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
LYSMD1	388695	hgsc.bcm.edu	hg19	1	151134570	151134570	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	LYSMD1	NM_212551	exon2	c.C187A	p.Q63K	TAATCTGTTCCAT	.	71.0	27.0	69.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
TOR1AIP2	163590	hgsc.bcm.edu	hg19	1	179815212	179815212	+	Silent	SNP	A	A	C	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	TOR1AIP2	NM_001199260	exon7	c.T1407G	p.L469L	TTAGAAAAGGCAC	.	110.0	6.0	118.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	hg19	1	248525639	248525639	+	Missense_Mutation	SNP	A	A	C	rs76878172	alternate_allele	TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	OR2T4,brain,glioma,0,1	OR2T4	NM_001004696	exon1	c.A757C	p.I253L	TTACTCATCCTCC	.	562.0	23.0	668.0	1.0	.	126	.	.	.	alt	.	.	PASS	Atlas-SNP
THUMPD2	80745	hgsc.bcm.edu	hg19	2	39964200	39964200	+	Splice_Site	SNP	C	C	G	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	THUMPD2	NM_025264	exon11	c.1188-1G>C	.	AGCACTCTGTGAC	.	94.0	8.0	92.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
TSGA10	80705	hgsc.bcm.edu	hg19	2	99634687	99634687	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	TSGA10	NM_182911	exon19	c.G2048A	p.R683Q	AGGCCTCGGTCAG	.	87.0	30.0	80.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM184C	55751	hgsc.bcm.edu	hg19	4	148545023	148545023	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	TMEM184C	NM_018241	exon2	c.C162G	p.I54M	TGGAATCTTTTTG	.	65.0	37.0	114.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
MAST4	375449	hgsc.bcm.edu	hg19	5	66456396	66456396	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	MAST4	NM_001164664	exon27	c.C3761A	p.S1254Y	AGAAATCCAAGAA	.	76.0	25.0	89.0	0.0	.	218	.	.	.	none	.	.	PASS	Atlas-SNP
EPB41L4A	64097	hgsc.bcm.edu	hg19	5	111506049	111506049	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	EPB41L4A	NM_022140	exon20	c.C1688T	p.P563L	CCGGATGGATCCA	.	68.0	22.0	71.0	0.0	.	130	.	.	.	none	.	.	PASS	Atlas-SNP
NMBR	4829	hgsc.bcm.edu	hg19	6	142396953	142396953	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	NMBR	NM_002511	exon3	c.C1005T	p.F335F	GCTGTTGAAATGC	.	138.0	8.0	149.0	0.0	.	62	.	.	.	none	.	.	PASS	Atlas-SNP
MEOX2	4223	hgsc.bcm.edu	hg19	7	15725797	15725797	+	Silent	SNP	A	A	G	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	MEOX2,rectum,carcinoma,0,2	MEOX2	NM_005924	exon1	c.T231C	p.H77H	GTGGTGATGGTGG	.	63.0	7.0	84.0	2.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
MEOX2	4223	hgsc.bcm.edu	hg19	7	15725800	15725800	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	MEOX2	NM_005924	exon1	c.C228T	p.H76H	GTGATGGTGGTGG	.	32.0	7.0	30.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
HOXA7	3204	hgsc.bcm.edu	hg19	7	27194707	27194707	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	HOXA7	NM_006896	exon2	c.C514T	p.R172C	TCTGGCGCTCGGT	.	119.0	32.0	111.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
PILRA	29992	hgsc.bcm.edu	hg19	7	99972037	99972037	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	PILRA	NM_013439	exon2	c.C435T	p.T145T	GGGGACCAAACTC	.	79.0	21.0	85.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
KIF13B	23303	hgsc.bcm.edu	hg19	8	28984749	28984749	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	KIF13B	NM_015254	exon25	c.G3112C	p.V1038L	CCTGCACTGACTT	.	132.0	9.0	121.0	0.0	.	192	.	.	.	none	.	.	PASS	Atlas-SNP
DCAF13	25879	hgsc.bcm.edu	hg19	8	104432551	104432551	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	DCAF13	NM_015420	exon2	c.G586T	p.A196S	ATAAGAGCTTTAA	.	135.0	48.0	165.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC171	203238	hgsc.bcm.edu	hg19	9	15745613	15745613	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	C9orf93_ENST00000380689,colon,carcinoma,0,4	.	NM_173550	exon18	c.C2655T	p.D885D	ACAAGACGTCATT	.	44.0	16.0	43.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ITIH5	80760	hgsc.bcm.edu	hg19	10	7621949	7621949	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	ITIH5	NM_001001851	exon9	c.G1187A	p.R396Q	ACGCTCCGGTCTC	.	60.0	33.0	75.0	0.0	.	343	.	.	.	none	.	.	PASS	Atlas-SNP
CREB3L1	90993	hgsc.bcm.edu	hg19	11	46342259	46342259	+	Splice_Site	SNP	A	A	G	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	CREB3L1,caecum,carcinoma,0,1	CREB3L1	NM_052854	exon12	c.1524-1A>G	.	CTCTCCAGGATCT	.	156.0	8.0	149.0	1.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
ACY3	91703	hgsc.bcm.edu	hg19	11	67413212	67413212	+	Missense_Mutation	SNP	G	G	A	rs368150084		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	ACY3	NM_080658	exon4	c.C383T	p.A128V	GACTTCGCGATTA	.	203.0	12.0	195.0	0.0	.	27	.	.	.	weak	.	.	PASS	Atlas-SNP
POU2AF1	5450	hgsc.bcm.edu	hg19	11	111228192	111228192	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	POU2AF1	NM_006235	exon4	c.C434T	p.P145L	AGTGGCGGAGAGG	.	338.0	131.0	370.0	1.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
HTR3A	3359	hgsc.bcm.edu	hg19	11	113846045	113846045	+	Missense_Mutation	SNP	G	G	A	rs200513646	bycluster	TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	HTR3A	NM_000869	exon1	c.G16A	p.A6T	AAGCTCGCTATGC	.	26.0	8.0	53.0	0.0	.	93	.	.	.	weak	.	.	PASS	Atlas-SNP
TP53BP1	7158	hgsc.bcm.edu	hg19	15	43748237	43748237	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	TP53BP1	NM_001141980	exon12	c.C2569T	p.Q857X	GGGGCTGCTGCAA	.	70.0	26.0	74.0	0.0	.	157	.	.	.	none	.	.	PASS	Atlas-SNP
ABCC1	4363	hgsc.bcm.edu	hg19	16	16177358	16177358	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	ABCC1	NM_004996	exon17	c.G2251A	p.E751K	GACCTGGAAATCC	.	253.0	52.0	209.0	0.0	.	156	.	.	.	none	.	.	PASS	Atlas-SNP
RLTPR	146206	hgsc.bcm.edu	hg19	16	67683208	67683208	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	RLTPR	NM_001013838	exon19	c.C1740T	p.D580D	GGACGACGATTGT	.	48.0	20.0	40.0	0.0	.	124	.	.	.	none	.	.	PASS	Atlas-SNP
KRTAP4-5	85289	hgsc.bcm.edu	hg19	17	39305774	39305774	+	Missense_Mutation	SNP	C	C	G	rs137947981	bycluster	TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	KRTAP4-5,NS,carcinoma,0,1	KRTAP4-5	NM_033188	exon1	c.G246C	p.Q82H	GGTGGTCTGGCAG	.	83.0	23.0	75.0	0.0	.	34	.	.	.	weak	.	.	PASS	Atlas-SNP
KRTAP4-5	85289	hgsc.bcm.edu	hg19	17	39305775	39305775	+	Missense_Mutation	SNP	T	T	C	rs141265645	bycluster	TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	KRTAP4-5,NS,carcinoma,+1,1	KRTAP4-5	NM_033188	exon1	c.A245G	p.Q82R	GTGGTCTGGCAGC	.	86.0	26.0	74.0	0.0	.	34	.	.	.	weak	.	.	PASS	Atlas-SNP
SP6	80320	hgsc.bcm.edu	hg19	17	45925061	45925061	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	SP6	NM_001258248	exon2	c.C735T	p.P245P	CCCATCGGGCCCA	.	83.0	31.0	101.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
DNAI2	64446	hgsc.bcm.edu	hg19	17	72306227	72306227	+	Silent	SNP	G	G	T	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	DNAI2	NM_023036	exon11	c.G1419T	p.L473L	CCAGCTGGGGACA	.	93.0	32.0	96.0	0.0	.	102	.	.	.	none	.	.	PASS	Atlas-SNP
RAB40B	10966	hgsc.bcm.edu	hg19	17	80617514	80617514	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	RAB40B	NM_006822	exon4	c.A284T	p.D95V	GCAATGTCATAGA	.	128.0	51.0	138.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
MBD1	4152	hgsc.bcm.edu	hg19	18	47802004	47802004	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	MBD1	NM_001204137	exon8	c.G758A	p.R253H	CACTGGCGCCTGA	.	224.0	74.0	239.0	0.0	.	228	.	.	.	none	.	.	PASS	Atlas-SNP
SPTBN4	57731	hgsc.bcm.edu	hg19	19	41076606	41076606	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	SPTBN4	NM_020971	exon33	c.C7291T	p.L2431F	CGCGAGCTCGACG	.	74.0	27.0	68.0	0.0	.	213	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	hg19	19	52376124	52376124	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	ZNF577,NS,carcinoma,0,1	ZNF577	NM_032679	exon7	c.G1119T	p.E373D	AGTTTTCTCATGT	.	84.0	40.0	67.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
EPB41L1	2036	hgsc.bcm.edu	hg19	20	34778710	34778710	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	EPB41L1	NM_001258329	exon12	c.C1291G	p.L431V	CGCAGCCTTGATG	.	38.0	12.0	45.0	0.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
FAM83D	81610	hgsc.bcm.edu	hg19	20	37570604	37570604	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	FAM83D	NM_030919	exon2	c.G576A	p.V192V	GTAGGTGATTGCA	.	151.0	53.0	155.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
PLXNB2	23654	hgsc.bcm.edu	hg19	22	50728592	50728592	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	PLXNB2	NM_012401	exon3	c.A422T	p.K141M	AAAGACTTCTCCC	.	113.0	39.0	115.0	0.0	.	172	.	.	.	none	.	.	PASS	Atlas-SNP
PLXNB2	23654	hgsc.bcm.edu	hg19	22	50728593	50728593	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	PLXNB2	NM_012401	exon3	c.A421G	p.K141E	AAGACTTCTCCCC	.	113.0	41.0	110.0	0.0	.	172	.	.	.	none	.	.	PASS	Atlas-SNP
ARSE	415	hgsc.bcm.edu	hg19	X	2861169	2861169	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	ARSE	NM_000047	exon8	c.G1063A	p.G355S	AACCGCCGTGATC	.	91.0	62.0	87.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	hg19	4	187629210	187629211	+	Frame_Shift_Del	DEL	AC	AC	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	FAT1	NM_005245	exon2	c.1772_1773del	p.591_591del	.	.	53.0	25.0	84.0	0.0	.	500	.	0.471698	0	none	.	.	PASS	Atlas-Indel,Pindel
DMXL1	1657	hgsc.bcm.edu	hg19	5	118556763	118556765	+	In_Frame_Del	DEL	GAG	GAG	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	DMXL1	NM_005509	exon36	c.8200_8202del	p.2734_2734del	.	.	313.0	96.0	385.0	0.0	.	268	.	0.306709	0	none	.	.	PASS	Atlas-Indel,Pindel
KIAA1217	56243	hgsc.bcm.edu	hg19	10	24832228	24832229	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	KIAA1217	NM_019590	exon19	c.4028_4029del	p.1343_1343del	.	.	309.0	132.0	304.0	0.0	.	235	.	0.427184	0	none	.	.	PASS	Atlas-Indel,Pindel
EIF4G3	8672	hgsc.bcm.edu	hg19	1	21133827	21133829	+	In_Frame_Del	DEL	CTC	CTC	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	EIF4G3	NM_001198801	exon35	c.4850_4852del	p.1617_1618del	.	.	99.0	33.0	108.0	0.0	.	300	.	0.333333	0	none	.	.	PASS	Atlas-Indel,Pindel
THUMPD2	80745	hgsc.bcm.edu	hg19	2	39964198	39964199	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	THUMPD2	NM_025264	exon10	c.1189_1190del	p.397_397del	.	.	124.0	23.0	94.0	0.0	.	35	.	0.185484	0	none	.	.	PASS	Atlas-Indel,Pindel
HIF1A	3091	hgsc.bcm.edu	hg19	14	62194216	62194223	+	Frame_Shift_Del	DEL	AACCAACC	AACCAACC	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AACCAACC	AACCAACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	HIF1A	NM_001243084	exon6	c.687_694del	p.229_232del	.	.	93.0	15.0	146.0	0.0	.	120	.	0.16129	0	none	.	.	PASS	Atlas-INDEL
NIPBL	25836	hgsc.bcm.edu	hg19	5	36986201	36986204	+	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AAAG	AAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	NIPBL	NM_133433	exon10	c.2918_2921del	p.973_974del	.	.	80.0	17.0	92.0	0.0	.	513	.	0.2125	0	none	.	.	PASS	Atlas-Indel,Pindel
SETD9	133383	hgsc.bcm.edu	hg19	5	56210690	56210691	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	.	NM_001171990	exon5	c.708_709del	p.236_237del	.	.	96.0	11.0	86.0	0.0	.	.	.	0.114583	0	none	.	.	PASS	Atlas-INDEL
HIF1A	3091	hgsc.bcm.edu	hg19	14	62194225	62194225	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	HIF1A	NM_001243084	exon6	c.696delT	p.P232fs	.	.	98.0	15.0	156.0	0.0	.	120	.	0.153061	0	none	.	.	PASS	Atlas-INDEL
IGFBP6	3489	hgsc.bcm.edu	hg19	12	53494509	53494509	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	IGFBP6	NM_002178	exon2	c.347delA	p.N116fs	.	.	71.0	30.0	62.0	0.0	.	16	.	0.422535	0	none	.	.	PASS	Atlas-Indel,Pindel
SAMD9	54809	hgsc.bcm.edu	hg19	7	92731495	92731495	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	SAMD9	NM_001193307	exon2	c.3917delT	p.I1306fs	.	.	32.0	12.0	28.0	0.0	.	239	.	0.375	0	none	.	.	PASS	Atlas-Indel,Pindel
GPR37L1	9283	hgsc.bcm.edu	hg19	1	202097307	202097311	+	Frame_Shift_Del	DEL	CTCAA	CTCAA	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	CTCAA	CTCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	GPR37L1	NM_004767	exon2	c.1068_1072del	p.356_358del	.	.	86.0	37.0	83.0	0.0	.	33	.	0.430233	0	none	.	.	PASS	Atlas-Indel,Pindel
GLS	2744	hgsc.bcm.edu	hg19	2	191788697	191788701	+	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AAAAG	AAAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	GLS	NM_001256310	exon10	c.1184_1188del	p.395_396del	.	.	120.0	34.0	132.0	0.0	.	47	.	0.283333	0	none	.	.	PASS	Atlas-Indel,Pindel
HOXD10	3236	hgsc.bcm.edu	hg19	2	176981597	176981599	+	In_Frame_Del	DEL	TTT	TTT	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	HOXD10	NM_002148	exon1	c.35_37del	p.12_13del	.	.	80.0	33.0	80.0	0.0	.	65	.	0.4125	0	none	.	.	PASS	Atlas-Indel,Pindel
TRIM39	56658	hgsc.bcm.edu	hg19	6	30303731	30303752	+	Frame_Shift_Del	DEL	GTCAGGCTTCGAGATGCTTAAG	GTCAGGCTTCGAGATGCTTAAG	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	GTCAGGCTTCGAGATGCTTAAG	GTCAGGCTTCGAGATGCTTAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	TRIM39	NM_172016	exon5	c.758_779del	p.253_260del	.	.	40.0	13.0	91.0	0.0	.	56	.	0.325	.	none	.	.	PASS	Pindel
HIF1A	3091	hgsc.bcm.edu	hg19	14	62194216	62194225	+	Frame_Shift_Del	DEL	AACCAACCTC	AACCAACCTC	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AACCAACCTC	AACCAACCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	HIF1A	NM_001243084	exon6	c.687_696del	p.229_232del	.	.	100.0	15.0	152.0	0.0	.	120	.	0.150	.	none	.	.	PASS	Pindel
MSH4	4438	hgsc.bcm.edu	hg19	1	76346929	76346934	+	Splice_Site	DEL	TTTCAG	TTTCAG	-	novel		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	TTTCAG	TTTCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	.	MSH4	.	.	.	.	.	.	59.0	11.0	82.0	0.0	.	147	.	0.186	.	none	.	.	PASS	Pindel