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
CROCC	9696	hgsc.bcm.edu	hg19	1	17298042	17298042	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	CROCC	NM_014675	exon36	c.A5867T	p.Q1956L	TGCAGCAGGAGGT	.	75.0	28.0	117.0	0.0	.	185	.	.	Atlas-SNP
VWA5B1	127731	hgsc.bcm.edu	hg19	1	20644146	20644146	+	Silent	SNP	C	C	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	VWA5B1	NM_001039500	exon5	c.C687A	p.I229I	GGAGATCCGTGGG	.	68.0	15.0	124.0	0.0	.	44	.	.	Atlas-SNP
RCAN3	11123	hgsc.bcm.edu	hg19	1	24859580	24859580	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	RCAN3	NM_001251979	exon4	c.T377C	p.M126T	TGCAGATGTCCGG	.	64.0	25.0	98.0	0.0	.	22	.	.	Atlas-SNP
NCDN	23154	hgsc.bcm.edu	hg19	1	36029507	36029507	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	NCDN	NM_014284	exon6	c.C1750A	p.P584T	ACCTCTCCAGGTA	.	54.0	32.0	65.0	0.0	.	79	.	.	Atlas-SNP
ZNF691	51058	hgsc.bcm.edu	hg19	1	43315395	43315395	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	ZNF691	NM_001242739	exon3	c.G66T	p.M22I	GGAAATGCTACCA	.	125.0	48.0	152.0	0.0	.	30	.	.	Atlas-SNP
EPS8L3	79574	hgsc.bcm.edu	hg19	1	110293318	110293318	+	Silent	SNP	G	G	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	EPS8L3	NM_139053	exon18	c.C1737T	p.I579I	GGACAGGATTCGT	.	97.0	5.0	127.0	0.0	.	73	.	.	Atlas-SNP
KCNN3	3782	hgsc.bcm.edu	hg19	1	154842095	154842095	+	Missense_Mutation	SNP	A	A	T	rs76110919	bycluster;alternate_allele	TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	KCNN3	NM_001204087	exon1	c.T346A	p.S116T	CGGTGGAGTTGGA	.	260.0	17.0	213.0	0.0	.	141	.	.	Atlas-SNP
SHC1	6464	hgsc.bcm.edu	hg19	1	154940971	154940971	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	SHC1	NM_183001	exon4	c.G750T	p.Q250H	ACCAACCTGTTTG	.	104.0	68.0	83.0	0.0	.	91	.	.	Atlas-SNP
DARC	2532	hgsc.bcm.edu	hg19	1	159176208	159176208	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	DARC	NM_001122951	exon1	c.T985A	p.S329T	TGGTCTTCTCATC	.	132.0	36.0	111.0	0.0	.	76	.	.	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	hg19	1	186281352	186281352	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	PRG4	NM_005807	exon11	c.A3839G	p.K1280R	TACAGAAGTGCCC	.	199.0	128.0	144.0	0.0	.	259	.	.	Atlas-SNP
PQLC3	130814	hgsc.bcm.edu	hg19	2	11317882	11317882	+	Silent	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	PQLC3	NM_152391	exon7	c.C537T	p.I179I	TGTGATCATGCTG	.	54.0	30.0	51.0	0.0	.	8	.	.	Atlas-SNP
EMILIN1	11117	hgsc.bcm.edu	hg19	2	27305559	27305559	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	EMILIN1	NM_007046	exon4	c.G1120A	p.G374S	GTGGCCGGCTCAG	.	103.0	24.0	114.0	0.0	.	75	.	.	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	hg19	2	73613036	73613036	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	ALMS1	NM_015120	exon1	c.G40C	p.E14Q	CTGGAGGAGGAGG	.	273.0	11.0	239.0	0.0	.	384	.	.	Atlas-SNP
DNAH7	56171	hgsc.bcm.edu	hg19	2	196681579	196681579	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	DNAH7	NM_018897	exon51	c.G9534T	p.L3178F	ATTAGCCAAGGCC	.	494.0	133.0	489.0	1.0	.	512	.	.	Atlas-SNP
COL4A3	1285	hgsc.bcm.edu	hg19	2	228141161	228141161	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	COL4A3	NM_000091	exon27	c.C1988T	p.P663L	CAGGGCCCCCTGG	.	121.0	65.0	98.0	0.0	.	293	.	.	Atlas-SNP
SH3BP4	23677	hgsc.bcm.edu	hg19	2	235949591	235949591	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	SH3BP4	NM_014521	exon4	c.G178T	p.V60L	AAGGAAGTGATTG	.	119.0	68.0	113.0	0.0	.	109	.	.	Atlas-SNP
GOLGA4	2803	hgsc.bcm.edu	hg19	3	37396591	37396591	+	Splice_Site	SNP	G	G	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	GOLGA4	NM_001172713	exon22	c.6622-1G>A	.	CTTGTAGACCATG	.	127.0	30.0	87.0	0.0	.	173	.	.	Atlas-SNP
CTNNB1	1499	hgsc.bcm.edu	hg19	3	41266137	41266137	+	Missense_Mutation	SNP	C	C	A	rs121913409	bycluster	TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	CTNNB1,NS,carcinoma,+1,2	CTNNB1	NM_001098209	exon3	c.C134A	p.S45Y	CTCCTTCTCTGAG	.	174.0	95.0	209.0	0.0	.	4904	.	.	Atlas-SNP
SACM1L	22908	hgsc.bcm.edu	hg19	3	45751119	45751119	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	SACM1L	NM_014016	exon5	c.G463C	p.E155Q	TTCCAAGAAATGA	.	127.0	27.0	126.0	0.0	.	38	.	.	Atlas-SNP
PDZRN3	23024	hgsc.bcm.edu	hg19	3	73433952	73433952	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	PDZRN3	NM_015009	exon10	c.A1765C	p.N589H	CGCCATTGTTCTC	.	79.0	21.0	70.0	0.0	.	196	.	.	Atlas-SNP
C3orf37	56941	hgsc.bcm.edu	hg19	3	129017267	129017267	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	C3orf37	NM_020187	exon5	c.C524T	p.T175I	TGCTGACAATGGC	.	195.0	103.0	214.0	1.0	.	27	.	.	Atlas-SNP
PDE6B	5158	hgsc.bcm.edu	hg19	4	661717	661717	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	PDE6B	NM_001145291	exon21	c.G2425A	p.A809T	TGGAAGGCGCTGG	.	77.0	24.0	89.0	0.0	.	80	.	.	Atlas-SNP
STK32B	55351	hgsc.bcm.edu	hg19	4	5500781	5500781	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	STK32B	NM_018401	exon12	c.C1216T	p.H406Y	CTCACCCACACCT	.	219.0	97.0	323.0	0.0	.	87	.	.	Atlas-SNP
GABRG1	2565	hgsc.bcm.edu	hg19	4	46067487	46067487	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	GABRG1,NS,carcinoma,0,1	GABRG1	NM_173536	exon4	c.C436A	p.P146T	TGTCAGGAATCCA	.	93.0	39.0	80.0	0.0	.	172	.	.	Atlas-SNP
CXCL13	10563	hgsc.bcm.edu	hg19	4	78528986	78528986	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	CXCL13	NM_006419	exon3	c.T194C	p.I65T	AAGAAATCATGTA	.	90.0	13.0	108.0	0.0	.	9	.	.	Atlas-SNP
FAM160A1	729830	hgsc.bcm.edu	hg19	4	152570857	152570857	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	FAM160A1	NM_001109977	exon11	c.C1664T	p.P555L	GGCTCCCGCAACA	.	154.0	63.0	130.0	0.0	.	60	.	.	Atlas-SNP
HEXB	3074	hgsc.bcm.edu	hg19	5	73981154	73981154	+	Silent	SNP	G	G	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	HEXB	NM_000521	exon1	c.G69A	p.L23L	ACTGCTGGCGGCG	.	97.0	49.0	104.0	0.0	.	34	.	.	Atlas-SNP
GFM2	84340	hgsc.bcm.edu	hg19	5	74021934	74021934	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	GFM2	NM_032380	exon18	c.T1744G	p.L582V	CTCCTAAAGTTCT	.	44.0	10.0	61.0	0.0	.	38	.	.	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	hg19	5	169412919	169412919	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	DOCK2	NM_004946	exon29	c.C2986T	p.Q996X	ATGGTTCAAAACA	.	107.0	33.0	164.0	0.0	.	389	.	.	Atlas-SNP
HIST1H2AH	85235	hgsc.bcm.edu	hg19	6	27114964	27114964	+	Silent	SNP	T	T	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	HIST1H2AH	NM_080596	exon1	c.T57C	p.S19S	CCGCTCTTCTCGG	.	266.0	54.0	268.0	0.0	.	26	.	.	Atlas-SNP
SKIV2L	6499	hgsc.bcm.edu	hg19	6	31927872	31927872	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	SKIV2L	NM_006929	exon3	c.T212A	p.L71Q	TGCCTCTGCATGG	.	120.0	41.0	92.0	0.0	.	97	.	.	Atlas-SNP
TEAD3	7005	hgsc.bcm.edu	hg19	6	35443156	35443156	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	TEAD3	NM_003214	exon12	c.A1151G	p.K384R	ATGTACTTCTCGG	.	58.0	24.0	64.0	0.0	.	52	.	.	Atlas-SNP
TJAP1	93643	hgsc.bcm.edu	hg19	6	43473578	43473578	+	Silent	SNP	C	C	G	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	TJAP1	NM_001146016	exon11	c.C1659G	p.G553G	GCAGGGCAACCTG	.	73.0	23.0	54.0	0.0	.	35	.	.	Atlas-SNP
TFAP2B	7021	hgsc.bcm.edu	hg19	6	50803851	50803851	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	TFAP2B	NM_003221	exon4	c.G679C	p.G227R	AACACCGGCGAGG	.	155.0	10.0	110.0	0.0	.	91	.	.	Atlas-SNP
HCRTR2	3062	hgsc.bcm.edu	hg19	6	55120007	55120007	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	HCRTR2	NM_001526	exon3	c.C476T	p.P159L	GTCACCCTTTGAT	.	132.0	70.0	81.0	0.0	.	112	.	.	Atlas-SNP
HMGCLL1	54511	hgsc.bcm.edu	hg19	6	55300495	55300495	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	HMGCLL1	NM_019036	exon10	c.A1078T	p.N360Y	TAGAGTTTGTGGT	.	117.0	32.0	122.0	0.0	.	70	.	.	Atlas-SNP
BAI3	577	hgsc.bcm.edu	hg19	6	70071152	70071152	+	Silent	SNP	T	T	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	BAI3	NM_001704	exon29	c.T3987C	p.N1329N	AATGAATATTGGC	.	77.0	35.0	109.0	0.0	.	451	.	.	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	hg19	6	152831461	152831461	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	SYNE1	NM_033071	exon8	c.A469C	p.S157R	CGCTGCTGGACAA	.	92.0	64.0	175.0	0.0	.	3227	.	.	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	hg19	7	5352817	5352817	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	TNRC18	NM_001080495	exon27	c.A7705G	p.S2569G	TGCTGCTACTGCT	.	49.0	12.0	64.0	0.0	.	311	.	.	Atlas-SNP
CCDC129	223075	hgsc.bcm.edu	hg19	7	31592634	31592634	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	CCDC129	NM_001257968	exon2	c.C74A	p.S25Y	ATTACTCTCCTAT	.	78.0	29.0	95.0	0.0	.	127	.	.	Atlas-SNP
ZNF3	7551	hgsc.bcm.edu	hg19	7	99674980	99674980	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	ZNF3	NM_032924	exon3	c.A1T	p.M1L	TTTCCATGGAAGG	.	99.0	34.0	122.0	0.0	.	54	.	.	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	hg19	7	128494870	128494870	+	Silent	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	FLNC	NM_001458	exon42	c.C7039T	p.L2347L	GGGGGCCTGTCCA	.	89.0	35.0	155.0	0.0	.	339	.	.	Atlas-SNP
CNOT4	4850	hgsc.bcm.edu	hg19	7	135099083	135099083	+	Silent	SNP	A	A	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	CNOT4	NM_001190850	exon5	c.T558A	p.L186L	TACCTTAAGTGTT	.	74.0	29.0	74.0	0.0	.	146	.	.	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	hg19	7	149518154	149518154	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	.	NM_198455	exon87	c.C12497A	p.S4166X	ACTGGTCGGCCTG	.	43.0	13.0	55.0	0.0	.	.	.	.	Atlas-SNP
HTR5A	3361	hgsc.bcm.edu	hg19	7	154876098	154876098	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	HTR5A	NM_024012	exon2	c.G975C	p.W325C	CCTGTGGCTTGGC	.	120.0	48.0	170.0	0.0	.	114	.	.	Atlas-SNP
XKR4	114786	hgsc.bcm.edu	hg19	8	56015588	56015588	+	Silent	SNP	T	T	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	XKR4	NM_052898	exon1	c.T540A	p.A180A	GGCCGCTGCTGCC	.	89.0	38.0	106.0	0.0	.	104	.	.	Atlas-SNP
TMEM67	91147	hgsc.bcm.edu	hg19	8	94770709	94770709	+	Splice_Site	SNP	A	A	G	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	TMEM67	NM_153704	exon3	c.313-2A>G	.	TAATTTAGAAAGG	.	114.0	66.0	91.0	0.0	.	187	.	.	Atlas-SNP
KIAA1429	25962	hgsc.bcm.edu	hg19	8	95550552	95550552	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	KIAA1429	NM_015496	exon3	c.C202T	p.Q68X	CTAATTGAAATGT	.	141.0	41.0	110.0	0.0	.	176	.	.	Atlas-SNP
AZIN1	51582	hgsc.bcm.edu	hg19	8	103855817	103855817	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	AZIN1	NM_015878	exon4	c.G64T	p.G22X	CATTTCCAAGGTT	.	194.0	20.0	166.0	0.0	.	26	.	.	Atlas-SNP
AGO2	27161	hgsc.bcm.edu	hg19	8	141559371	141559371	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	.	NM_012154	exon12	c.T1430A	p.I477N	CTCGAGATCTTTC	.	64.0	42.0	65.0	0.0	.	.	.	.	Atlas-SNP
JAK2	3717	hgsc.bcm.edu	hg19	9	5044434	5044434	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	JAK2	NM_004972	exon5	c.A382T	p.S128C	AGTGGCAGCAACA	.	102.0	34.0	102.0	0.0	.	35466	.	.	Atlas-SNP
ZMYND11	10771	hgsc.bcm.edu	hg19	10	226050	226050	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	ZMYND11	NM_001202465	exon2	c.A98G	p.N33S	TTGCCAACATTGA	.	113.0	44.0	129.0	0.0	.	72	.	.	Atlas-SNP
UPF2	26019	hgsc.bcm.edu	hg19	10	12041933	12041933	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	UPF2	NM_080599	exon7	c.A1730C	p.N577T	ACACAGTTGGGTA	.	80.0	31.0	124.0	0.0	.	111	.	.	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	hg19	10	50534397	50534397	+	Silent	SNP	G	G	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	C10orf71	NM_001135196	exon3	c.G3807A	p.A1269A	GCCCGCGTACCCC	.	114.0	38.0	175.0	0.0	.	179	.	.	Atlas-SNP
ADAM12	8038	hgsc.bcm.edu	hg19	10	127753571	127753571	+	Splice_Site	SNP	C	C	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	ADAM12	NM_003474	exon15	c.1423-1G>T	.	CTTCAGCTGGAAG	.	31.0	14.0	38.0	0.0	.	388	.	.	Atlas-SNP
KRTAP5-1	387264	hgsc.bcm.edu	hg19	11	1606214	1606214	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	KRTAP5-1	NM_001005922	exon1	c.G266A	p.C89Y	GAGCCACAGCCCC	.	127.0	44.0	190.0	0.0	.	74	.	.	Atlas-SNP
MAP3K11	4296	hgsc.bcm.edu	hg19	11	65365864	65365864	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	MAP3K11	NM_002419	exon10	c.C2442A	p.D814E	TGGGGAGTCCCAG	.	127.0	42.0	218.0	0.0	.	67	.	.	Atlas-SNP
ADAMTS20	80070	hgsc.bcm.edu	hg19	12	43833794	43833794	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	ADAMTS20	NM_025003	exon17	c.A2369G	p.Q790R	GTTCCTTGCACAT	.	56.0	22.0	87.0	0.0	.	635	.	.	Atlas-SNP
SYCP3	50511	hgsc.bcm.edu	hg19	12	102125389	102125389	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	SYCP3,NS,carcinoma,0,1	SYCP3	NM_001177949	exon7	c.A509T	p.Q170L	AATCTCTGGCTCT	.	39.0	12.0	60.0	0.0	.	19	.	.	Atlas-SNP
OLFM4	10562	hgsc.bcm.edu	hg19	13	53624703	53624703	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	OLFM4	NM_006418	exon5	c.C1330A	p.R444S	GCCACCCGTACTA	.	117.0	43.0	161.0	0.0	.	94	.	.	Atlas-SNP
HECTD1	25831	hgsc.bcm.edu	hg19	14	31597196	31597196	+	Silent	SNP	A	A	G	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	HECTD1	NM_015382	exon26	c.T4776C	p.G1592G	CTGAGCACCCATA	.	79.0	29.0	106.0	0.0	.	159	.	.	Atlas-SNP
MTHFD1	4522	hgsc.bcm.edu	hg19	14	64920556	64920556	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	MTHFD1	NM_005956	exon25	c.A2542C	p.K848Q	CAACACAAAGCTG	.	127.0	52.0	139.0	0.0	.	61	.	.	Atlas-SNP
PLEKHD1	400224	hgsc.bcm.edu	hg19	14	69994592	69994592	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	PLEKHD1	NM_001161498	exon12	c.C1294T	p.R432C	GCCACTCGCCGCA	.	90.0	41.0	121.0	0.0	.	24	.	.	Atlas-SNP
UNC79	57578	hgsc.bcm.edu	hg19	14	94139742	94139742	+	Silent	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	UNC79	NM_020818	exon42	c.C6268T	p.L2090L	GAACTTCTGCAGG	.	84.0	23.0	98.0	0.0	.	366	.	.	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	hg19	14	105411351	105411351	+	Silent	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	AHNAK2	NM_138420	exon7	c.G10437A	p.K3479K	GGGCATCTTGAAC	.	83.0	17.0	98.0	0.0	.	719	.	.	Atlas-SNP
BAHD1	22893	hgsc.bcm.edu	hg19	15	40751536	40751536	+	Silent	SNP	A	A	G	rs144909314	byfrequency;alternate_allele	TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	BAHD1	NM_014952	exon2	c.A873G	p.P291P	TGGGCCATCCGTC	.	106.0	47.0	147.0	0.0	.	68	.	A|0.997;C|0.003	Atlas-SNP
CORO2B	10391	hgsc.bcm.edu	hg19	15	69011783	69011783	+	Silent	SNP	T	T	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	CORO2B	NM_006091	exon11	c.T1203C	p.Y401Y	AGGCTATAAGAAG	.	127.0	54.0	191.0	0.0	.	68	.	.	Atlas-SNP
RCN2	5955	hgsc.bcm.edu	hg19	15	77224707	77224707	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	RCN2	NM_002902	exon2	c.T150A	p.D50E	GGAAGATGTGGAT	.	67.0	23.0	68.0	0.0	.	16	.	.	Atlas-SNP
PRPF8	10594	hgsc.bcm.edu	hg19	17	1584082	1584082	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	PRPF8	NM_006445	exon8	c.G1036T	p.D346Y	GCAAGTCAGGATC	.	119.0	52.0	170.0	0.0	.	169	.	.	Atlas-SNP
TTC19	54902	hgsc.bcm.edu	hg19	17	15903501	15903501	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	TTC19	NM_017775	exon2	c.C254T	p.A85V	CCGCTGCCGAGGA	.	867.0	91.0	1107.0	0.0	.	10	.	.	Atlas-SNP
TAOK1	57551	hgsc.bcm.edu	hg19	17	27849536	27849536	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	TAOK1	NM_020791	exon17	c.A2147T	p.K716M	GTTTGAAGGTATG	.	114.0	13.0	180.0	0.0	.	151	.	.	Atlas-SNP
SLFN14	342618	hgsc.bcm.edu	hg19	17	33875849	33875849	+	Silent	SNP	A	A	G	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	SLFN14	NM_001129820	exon4	c.T2148C	p.L716L	AGGGGGAAGGCCA	.	117.0	5.0	145.0	0.0	.	43	.	.	Atlas-SNP
ATP6V0A1	535	hgsc.bcm.edu	hg19	17	40650998	40650998	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	ATP6V0A1	NM_001130020	exon15	c.G1638A	p.M546I	GAAGATGTCTGTT	.	112.0	41.0	171.0	0.0	.	67	.	.	Atlas-SNP
ABCA5	23461	hgsc.bcm.edu	hg19	17	67285417	67285417	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	ABCA5	NM_018672	exon13	c.T1803G	p.D601E	GTCTAAATCTAGT	.	62.0	29.0	84.0	0.0	.	162	.	.	Atlas-SNP
SBNO2	22904	hgsc.bcm.edu	hg19	19	1109536	1109536	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	SBNO2	NM_014963	exon28	c.G3185A	p.G1062D	TAGGGGCCCGTCA	.	106.0	37.0	176.0	0.0	.	112	.	.	Atlas-SNP
PTPRS	5802	hgsc.bcm.edu	hg19	19	5244107	5244107	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	PTPRS	NM_002850	exon11	c.G1375T	p.G459C	GGTAGCCGCGGAT	.	40.0	15.0	55.0	0.0	.	169	.	.	Atlas-SNP
FUT6	2528	hgsc.bcm.edu	hg19	19	5832522	5832522	+	Silent	SNP	C	C	A	rs371867552	alternate_allele	TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	FUT6	NM_000150	exon3	c.G57T	p.T19T	CAGCAGCGTGGTC	.	113.0	35.0	183.0	0.0	.	30	.	.	Atlas-SNP
CACNA1A	773	hgsc.bcm.edu	hg19	19	13616903	13616903	+	Silent	SNP	T	T	G	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	CACNA1A	NM_001127221	exon1	c.A136C	p.R46R	ACATCCTTTGCGC	.	935.0	368.0	1172.0	1.0	.	715	.	.	Atlas-SNP
CEACAM5	1048	hgsc.bcm.edu	hg19	19	42221465	42221465	+	Silent	SNP	G	G	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	CEACAM5	NM_004363	exon5	c.G1050A	p.Q350Q	GATTCAGAACACA	.	89.0	31.0	133.0	0.0	.	84	.	.	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	hg19	19	54726002	54726002	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	LILRB3	NM_006864	exon4	c.G356T	p.G119V	TAGGCTCCTAGGA	.	141.0	18.0	214.0	0.0	.	67	.	.	Atlas-SNP
C20orf26	26074	hgsc.bcm.edu	hg19	20	20144770	20144770	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	C20orf26	NM_015585	exon11	c.T1103C	p.L368P	CATCGCTCGTACT	.	67.0	24.0	65.0	0.0	.	188	.	.	Atlas-SNP
SYS1	90196	hgsc.bcm.edu	hg19	20	43995750	43995750	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	SYS1	NM_001197129	exon5	c.G466A	p.V156I	TCCAATGTCTAGA	.	79.0	35.0	106.0	0.0	.	15	.	.	Atlas-SNP
KCNB1	3745	hgsc.bcm.edu	hg19	20	47990403	47990403	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	KCNB1	NM_004975	exon2	c.T1694C	p.I565T	CTGGGGATACTCT	.	94.0	33.0	110.0	0.0	.	142	.	.	Atlas-SNP
BACH1	571	hgsc.bcm.edu	hg19	21	30701998	30701998	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	BACH1	NM_206866	exon4	c.C1760A	p.S587X	TTGAATCAGAAAT	.	78.0	40.0	175.0	0.0	.	66	.	.	Atlas-SNP
IFNAR2	3455	hgsc.bcm.edu	hg19	21	34635391	34635391	+	Silent	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	IFNAR2	NM_207585	exon9	c.C1134T	p.P378P	GCTCCCCACGATG	.	66.0	42.0	138.0	0.0	.	44	.	.	Atlas-SNP
SFI1	9814	hgsc.bcm.edu	hg19	22	32009644	32009644	+	Silent	SNP	A	A	G	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	SFI1	NM_001007467	exon27	c.A2799G	p.K933K	ACAGAAAGTGCTG	.	110.0	35.0	135.0	0.0	.	78	.	.	Atlas-SNP
AFF2	2334	hgsc.bcm.edu	hg19	X	148037839	148037839	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	AFF2	NM_002025	exon11	c.C2264T	p.T755I	GCCTGACCCTCAG	.	162.0	69.0	128.0	0.0	.	679	.	.	Atlas-SNP
ND4L	0	hgsc.bcm.edu	hg19	MT	10725	10725	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	.	ENST00000361335	exon1	c.G256A	p.G86S	ACATATGGCCTAG	.	63.0	14.0	52.0	0.0	.	.	.	.	Atlas-SNP
RRM2	6241	hgsc.bcm.edu	hg19	2	10262771	10262797	+	In_Frame_Del	DEL	AGCCAATGGGAAGGGCCGGGGCACCAA	AGCCAATGGGAAGGGCCGGGGCACCAA	-	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	AGCCAATGGGAAGGGCCGGGGCACCAA	AGCCAATGGGAAGGGCCGGGGCACCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	RRM2	NM_001165931	exon1	c.25_51del	p.9_17del	.	.	192.0	45.0	265.0	0.0	.	63	.	.	Atlas-Indel,Pindel
HMCN1	83872	hgsc.bcm.edu	hg19	1	185986178	185986179	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	HMCN1	NM_031935	exon33	c.5275_5276insC	p.T1759fs	.	.	250.0	112.0	148.0	0.0	.	797	.	.	Atlas-Indel,Pindel
ATG5	9474	hgsc.bcm.edu	hg19	6	106764056	106764058	+	In_Frame_Del	DEL	CTC	CTC	-	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	ATG5	NM_004849	exon2	c.27_29del	p.9_10del	.	.	39.0	28.0	117.0	0.0	.	23	.	.	Atlas-Indel,Pindel
NCOR1	9611	hgsc.bcm.edu	hg19	17	16029431	16029435	+	Frame_Shift_Del	DEL	TTTCT	TTTCT	-	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	TTTCT	TTTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	NCOR1	NM_001190440	exon14	c.1596_1600del	p.532_534del	.	.	292.0	21.0	314.0	0.0	.	240	.	.	Atlas-Indel,Pindel
MAP2K4	6416	hgsc.bcm.edu	hg19	17	12016647	12016648	+	Frame_Shift_Del	DEL	AA	AA	-	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	.	MAP2K4	NM_003010	exon7	c.782_783del	p.261_261del	.	.	66.0	23.0	93.0	0.0	.	176	.	.	Atlas-Indel,Pindel
MUC4	4585	hgsc.bcm.edu	hg19	3	195506454	195506549	+	In_Frame_Del	DEL	GGTGGCGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGGGGGGTGGCGTGACCTGTGGATGCTGAGGAACGGCTGGTGACAGGAAGAGA	GGTGGCGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGGGGGGTGGCGTGACCTGTGGATGCTGAGGAACGGCTGGTGACAGGAAGAGA	-	novel		TCGA-5R-AA1C-01A-11D-A40R-10	TCGA-5R-AA1C-10A-01D-A40U-10	GGTGGCGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGGGGGGTGGCGTGACCTGTGGATGCTGAGGAACGGCTGGTGACAGGAAGAGA	GGTGGCGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGGGGGGTGGCGTGACCTGTGGATGCTGAGGAACGGCTGGTGACAGGAAGAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d37f1231-13b4-442e-8844-8e3980be1ef0	da5a5303-fdce-40d4-86d1-4cf45f39aa20	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	NM_018406	exon2	c.11903_11998del	p.3968_4000del	.	.	89.0	11.0	82.0	0.0	.	1505	.	.	Pindel