	2	32724628	32724628	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	BIRC6	NM_016252	exon46	c.C8483T	p.T2828I	TCCAGACAGGCCA	.	67.0	31.0	42.0	0.0	.	838	.	.	Atlas-SNP
CYTIP	9595	hgsc.bcm.edu	hg19	2	158300471	158300471	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	CYTIP	NM_004288	exon1	c.G62A	p.G21E	GCTGGCCCAGCGC	.	74.0	35.0	69.0	0.0	.	45	.	.	Atlas-SNP
RBM45	129831	hgsc.bcm.edu	hg19	2	178985043	178985043	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	RBM45	NM_152945	exon4	c.A580T	p.N194Y	CCTAAAAATAAAG	.	177.0	64.0	133.0	0.0	.	49	.	.	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179451970	179451970	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	TTN	NM_001267550	exon307	c.C63968T	p.T21323I	AAGCTTGTTTTCT	.	134.0	64.0	111.0	0.0	.	18412	.	.	Atlas-SNP
ADAM23	8745	hgsc.bcm.edu	hg19	2	207437863	207437863	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	ADAM23	NM_003812	exon18	c.C1681T	p.R561W	GAATGCCGGGATG	.	113.0	46.0	94.0	0.0	.	239	.	.	Atlas-SNP
SETD2	29072	hgsc.bcm.edu	hg19	3	47129617	47129617	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	SETD2	NM_014159	exon10	c.C5263G	p.L1755V	GTTCCAGACAGGT	.	81.0	22.0	55.0	0.0	.	721	.	.	Atlas-SNP
EOGT	285203	hgsc.bcm.edu	hg19	3	69028841	69028841	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	.	NM_173654	exon13	c.G1060A	p.D354N	CCCAGTCTGGAAG	.	110.0	70.0	108.0	0.0	.	.	.	.	Atlas-SNP
TRMT10C	54931	hgsc.bcm.edu	hg19	3	101284816	101284816	+	Silent	SNP	A	A	G	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	.	NM_017819	exon2	c.A1191G	p.R397R	CAACAGACTAAAG	.	170.0	8.0	189.0	0.0	.	.	.	.	Atlas-SNP
CCDC39	339829	hgsc.bcm.edu	hg19	3	180334069	180334069	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	CCDC39	NM_181426	exon19	c.G2669A	p.R890K	GCTTACCTTGCTG	.	91.0	41.0	91.0	0.0	.	242	.	.	Atlas-SNP
GABRG1	2565	hgsc.bcm.edu	hg19	4	46043146	46043146	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	GABRG1	NM_173536	exon9	c.T1257G	p.F419L	GTCTTCAAAGCAA	.	198.0	8.0	146.0	0.0	.	172	.	.	Atlas-SNP
IMPG1	3617	hgsc.bcm.edu	hg19	6	76712648	76712648	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	IMPG1	NM_001563	exon12	c.G1278T	p.E426D	ACCATGCTCTGCT	.	143.0	63.0	105.0	0.0	.	143	.	.	Atlas-SNP
SASH1	23328	hgsc.bcm.edu	hg19	6	148846451	148846451	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	SASH1	NM_015278	exon11	c.G1234C	p.D412H	GGATTTGACTTGA	.	65.0	22.0	57.0	0.0	.	123	.	.	Atlas-SNP
ZNF703	80139	hgsc.bcm.edu	hg19	8	37554679	37554679	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	ZNF703	NM_025069	exon2	c.G260A	p.S87N	AGAAGAGCCCCTT	.	32.0	21.0	79.0	0.0	.	16	.	.	Atlas-SNP
UBR5	51366	hgsc.bcm.edu	hg19	8	103335715	103335715	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	UBR5,NS,carcinoma,0,1	UBR5	NM_015902	exon14	c.G1608C	p.L536F	ATTTCTCAAGCAT	.	136.0	30.0	97.0	0.0	.	285	.	.	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	hg19	8	113697726	113697726	+	Silent	SNP	A	A	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	CSMD3	NM_198123	exon15	c.T2391A	p.P797P	ATGGGAAGGCACC	.	112.0	107.0	106.0	0.0	.	2325	.	.	Atlas-SNP
TRPS1	7227	hgsc.bcm.edu	hg19	8	116426936	116426936	+	Missense_Mutation	SNP	G	G	T	rs78385846	bycluster	TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	TRPS1	NM_014112	exon7	c.C3200A	p.S1067Y	GATACGGATGAAC	.	141.0	128.0	106.0	0.0	.	516	.	.	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	hg19	9	113170455	113170455	+	Silent	SNP	A	A	G	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	SVEP1	NM_153366	exon38	c.T7425C	p.N2475N	GGTAGTATTTCCC	.	67.0	54.0	77.0	0.0	.	326	.	.	Atlas-SNP
TNC	3371	hgsc.bcm.edu	hg19	9	117849523	117849523	+	Missense_Mutation	SNP	C	C	T	rs368041702	alternate_allele	TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	TNC	NM_002160	exon3	c.G487A	p.G163S	CCCGACCGCTACA	.	162.0	75.0	132.0	0.0	.	282	.	.	Atlas-SNP
LCN15	389812	hgsc.bcm.edu	hg19	9	139656673	139656673	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	LCN15	NM_203347	exon5	c.C487A	p.P163T	CCTTGGGGAGCCC	.	186.0	77.0	154.0	0.0	.	11	.	.	Atlas-SNP
VTI1A	143187	hgsc.bcm.edu	hg19	10	114220309	114220309	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	VTI1A	NM_145206	exon2	c.G121T	p.V41L	GCAAATGTGGAGA	.	471.0	132.0	528.0	1.0	.	15	.	.	Atlas-SNP
VTI1A	143187	hgsc.bcm.edu	hg19	10	114220314	114220314	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	VTI1A	NM_145206	exon2	c.G126T	p.E42D	TGTGGAGAAACAG	.	454.0	111.0	538.0	1.0	.	15	.	.	Atlas-SNP
VTI1A	143187	hgsc.bcm.edu	hg19	10	114220315	114220315	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	VTI1A	NM_145206	exon2	c.A127T	p.K43X	GTGGAGAAACAGC	.	451.0	112.0	536.0	1.0	.	15	.	.	Atlas-SNP
SFXN4	119559	hgsc.bcm.edu	hg19	10	120916266	120916266	+	Silent	SNP	T	T	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	SFXN4	NM_213649	exon10	c.A540T	p.V180V	AGGGATTACCTAG	.	60.0	24.0	53.0	0.0	.	24	.	.	Atlas-SNP
OR10A3	26496	hgsc.bcm.edu	hg19	11	7960486	7960486	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	OR10A3,NS,carcinoma,0,1	OR10A3	NM_001003745	exon1	c.A582T	p.L194F	TTCAAATAAGAAG	.	175.0	47.0	173.0	0.0	.	54	.	.	Atlas-SNP
OR4A16	81327	hgsc.bcm.edu	hg19	11	55111591	55111591	+	Silent	SNP	T	T	C	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	OR4A16	NM_001005274	exon1	c.T915C	p.S305S	GTTAAGTATAGTT	.	24.0	8.0	40.0	0.0	.	120	.	.	Atlas-SNP
C12orf57	113246	hgsc.bcm.edu	hg19	12	7053299	7053299	+	Silent	SNP	G	G	T	rs144652065	alternate_allele	TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	C12orf57	NM_138425	exon1	c.G15T	p.S5S	CGCCTCGACCCAA	.	83.0	4.0	84.0	0.0	.	10	.	G|1.000;A|0.000	Atlas-SNP
SOX5	6660	hgsc.bcm.edu	hg19	12	23793762	23793762	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	SOX5	NM_006940	exon8	c.G1001A	p.G334D	AGTGGGCCTAAGC	.	53.0	28.0	54.0	0.0	.	134	.	.	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	hg19	12	26640009	26640009	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	ITPR2	NM_002223	exon40	c.G5546T	p.R1849L	CTCATTCGTGGAC	.	102.0	53.0	91.0	0.0	.	270	.	.	Atlas-SNP
LRIG3	121227	hgsc.bcm.edu	hg19	12	59266374	59266374	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	LRIG3	NM_153377	exon19	c.T3340A	p.S1114T	CATAAGACTGAAA	.	55.0	36.0	56.0	0.0	.	120	.	.	Atlas-SNP
MYF5	4617	hgsc.bcm.edu	hg19	12	81112793	81112793	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	MYF5	NM_005593	exon3	c.G731C	p.G244A	CTCCAGGGGCTTC	.	56.0	33.0	67.0	0.0	.	78	.	.	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	hg19	12	124341720	124341720	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	DNAH10_same_name,NS,carcinoma,0,2	DNAH10	NM_207437	exon36	c.G6202A	p.V2068I	CCTCGCGTCCGCT	.	105.0	32.0	104.0	0.0	.	888	.	.	Atlas-SNP
FLT1	2321	hgsc.bcm.edu	hg19	13	28959141	28959141	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	FLT1	NM_002019	exon14	c.A1997T	p.N666I	CTGAGGTTTCGCA	.	68.0	59.0	119.0	0.0	.	393	.	.	Atlas-SNP
OR4N2	390429	hgsc.bcm.edu	hg19	14	20296476	20296476	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	OR4N2,NS,carcinoma,+1,2	OR4N2	NM_001004723	exon1	c.G869A	p.R290H	CCCTTCGCAACCA	.	99.0	4.0	93.0	1.0	.	125	.	.	Atlas-SNP
C14orf166	51637	hgsc.bcm.edu	hg19	14	52458049	52458049	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	C14orf166	NM_016039	exon2	c.A76G	p.R26G	GAATTTAGAAACT	.	278.0	166.0	277.0	0.0	.	23	.	.	Atlas-SNP
ZSCAN29	146050	hgsc.bcm.edu	hg19	15	43661977	43661977	+	Silent	SNP	C	C	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	ZSCAN29,NS,carcinoma,0,1	ZSCAN29	NM_152455	exon1	c.G135T	p.R45R	TAGCCACCGACAG	.	65.0	21.0	66.0	0.0	.	57	.	.	Atlas-SNP
AXIN1	8312	hgsc.bcm.edu	hg19	16	360070	360070	+	Splice_Site	SNP	C	C	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	AXIN1	NM_181050	exon5	c.1020-1G>T	.	CCATCCCTGTCCA	.	56.0	46.0	85.0	0.0	.	290	.	.	Atlas-SNP
MAP2K3	5606	hgsc.bcm.edu	hg19	17	21203869	21203869	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	MAP2K3	NM_145109	exon4	c.G178C	p.E60Q	GAGGTGGAGGCTG	.	120.0	31.0	117.0	0.0	.	135	.	.	Atlas-SNP
PIGS	94005	hgsc.bcm.edu	hg19	17	26885512	26885512	+	Missense_Mutation	SNP	G	G	A	rs201018217	alternate_allele	TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	PIGS	NM_033198	exon8	c.C916T	p.P306S	CCACTGGGTTGAT	.	72.0	47.0	85.0	0.0	.	42	.	G|0.999;C|0.001	Atlas-SNP
MEOX1	4222	hgsc.bcm.edu	hg19	17	41738601	41738601	+	Missense_Mutation	SNP	G	G	A	rs183202008	bycluster;by1000genomes;alternate_allele	TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	MEOX1	NM_004527	exon1	c.C302T	p.A101V	CGCCGGGCGTCTG	.	89.0	21.0	125.0	0.0	.	29	.	G|0.999;T|0.001	Atlas-SNP
PNMAL2	57469	hgsc.bcm.edu	hg19	19	46997793	46997793	+	Silent	SNP	G	G	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	PNMAL2	NM_020709	exon1	c.C930T	p.D310D	CGAAGTGTCGCTG	.	154.0	14.0	88.0	0.0	.	44	.	.	Atlas-SNP
TTYH1	57348	hgsc.bcm.edu	hg19	19	54930426	54930426	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	TTYH1	NM_020659	exon2	c.C251G	p.S84W	TCCCCTCGCCCGG	.	75.0	64.0	36.0	0.0	.	78	.	.	Atlas-SNP
TIAM1	7074	hgsc.bcm.edu	hg19	21	32595765	32595765	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	TIAM1	NM_003253	exon9	c.T1952A	p.M651K	CGGCCCATGGCCA	.	96.0	4.0	92.0	0.0	.	522	.	.	Atlas-SNP
DGCR14	8220	hgsc.bcm.edu	hg19	22	19124915	19124915	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	DGCR14	NM_022719	exon8	c.G956T	p.G319V	ACCTCCCCCCAGG	.	82.0	35.0	88.0	0.0	.	43	.	.	Atlas-SNP
FAM5C	339479	hgsc.bcm.edu	hg19	1	190068224	190068228	+	Frame_Shift_Del	DEL	AGAGA	AGAGA	-	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	AGAGA	AGAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	FAM5C	NM_199051	exon8	c.1222_1226del	p.408_409del	.	.	298.0	66.0	175.0	0.0	.	343	.	.	Atlas-Indel,Pindel
REXO1	57455	hgsc.bcm.edu	hg19	19	1827911	1827912	+	Frame_Shift_Ins	INS	-	-	CTCAT	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	REXO1	NM_020695	exon2	c.877_878insATGAG	p.A293fs	.	.	62.0	46.0	63.0	0.0	.	55	.	.	Atlas-Indel,Pindel
LPA	4018	hgsc.bcm.edu	hg19	6	160953610	160953611	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	LPA	NM_005577	exon39	c.5914_5915insT	p.K1972_Y1973delinsX	.	.	46.0	18.0	32.0	0.0	.	237	.	.	Atlas-Indel,Pindel
BRSK1	84446	hgsc.bcm.edu	hg19	19	55815479	55815480	+	Splice_Site	INS	-	-	TAA	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	BRSK1	NM_032430	exon13	c.1347+1->TAA	.	.	.	86.0	17.0	53.0	0.0	.	192	.	.	Atlas-Indel,Pindel
DSPP	1834	hgsc.bcm.edu	hg19	4	88536956	88536973	+	In_Frame_Del	DEL	AGCAGTGACAGCAGTGAC	AGCAGTGACAGCAGTGAC	-	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	AGCAGTGACAGCAGTGAC	AGCAGTGACAGCAGTGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	DSPP	NM_014208	exon5	c.3141_3158del	p.1047_1053del	.	.	172.0	10.0	204.0	0.0	.	174	.	.	Pindel
VTI1A	143187	hgsc.bcm.edu	hg19	10	114220309	114220315	+	Frame_Shift_Del	DEL	GTGGAGA	GTGGAGA	-	novel		TCGA-CC-A9FU-01A-11D-A36X-10	TCGA-CC-A9FU-10A-01D-A370-10	GTGGAGA	GTGGAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	07019fc1-db55-4a50-806c-4e370020cf28	b19b1b61-ed1e-48d0-a04b-759095dacf7c	.	VTI1A	NM_145206	exon2	c.120_126del	p.40_42del	.	.	480.0	87.0	533.0	0.0	.	15	.	.	Pindel
