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	TVarRat	NVarRat	dbSNP_Strength	dbSNP_AF	dbSNP_PopFreq	Confidence	Algorithm
SSU72	29101	hgsc.bcm.edu	hg19	1	1480325	1480325	+	Silent	SNP	C	C	T	rs138912153	alternate_allele	TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SSU72	NM_014188	exon3	c.G282A	p.R94R	TTCTGGCCGGGGC	.	197.0	71.0	265.0	0.0	.	15	.	.	.	alt	C|1.000;A|0.000	.	PASS	Atlas-SNP
CELA3B	23436	hgsc.bcm.edu	hg19	1	22310247	22310247	+	Silent	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	CELA3B	NM_007352	exon5	c.C423T	p.L141L	CCAGCTCGCCTCA	.	119.0	38.0	136.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
ASAP3	55616	hgsc.bcm.edu	hg19	1	23759922	23759922	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ASAP3	NM_017707	exon21	c.A2123T	p.E708V	ACCTTCTCTTCCT	.	90.0	47.0	119.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
CSMD2	114784	hgsc.bcm.edu	hg19	1	33985175	33985175	+	Silent	SNP	T	T	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	CSMD2	NM_052896	exon69	c.A10407T	p.T3469T	GATGTCTGTGGGC	.	235.0	90.0	330.0	0.0	.	946	.	.	.	none	.	.	PASS	Atlas-SNP
TTF2	8458	hgsc.bcm.edu	hg19	1	117618867	117618867	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TTF2	NM_003594	exon6	c.C1341G	p.I447M	ACAAATCCAGGAG	.	48.0	19.0	75.0	0.0	.	92	.	.	.	none	.	.	PASS	Atlas-SNP
RRNAD1	51093	hgsc.bcm.edu	hg19	1	156706431	156706431	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	RRNAD1,NS,carcinoma,0,1	RRNAD1	NM_001142560	exon7	c.T829C	p.C277R	TTTCCATGCTGAG	.	135.0	52.0	154.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
PRRC2C	23215	hgsc.bcm.edu	hg19	1	171482181	171482181	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	.	NM_015172	exon3	c.C154G	p.R52G	ATTTCACGGCGTA	.	56.0	20.0	65.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
TRIM11	81559	hgsc.bcm.edu	hg19	1	228584695	228584695	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TRIM11	NM_145214	exon5	c.C812A	p.T271N	CACACGGTCCTCA	.	80.0	35.0	101.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
SLC8A1	6546	hgsc.bcm.edu	hg19	2	40405590	40405590	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	SLC8A1,NS,carcinoma,0,1	SLC8A1	NM_021097	exon2	c.A1852G	p.K618E	TGTTTTTCTCATA	.	241.0	108.0	270.0	0.0	.	221	.	.	.	none	.	.	PASS	Atlas-SNP
FBXO11	80204	hgsc.bcm.edu	hg19	2	48049436	48049436	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	FBXO11	NM_001190274	exon13	c.T1623G	p.N541K	TATAGAATTTCCC	.	54.0	19.0	54.0	0.0	.	127	.	.	.	none	.	.	PASS	Atlas-SNP
VGLL4	9686	hgsc.bcm.edu	hg19	3	11600049	11600049	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	VGLL4	NM_001128219	exon5	c.C872T	p.S291F	GAGGGGGAGTGAC	.	101.0	18.0	97.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
B4GALT4	8702	hgsc.bcm.edu	hg19	3	118945881	118945881	+	Silent	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	B4GALT4	NM_212543	exon5	c.G261A	p.Q87Q	CTTGCTCTGGCCT	.	81.0	4.0	67.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
ITGB5	3693	hgsc.bcm.edu	hg19	3	124487860	124487860	+	Missense_Mutation	SNP	C	C	T	rs375122712		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ITGB5	NM_002213	exon12	c.G2017A	p.V673M	ACTCACCGATGGT	.	101.0	29.0	71.0	0.0	.	66	.	.	.	weak	.	.	PASS	Atlas-SNP
FGFR3	2261	hgsc.bcm.edu	hg19	4	1807787	1807787	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	FGFR3	NM_001163213	exon14	c.A1852G	p.R618G	ATCCACAGGGACC	.	27.0	11.0	59.0	0.0	.	3320	.	.	.	none	.	.	PASS	Atlas-SNP
SLAIN2	57606	hgsc.bcm.edu	hg19	4	48384849	48384849	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SLAIN2	NM_020846	exon5	c.T1127A	p.V376E	GTAGAGTGTCCCC	.	46.0	23.0	57.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
TBCK	93627	hgsc.bcm.edu	hg19	4	106967781	106967781	+	Silent	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TBCK	NM_001163436	exon26	c.C2628T	p.G876G	ATTAATGCCACCA	.	50.0	15.0	66.0	0.0	.	89	.	.	.	none	.	.	PASS	Atlas-SNP
JMY	133746	hgsc.bcm.edu	hg19	5	78610483	78610483	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	JMY	NM_152405	exon9	c.C2468T	p.P823L	CACCACCACCACC	.	20.0	7.0	41.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
RAD50	10111	hgsc.bcm.edu	hg19	5	131953819	131953819	+	Silent	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	RAD50	NM_005732	exon21	c.A3222G	p.A1074A	TTTGGCATTAGGG	.	249.0	110.0	226.0	0.0	.	246	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF346	23567	hgsc.bcm.edu	hg19	5	176471535	176471535	+	Splice_Site	SNP	G	G	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ZNF346	NM_012279	exon4	c.517+1G>C	.	TGGAAGGTACTGG	.	80.0	28.0	81.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
ECI2	10455	hgsc.bcm.edu	hg19	6	4117677	4117677	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ECI2	NM_206836	exon9	c.G894C	p.E298D	AAGCATCTCTGTT	.	83.0	29.0	105.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC146	57639	hgsc.bcm.edu	hg19	7	76866323	76866323	+	Silent	SNP	C	C	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	CCDC146	NM_020879	exon3	c.C216G	p.T72T	GTATACCTTGCTG	.	98.0	4.0	54.0	0.0	.	87	.	.	.	none	.	.	PASS	Atlas-SNP
HSF1	3297	hgsc.bcm.edu	hg19	8	145535422	145535422	+	Missense_Mutation	SNP	G	G	A	rs201143946	bycluster	TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	HSF1	NM_005526	exon8	c.G760A	p.A254T	CTCTACGCCCCTG	.	86.0	4.0	77.0	0.0	.	29	.	.	.	weak	.	.	PASS	Atlas-SNP
AGTPBP1	23287	hgsc.bcm.edu	hg19	9	88284416	88284416	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	AGTPBP1	NM_015239	exon8	c.A646C	p.N216H	TGGAATTCTTCTT	.	65.0	26.0	63.0	0.0	.	128	.	.	.	none	.	.	PASS	Atlas-SNP
CCBL1	883	hgsc.bcm.edu	hg19	9	131597888	131597888	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	CCBL1	NM_001122671	exon10	c.A914T	p.Y305F	ACAAAGTAGCTGC	.	57.0	23.0	63.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
NFKB2	4791	hgsc.bcm.edu	hg19	10	104158555	104158555	+	Missense_Mutation	SNP	G	G	A	rs45580031	alternate_allele	TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	NFKB2	NM_001077494	exon12	c.G1051A	p.G351R	CCCTTCGGGGGTG	.	35.0	16.0	54.0	0.0	.	48	.	.	.	alt	G|0.993;C|0.007	.	PASS	Atlas-SNP
CTSC	1075	hgsc.bcm.edu	hg19	11	88045694	88045694	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	CTSC	NM_001814	exon3	c.C347G	p.T116S	CAGTAAGTGGTCA	.	283.0	119.0	316.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
NELL2	4753	hgsc.bcm.edu	hg19	12	44915902	44915902	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	NELL2_ENST00000437801,rectum,carcinoma,0,2	NELL2	NM_001145107	exon19	c.C2206G	p.L736V	AAAAAAGATCAAC	.	50.0	2.0	76.0	0.0	.	286	.	.	.	none	.	.	PASS	Atlas-SNP
DIP2B	57609	hgsc.bcm.edu	hg19	12	51102296	51102296	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	DIP2B	NM_173602	exon22	c.C2600A	p.P867H	AAAGACCTGATGC	.	17.0	9.0	15.0	0.0	.	167	.	.	.	none	.	.	PASS	Atlas-SNP
LETMD1	25875	hgsc.bcm.edu	hg19	12	51450186	51450186	+	Silent	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	LETMD1	NM_001243689	exon7	c.G855A	p.L285L	CTTGTTGAGACAT	.	171.0	71.0	230.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
PTPN11	5781	hgsc.bcm.edu	hg19	12	112892458	112892458	+	Silent	SNP	T	T	C	rs78376169	bycluster	TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	PTPN11,NS,carcinoma,0,2	PTPN11	NM_080601	exon5	c.T616C	p.L206L	GAAACATTGGGTA	.	58.0	4.0	64.0	0.0	.	623	.	.	.	weak	.	.	PASS	Atlas-SNP
TDRD3	81550	hgsc.bcm.edu	hg19	13	61034625	61034625	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TDRD3	NM_001146070	exon4	c.G304A	p.G102S	ACTGATGGTCATA	.	111.0	23.0	89.0	0.0	.	123	.	.	.	none	.	.	PASS	Atlas-SNP
RALGAPA1	253959	hgsc.bcm.edu	hg19	14	36104756	36104756	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	RALGAPA1	NM_194301	exon31	c.C4207G	p.P1403A	TTAGAGGTAAGGC	.	33.0	15.0	51.0	0.0	.	289	.	.	.	none	.	.	PASS	Atlas-SNP
DUOXA2	405753	hgsc.bcm.edu	hg19	15	45410080	45410080	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	DUOXA2	NM_207581	exon6	c.C936A	p.D312E	CCCAGACTTAAAA	.	113.0	48.0	140.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
MYO9A	4649	hgsc.bcm.edu	hg19	15	72172105	72172105	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	MYO9A	NM_006901	exon30	c.A5696G	p.E1899G	CGAAATTCCTTCA	.	76.0	35.0	88.0	0.0	.	203	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM204	79652	hgsc.bcm.edu	hg19	16	1604905	1604905	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TMEM204	NM_024600	exon3	c.A559T	p.I187F	ATGCTCATCTGGA	.	85.0	23.0	74.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
SCNN1B	6338	hgsc.bcm.edu	hg19	16	23387095	23387095	+	Missense_Mutation	SNP	C	C	T	rs372303239		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SCNN1B	NM_000336	exon8	c.C1189T	p.R397C	ATGATCCGTAACT	.	179.0	42.0	124.0	0.0	.	81	.	.	.	weak	.	.	PASS	Atlas-SNP
ELMO3	79767	hgsc.bcm.edu	hg19	16	67236622	67236622	+	Silent	SNP	T	T	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ELMO3	NM_024712	exon15	c.T1650A	p.T550T	GCTCACTTATGGG	.	69.0	44.0	91.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
TEKT1	83659	hgsc.bcm.edu	hg19	17	6703554	6703554	+	Splice_Site	SNP	C	C	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TEKT1	NM_053285	exon9	c.1050-1G>T	.	TTCAATCTAGGAG	.	101.0	29.0	82.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
RAI1	10743	hgsc.bcm.edu	hg19	17	17701717	17701717	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	RAI1	NM_030665	exon3	c.G5455A	p.A1819T	GGGGAGGCCCAGG	.	26.0	17.0	37.0	0.0	.	121	.	.	.	none	.	.	PASS	Atlas-SNP
ALDH3A2	224	hgsc.bcm.edu	hg19	17	19566808	19566808	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ALDH3A2	NM_001031806	exon7	c.A1103G	p.H368R	ATAACCATAAGGT	.	82.0	37.0	78.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
TAF15	8148	hgsc.bcm.edu	hg19	17	34171754	34171754	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TAF15	NM_139215	exon15	c.G1451A	p.G484D	ATCGAGGTGGCTA	.	36.0	17.0	21.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
HELZ	9931	hgsc.bcm.edu	hg19	17	65074431	65074431	+	Silent	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	HELZ	NM_014877	exon33	c.C5766T	p.L1922L	CTGGAAGAGAGAC	.	124.0	35.0	128.0	0.0	.	160	.	.	.	none	.	.	PASS	Atlas-SNP
SMCHD1	23347	hgsc.bcm.edu	hg19	18	2718194	2718194	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SMCHD1	NM_015295	exon18	c.C2299T	p.Q767X	ATTAGTCAACATG	.	46.0	19.0	46.0	0.0	.	88	.	.	.	none	.	.	PASS	Atlas-SNP
TCF4	6925	hgsc.bcm.edu	hg19	18	52921812	52921812	+	Silent	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TCF4	NM_001243226	exon16	c.T1572C	p.I524I	AGGTCCAATGATT	.	53.0	22.0	52.0	0.0	.	178	.	.	.	none	.	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	hg19	19	9056220	9056220	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	MUC16	NM_024690	exon3	c.C31226G	p.T10409R	GTCACTGTTCCCA	.	246.0	94.0	268.0	0.0	.	4315	.	.	.	none	.	.	PASS	Atlas-SNP
CHERP	10523	hgsc.bcm.edu	hg19	19	16640580	16640580	+	Silent	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	CHERP,NS,carcinoma,0,2	CHERP	NM_006387	exon8	c.A1008G	p.Q336Q	CTGCTGTTGCTGC	.	38.0	2.0	36.0	1.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF93	81931	hgsc.bcm.edu	hg19	19	20044771	20044771	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ZNF93	NM_031218	exon4	c.C1007T	p.T336I	TTCATACTGGAGA	.	53.0	21.0	53.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF585A	199704	hgsc.bcm.edu	hg19	19	37642653	37642653	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ZNF585A	NM_199126	exon6	c.G1983T	p.K661N	GTAAGGCTTCTCT	.	106.0	46.0	153.0	0.0	.	117	.	.	.	none	.	.	PASS	Atlas-SNP
SBF1	6305	hgsc.bcm.edu	hg19	22	50903300	50903300	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SBF1	NM_002972	exon13	c.C1379T	p.P460L	CGCTGGGGGTGGT	.	68.0	25.0	78.0	0.0	.	211	.	.	.	none	.	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179429832	179429834	+	In_Frame_Del	DEL	AAT	AAT	-	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TTN	NM_001267550	exon326	c.81026_81028del	p.27009_27010del	.	.	138.0	58.0	158.0	0.0	.	18412	.	0.42029	0	none	.	.	PASS	Atlas-INDEL
ADAM7	8756	hgsc.bcm.edu	hg19	8	24339727	24339728	+	Frame_Shift_Ins	INS	-	-	TA	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ADAM7	NM_003817	exon9	c.778_779insTA	p.L260fs	.	.	101.0	27.0	57.0	0.0	.	165	.	0.267327	0	none	.	.	PASS	Atlas-INDEL
ASNS	440	hgsc.bcm.edu	hg19	7	97482647	97482647	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ASNS	NM_001673	exon11	c.1291delT	p.S431fs	.	.	109.0	25.0	72.0	0.0	.	97	.	0.229358	0	none	.	.	PASS	Atlas-INDEL
SMG5	23381	hgsc.bcm.edu	hg19	1	156221203	156221203	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SMG5	NM_015327	exon20	c.2820delA	p.A940fs	.	.	197.0	69.0	226.0	0.0	.	98	.	0.350254	0	none	.	.	PASS	Atlas-INDEL
AMPH	273	hgsc.bcm.edu	hg19	7	38431574	38431574	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	AMPH	NM_001635	exon19	c.1654delG	p.E552fs	.	.	90.0	55.0	85.0	0.0	.	157	.	0.611111	0	none	.	.	PASS	Atlas-INDEL
SUPT16H	11198	hgsc.bcm.edu	hg19	14	21821646	21821648	+	Frame_Shift_Del	DEL	CCT	CCT	-	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SUPT16H	NM_007192	exon25	c.2998_2998del	p.1000_1000del	.	.	62.0	24.0	109.0	0.0	.	84	.	0.387097	0	none	.	.	PASS	Atlas-INDEL
