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
GPBP1L1	60313	hgsc.bcm.edu	hg19	1	46124754	46124754	+	Silent	SNP	C	C	A	rs144406702	alternate_allele	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	GPBP1L1,colon,carcinoma,0,1	GPBP1L1	NM_021639	exon4	c.G6T	p.A2A	ATGCTGCGCCATT	.	51.0	3.0	112.0	0.0	.	43	.	C|1.000;T|0.000	Atlas-SNP
INSRR	3645	hgsc.bcm.edu	hg19	1	156815550	156815550	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	INSRR	NM_014215	exon10	c.C2035A	p.P679T	CCTCAGGATCCCC	.	81.0	4.0	76.0	0.0	.	309	.	.	Atlas-SNP
POU2F1	5451	hgsc.bcm.edu	hg19	1	167384897	167384897	+	Silent	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	POU2F1	NM_002697	exon16	c.T2151C	p.S717S	GGTCTCTGCCGCC	.	80.0	21.0	133.0	0.0	.	120	.	.	Atlas-SNP
PKP1	5317	hgsc.bcm.edu	hg19	1	201294914	201294914	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PKP1	NM_000299	exon13	c.T2117C	p.L706P	CCCGGCTTCTCCT	.	116.0	25.0	139.0	0.0	.	127	.	.	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	hg19	1	215802343	215802343	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	USH2A	NM_206933	exon71	c.C15332T	p.T5111I	ACAGGTGTCCCAG	.	109.0	13.0	164.0	0.0	.	1168	.	.	Atlas-SNP
AMMECR1L	83607	hgsc.bcm.edu	hg19	2	128628831	128628831	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	AMMECR1L	NM_031445	exon4	c.G510A	p.T170T	GGTTAACGTGTAT	.	44.0	10.0	74.0	0.0	.	22	.	.	Atlas-SNP
IL5RA	3568	hgsc.bcm.edu	hg19	3	3137002	3137002	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	IL5RA	NM_001243099	exon8	c.C836A	p.T279K	TTCCTTGTATTGT	.	116.0	51.0	161.0	0.0	.	55	.	.	Atlas-SNP
ATP2B2	491	hgsc.bcm.edu	hg19	3	10417206	10417206	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ATP2B2	NM_001001331	exon11	c.A1324G	p.K442E	AGAACTTGACAAA	.	126.0	13.0	135.0	0.0	.	304	.	.	Atlas-SNP
PXK	54899	hgsc.bcm.edu	hg19	3	58395296	58395296	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PXK	NM_017771	exon15	c.A1346G	p.H449R	AGTCCCACCATGG	.	196.0	93.0	253.0	1.0	.	89	.	.	Atlas-SNP
FGFR3	2261	hgsc.bcm.edu	hg19	4	1807577	1807577	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	FGFR3	NM_001163213	exon13	c.C1752T	p.C584C	CACCTGCAAGCCG	.	54.0	16.0	76.0	0.0	.	3320	.	.	Atlas-SNP
SH3BP2	6452	hgsc.bcm.edu	hg19	4	2829348	2829348	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SH3BP2	NM_001145856	exon7	c.A704G	p.D235G	ACGACGATGAGGA	.	67.0	30.0	127.0	0.0	.	43	.	.	Atlas-SNP
FHDC1	85462	hgsc.bcm.edu	hg19	4	153896514	153896514	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	FHDC1	NM_033393	exon11	c.G2071T	p.E691X	GGCATGGAGGAGA	.	29.0	12.0	71.0	0.0	.	102	.	.	Atlas-SNP
CYFIP2	26999	hgsc.bcm.edu	hg19	5	156712348	156712348	+	Splice_Site	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CYFIP2	.	.	.	.	CCTTCAGTGCAGA	.	39.0	6.0	39.0	0.0	.	354	.	.	Atlas-SNP
CCNJL	79616	hgsc.bcm.edu	hg19	5	159686508	159686508	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CCNJL	NM_024565	exon5	c.A695C	p.Y232S	TGGGCATACTCCT	.	31.0	7.0	48.0	0.0	.	36	.	.	Atlas-SNP
EYS	346007	hgsc.bcm.edu	hg19	6	65612320	65612320	+	Silent	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	EYS	NM_001142800	exon17	c.T2715C	p.C905C	ATCTTCACAGTCA	.	121.0	26.0	203.0	0.0	.	527	.	.	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	hg19	8	3165845	3165845	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CSMD1	NM_033225	exon24	c.C3812A	p.P1271H	CACGAAGGTAGTG	.	22.0	4.0	71.0	0.0	.	1469	.	.	Atlas-SNP
MTMR7	9108	hgsc.bcm.edu	hg19	8	17163407	17163407	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	MTMR7	NM_004686	exon11	c.A1211C	p.E404A	ACACACTCAATGA	.	33.0	14.0	142.0	0.0	.	75	.	.	Atlas-SNP
RFX3	5991	hgsc.bcm.edu	hg19	9	3247979	3247979	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RFX3	NM_002919	exon16	c.A2021T	p.E674V	TGTAATTCTGGCT	.	32.0	12.0	66.0	0.0	.	156	.	.	Atlas-SNP
PLAA	9373	hgsc.bcm.edu	hg19	9	26905887	26905887	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PLAA	NM_001031689	exon14	c.G2010C	p.Q670H	TCCTGCCTGGCCA	.	93.0	22.0	198.0	0.0	.	48	.	.	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	hg19	9	104499796	104499796	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	GRIN3A	NM_133445	exon1	c.G466C	p.A156P	GGCCTGCCTCGAT	.	54.0	19.0	108.0	0.0	.	186	.	.	Atlas-SNP
TMEM38B	55151	hgsc.bcm.edu	hg19	9	108536210	108536210	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	TMEM38B	NM_018112	exon6	c.G725A	p.W242X	TGAGTTGGATGCT	.	95.0	34.0	158.0	0.0	.	31	.	.	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	hg19	9	113312149	113312149	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SVEP1	NM_153366	exon2	c.C767G	p.A256G	CGGCGAGCTAAAG	.	83.0	16.0	171.0	0.0	.	326	.	.	Atlas-SNP
FAM78A	286336	hgsc.bcm.edu	hg19	9	134136583	134136583	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	FAM78A	NM_033387	exon2	c.G478A	p.D160N	AGTTGTCATTCAT	.	30.0	7.0	57.0	0.0	.	28	.	.	Atlas-SNP
RET	5979	hgsc.bcm.edu	hg19	10	43600449	43600449	+	Silent	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RET	NM_020630	exon4	c.G675A	p.T225T	GAGCACGCGCTGG	.	40.0	13.0	59.0	0.0	.	916	.	.	Atlas-SNP
RBP3	5949	hgsc.bcm.edu	hg19	10	48389747	48389747	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RBP3	NM_002900	exon1	c.G1131A	p.Q377Q	CGCAGCCTGCAGG	.	41.0	15.0	57.0	0.0	.	152	.	.	Atlas-SNP
CTSD	1509	hgsc.bcm.edu	hg19	11	1778644	1778644	+	Missense_Mutation	SNP	C	C	T	rs371522391		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CTSD	NM_001909	exon5	c.G614A	p.R205H	GAGATGCGGGGGT	.	68.0	34.0	61.0	0.0	.	26	.	.	Atlas-SNP
OR52N4	390072	hgsc.bcm.edu	hg19	11	5776243	5776243	+	Silent	SNP	C	C	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	OR52N4,right_upper_lobe,carcinoma,0,1	OR52N4	NM_001005175	exon1	c.C273G	p.L91L	TCATCTCAAGGAC	.	74.0	12.0	123.0	0.0	.	55	.	.	Atlas-SNP
NRXN2	9379	hgsc.bcm.edu	hg19	11	64434901	64434901	+	Missense_Mutation	SNP	C	C	A	rs143130600	bycluster;by1000genomes;alternate_allele	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	NRXN2	NM_015080	exon9	c.G1619T	p.G540V	GCTCCACCCCCAG	.	49.0	11.0	81.0	0.0	.	247	.	C|1.000;T|0.000	Atlas-SNP
NLRX1	79671	hgsc.bcm.edu	hg19	11	119052990	119052990	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	NLRX1	NM_024618	exon9	c.G2542A	p.G848S	GGTGCTGGTGACA	.	25.0	7.0	56.0	0.0	.	128	.	.	Atlas-SNP
EEA1	8411	hgsc.bcm.edu	hg19	12	93205205	93205205	+	Silent	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	EEA1	NM_003566	exon17	c.A2049G	p.L683L	CTTATTTAACTCC	.	43.0	11.0	48.0	0.0	.	104	.	.	Atlas-SNP
MAP4K5	11183	hgsc.bcm.edu	hg19	14	50911780	50911780	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	MAP4K5	NM_006575	exon18	c.G1318T	p.V440L	CTGCCACAGGCCC	.	73.0	16.0	122.0	0.0	.	48	.	.	Atlas-SNP
CYLD	1540	hgsc.bcm.edu	hg19	16	50815217	50815217	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CYLD	NM_015247	exon11	c.G1579A	p.A527T	ACCTGTGCCCTGA	.	55.0	17.0	105.0	0.0	.	150	.	.	Atlas-SNP
TAF1C	9013	hgsc.bcm.edu	hg19	16	84214736	84214736	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	TAF1C	NM_005679	exon11	c.G1299T	p.Q433H	CCCTTTCTGGCAC	.	54.0	28.0	114.0	0.0	.	60	.	.	Atlas-SNP
FASN	2194	hgsc.bcm.edu	hg19	17	80051623	80051623	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	FASN	NM_004104	exon4	c.G305A	p.G102E	TGTGTTCCTCGGA	.	68.0	40.0	45.0	0.0	.	154	.	.	Atlas-SNP
FOXK2	3607	hgsc.bcm.edu	hg19	17	80477826	80477826	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	FOXK2,NS,carcinoma,0,1	FOXK2	NM_004514	exon1	c.G62C	p.G21A	GGGCCGGGGGCGG	.	4.0	2.0	1.0	0.0	.	46	.	.	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	hg19	18	7002349	7002349	+	Silent	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	LAMA1	NM_005559	exon30	c.T4296C	p.D1432D	ACACACATCACAA	.	37.0	9.0	52.0	0.0	.	458	.	.	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	hg19	19	17040002	17040002	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CPAMD8	NM_015692	exon24	c.A3035T	p.Q1012L	GGCCGCTGCACAT	.	30.0	5.0	37.0	0.0	.	192	.	.	Atlas-SNP
CILP2	148113	hgsc.bcm.edu	hg19	19	19655201	19655201	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CILP2	NM_153221	exon8	c.C1847A	p.T616N	ACCTCACCTCGGC	.	41.0	17.0	71.0	0.0	.	84	.	.	Atlas-SNP
RBM42	79171	hgsc.bcm.edu	hg19	19	36120133	36120133	+	Silent	SNP	G	G	T	rs371589146	alternate_allele	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RBM42	NM_024321	exon1	c.G78T	p.P26P	CATCCCGGGCAAA	.	27.0	11.0	35.0	0.0	.	40	.	.	Atlas-SNP
ZBTB32	27033	hgsc.bcm.edu	hg19	19	36207170	36207170	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ZBTB32	NM_014383	exon5	c.A1160T	p.Q387L	AGCATCAGATGGA	.	81.0	27.0	82.0	0.0	.	33	.	.	Atlas-SNP
PTOV1	53635	hgsc.bcm.edu	hg19	19	50361895	50361895	+	Silent	SNP	C	C	A	rs376020024		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PTOV1	NM_017432	exon10	c.C1026A	p.I342I	CCGGATCATGGAC	.	52.0	25.0	81.0	0.0	.	41	.	.	Atlas-SNP
SYNDIG1	79953	hgsc.bcm.edu	hg19	20	24565510	24565510	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	SYNDIG1,NS,carcinoma,0,1	SYNDIG1	NM_024893	exon3	c.A499G	p.T167A	AGCGACACAGAGA	.	64.0	29.0	60.0	1.0	.	58	.	.	Atlas-SNP
DSCAM	1826	hgsc.bcm.edu	hg19	21	42080424	42080424	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	DSCAM	NM_001271534	exon2	c.A317T	p.N106I	GAAGGATTTTCAG	.	46.0	15.0	69.0	0.0	.	347	.	.	Atlas-SNP
SIK1	150094	hgsc.bcm.edu	hg19	21	44841639	44841639	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	SIK1,caecum,carcinoma,0,1	SIK1	NM_173354	exon5	c.G378A	p.A126A	CTTCCGCGCCTCG	.	78.0	24.0	111.0	0.0	.	65	.	.	Atlas-SNP
SHROOM4	57477	hgsc.bcm.edu	hg19	X	50350826	50350826	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SHROOM4	NM_020717	exon6	c.C3316A	p.P1106T	TGGGAGGAGGAGG	.	30.0	17.0	92.0	0.0	.	171	.	.	Atlas-SNP
PABPC5	140886	hgsc.bcm.edu	hg19	X	90690699	90690699	+	Silent	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PABPC5	NM_080832	exon2	c.T123A	p.A41A	GCCTGCTGGCCCT	.	16.0	10.0	53.0	0.0	.	92	.	.	Atlas-SNP
GLRA4	441509	hgsc.bcm.edu	hg19	X	102978843	102978843	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	GLRA4	NM_001024452	exon5	c.T518G	p.L173R	TCCATCAGGCAGG	.	102.0	69.0	280.0	1.0	.	86	.	.	Atlas-SNP
RAB9B	51209	hgsc.bcm.edu	hg19	X	103080318	103080318	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RAB9B	NM_016370	exon3	c.G397A	p.V133M	TAGTCACTTGCCT	.	24.0	17.0	91.0	0.0	.	24	.	.	Atlas-SNP
HGS	9146	hgsc.bcm.edu	hg19	17	79660939	79660939	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	HGS	NM_004712	exon11	c.879delG	p.E293fs	.	.	54.0	15.0	28.0	0.0	.	54	.	.	Atlas-Indel,Pindel
TP53	7157	hgsc.bcm.edu	hg19	17	7579389	7579399	+	Frame_Shift_Del	DEL	GGGAAGGGACA	GGGAAGGGACA	-	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	GGGAAGGGACA	GGGAAGGGACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	TP53	NM_001126112	exon4	c.289_299del	p.97_100del	.	.	64.0	23.0	190.0	0.0	.	33396	.	.	Atlas-Indel,Pindel
SUN5	140732	hgsc.bcm.edu	hg19	20	31577506	31577506	+	Splice_Site	DEL	T	T	-	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SUN5	NM_080675	exon10	c.535-1A>-	.	.	.	66.0	18.0	79.0	0.0	.	63	.	.	Pindel
MSN	4478	hgsc.bcm.edu	hg19	X	64951035	64951044	+	Frame_Shift_Del	DEL	ACACCGTGGC	ACACCGTGGC	-	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	ACACCGTGGC	ACACCGTGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	MSN	NM_002444	exon5	c.533_542del	p.178_181del	.	.	56.0	17.0	154.0	0.0	.	89	.	.	Pindel
