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
UBE2J2	118424	hgsc.bcm.edu	hg19	1	1190842	1190842	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	UBE2J2	NM_194315	exon8	c.A569T	p.Q190L	TCGTCTTGTGCTT	.	258.0	70.0	243.0	0.0	.	25	.	.	Atlas-SNP
COL16A1	1307	hgsc.bcm.edu	hg19	1	32151294	32151294	+	Silent	SNP	T	T	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	COL16A1	NM_001856	exon29	c.A1962C	p.P654P	TCCGGATGGGCCA	.	162.0	36.0	107.0	0.0	.	137	.	.	Atlas-SNP
CLCA2	9635	hgsc.bcm.edu	hg19	1	86916353	86916353	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	CLCA2	NM_006536	exon12	c.A2092T	p.S698C	AGCATAAGCACCC	.	129.0	14.0	165.0	0.0	.	102	.	.	Atlas-SNP
VTCN1	79679	hgsc.bcm.edu	hg19	1	117699311	117699311	+	Silent	SNP	A	A	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	VTCN1	NM_024626	exon3	c.T330C	p.V110V	ATTGCCAACTATC	.	132.0	38.0	115.0	0.0	.	26	.	.	Atlas-SNP
PGLYRP3	114771	hgsc.bcm.edu	hg19	1	153279733	153279733	+	Silent	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	PGLYRP3	NM_052891	exon2	c.C66T	p.T22T	GACGATGGTGGGA	.	45.0	18.0	39.0	0.0	.	55	.	.	Atlas-SNP
NOS1AP	9722	hgsc.bcm.edu	hg19	1	162337003	162337003	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	NOS1AP	NM_014697	exon10	c.G1267T	p.D423Y	AGGCGCGACTGCT	.	43.0	12.0	41.0	0.0	.	139	.	.	Atlas-SNP
KIF21B	23046	hgsc.bcm.edu	hg19	1	200973575	200973575	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	KIF21B	NM_017596	exon7	c.G909T	p.L303F	ATTGCCCAAGGCC	.	95.0	23.0	59.0	0.0	.	208	.	.	Atlas-SNP
ZC3H11A	9877	hgsc.bcm.edu	hg19	1	203816541	203816541	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	ZC3H11A	NM_014827	exon15	c.A1272C	p.K424N	ACAAAAAAGCAAA	.	172.0	37.0	167.0	0.0	.	71	.	.	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	hg19	1	215916665	215916665	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	USH2A	NM_206933	exon59	c.C11402T	p.P3801L	ATTTCGGGGATGA	.	37.0	8.0	25.0	0.0	.	1168	.	.	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	hg19	1	216062251	216062251	+	Silent	SNP	T	T	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	USH2A	NM_206933	exon41	c.A7740T	p.G2580G	GACATTTCCAGGA	.	108.0	29.0	91.0	0.0	.	1168	.	.	Atlas-SNP
RYR2	6262	hgsc.bcm.edu	hg19	1	237923107	237923107	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	RYR2	NM_001035	exon83	c.A11357C	p.D3786A	AAAAGGATGTGGG	.	166.0	43.0	144.0	0.0	.	1273	.	.	Atlas-SNP
NLRP3	114548	hgsc.bcm.edu	hg19	1	247582364	247582364	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	NLRP3	NM_183395	exon1	c.G268T	p.D90Y	AAAAGAGATGAGC	.	19.0	10.0	16.0	0.0	.	286	.	.	Atlas-SNP
GTF3C2	2976	hgsc.bcm.edu	hg19	2	27552031	27552031	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	GTF3C2	NM_001521	exon15	c.T1996G	p.C666G	TGTAGGGAAGCAG	.	97.0	25.0	65.0	0.0	.	73	.	.	Atlas-SNP
EIF2B4	8890	hgsc.bcm.edu	hg19	2	27590024	27590024	+	Silent	SNP	C	C	T	rs373520608		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	EIF2B4	NM_172195	exon9	c.G990A	p.E330E	AATCTTCTCTTGC	.	81.0	22.0	79.0	0.0	.	48	.	.	Atlas-SNP
FAM98A	25940	hgsc.bcm.edu	hg19	2	33810097	33810097	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	FAM98A	NM_015475	exon8	c.A1303G	p.S435G	ATCCACTTCCTGT	.	116.0	32.0	109.0	0.0	.	42	.	.	Atlas-SNP
LY75	4065	hgsc.bcm.edu	hg19	2	160665051	160665051	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	LY75	NM_002349	exon33	c.T4731A	p.D1577E	ATCTTCATCTTTT	.	140.0	40.0	163.0	0.0	.	151	.	.	Atlas-SNP
DFNB59	494513	hgsc.bcm.edu	hg19	2	179325171	179325171	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	DFNB59	NM_001042702	exon6	c.G764C	p.R255T	TTGAAAGAAGTAT	.	105.0	20.0	126.0	0.0	.	37	.	.	Atlas-SNP
OSGEPL1	64172	hgsc.bcm.edu	hg19	2	190617632	190617632	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	OSGEPL1	NM_022353	exon6	c.G1037A	p.C346Y	AAAGTGCACTGTG	.	271.0	60.0	312.0	0.0	.	19	.	.	Atlas-SNP
PMS1	5378	hgsc.bcm.edu	hg19	2	190718971	190718971	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	PMS1	NM_001128144	exon9	c.G973A	p.V325I	GAATCTGTTTTAA	.	133.0	28.0	159.0	0.0	.	78	.	.	Atlas-SNP
ASIC4	55515	hgsc.bcm.edu	hg19	2	220379823	220379823	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	.	NM_182847	exon1	c.C758A	p.S253X	GGCATTCGGCACT	.	77.0	21.0	54.0	0.0	.	.	.	.	Atlas-SNP
RBMS3	27303	hgsc.bcm.edu	hg19	3	29781252	29781252	+	Silent	SNP	C	C	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	RBMS3	NM_001003793	exon5	c.C441G	p.L147L	AAATCTCCCCATT	.	98.0	19.0	124.0	0.0	.	62	.	.	Atlas-SNP
VIPR1	7433	hgsc.bcm.edu	hg19	3	42577594	42577594	+	Silent	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	VIPR1	NM_004624	exon13	c.C1195T	p.L399L	GCGGAGCTGAGGC	.	56.0	12.0	55.0	0.0	.	45	.	.	Atlas-SNP
SACM1L	22908	hgsc.bcm.edu	hg19	3	45748365	45748365	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	SACM1L	NM_014016	exon4	c.A299G	p.Y100C	TTTCTTATAAGAA	.	188.0	52.0	240.0	0.0	.	38	.	.	Atlas-SNP
EPHB1	2047	hgsc.bcm.edu	hg19	3	134920367	134920367	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	EPHB1	NM_004441	exon12	c.A2182T	p.I728F	AGGGGCATCGCTG	.	153.0	32.0	133.0	0.0	.	519	.	.	Atlas-SNP
AADAC	13	hgsc.bcm.edu	hg19	3	151545693	151545693	+	Nonsense_Mutation	SNP	T	T	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	AADAC	NM_001086	exon5	c.T933G	p.Y311X	AAAATATCCAGGG	.	55.0	17.0	65.0	0.0	.	49	.	.	Atlas-SNP
DGKG	1608	hgsc.bcm.edu	hg19	3	185993350	185993350	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	DGKG	NM_001346	exon10	c.G896A	p.G299D	CACAGGCCTTGCT	.	54.0	17.0	46.0	0.0	.	98	.	.	Atlas-SNP
KDR	3791	hgsc.bcm.edu	hg19	4	55955862	55955862	+	Silent	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	KDR	NM_002253	exon24	c.C3300T	p.S1100S	ACCTAAGGAAAAT	.	120.0	28.0	139.0	0.0	.	307	.	.	Atlas-SNP
EXOC1	55763	hgsc.bcm.edu	hg19	4	56759928	56759928	+	Silent	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	EXOC1	NM_018261	exon15	c.G1935A	p.R645R	CAAAAGGAACTTT	.	76.0	23.0	78.0	0.0	.	103	.	.	Atlas-SNP
AASDH	132949	hgsc.bcm.edu	hg19	4	57204730	57204730	+	Silent	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	AASDH	NM_181806	exon15	c.G3135T	p.G1045G	CACTTTCCCATCA	.	222.0	54.0	201.0	0.0	.	101	.	.	Atlas-SNP
TMPRSS11F	389208	hgsc.bcm.edu	hg19	4	68934361	68934361	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	TMPRSS11F,NS,carcinoma,0,1	TMPRSS11F	NM_207407	exon7	c.C730A	p.L244I	CTGTGAGCAGCCA	.	148.0	44.0	92.0	0.0	.	79	.	.	Atlas-SNP
RASSF6	166824	hgsc.bcm.edu	hg19	4	74451010	74451010	+	Silent	SNP	T	T	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	RASSF6	NM_201431	exon6	c.A550C	p.R184R	TGGTTCTATAGAG	.	249.0	77.0	259.0	0.0	.	68	.	.	Atlas-SNP
SLC39A8	64116	hgsc.bcm.edu	hg19	4	103228652	103228652	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	SLC39A8	NM_022154	exon3	c.T493G	p.F165V	CCACAAAAAAGGT	.	294.0	80.0	364.0	0.0	.	24	.	.	Atlas-SNP
RBM46	166863	hgsc.bcm.edu	hg19	4	155719022	155719022	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	RBM46	NM_144979	exon3	c.G211C	p.D71H	CCTCGTGATATGT	.	135.0	36.0	161.0	0.0	.	76	.	.	Atlas-SNP
PDZD2	23037	hgsc.bcm.edu	hg19	5	31983740	31983740	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	PDZD2	NM_178140	exon2	c.A956T	p.Q319L	ACTTCCAATCGAG	.	156.0	45.0	164.0	0.0	.	306	.	.	Atlas-SNP
MCCC2	64087	hgsc.bcm.edu	hg19	5	70936898	70936898	+	Silent	SNP	T	T	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	MCCC2	NM_022132	exon11	c.T1068A	p.V356V	ATTAGTTACAGGT	.	93.0	19.0	88.0	0.0	.	47	.	.	Atlas-SNP
FBN2	2201	hgsc.bcm.edu	hg19	5	127727761	127727761	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	FBN2	NM_001999	exon11	c.G1553C	p.R518P	TCACATCGGTAGC	.	136.0	24.0	171.0	0.0	.	858	.	.	Atlas-SNP
KDM3B	51780	hgsc.bcm.edu	hg19	5	137759953	137759953	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	KDM3B	NM_016604	exon16	c.G4162T	p.G1388W	TGTGATGGGAGGC	.	260.0	74.0	243.0	0.0	.	177	.	.	Atlas-SNP
KDM3B	51780	hgsc.bcm.edu	hg19	5	137759954	137759954	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	KDM3B	NM_016604	exon16	c.G4163T	p.G1388V	GTGATGGGAGGCT	.	259.0	73.0	243.0	0.0	.	177	.	.	Atlas-SNP
PCDHA2	56146	hgsc.bcm.edu	hg19	5	140176834	140176834	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	PCDHA2	NM_031495	exon1	c.A2285T	p.E762V	CTGGGGAGGACCC	.	225.0	59.0	201.0	0.0	.	404	.	.	Atlas-SNP
PCDHA6	56142	hgsc.bcm.edu	hg19	5	140208267	140208267	+	Silent	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	PCDHA6_ENST00000529310,colon,carcinoma,0,4	PCDHA6	NM_018909	exon1	c.G591A	p.K197K	ATTAAAGAAATCC	.	74.0	20.0	82.0	0.0	.	442	.	.	Atlas-SNP
KCTD16	57528	hgsc.bcm.edu	hg19	5	143586733	143586733	+	Silent	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	KCTD16	NM_020768	exon3	c.C456T	p.P152P	CTGCCCCCCTTCC	.	77.0	21.0	72.0	0.0	.	70	.	.	Atlas-SNP
SLC36A1	206358	hgsc.bcm.edu	hg19	5	150843185	150843185	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	SLC36A1	NM_078483	exon3	c.T215A	p.V72E	TGGCGGTGAAAAA	.	109.0	24.0	113.0	0.0	.	50	.	.	Atlas-SNP
SLIT3	6586	hgsc.bcm.edu	hg19	5	168244433	168244433	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	SLIT3	NM_001271946	exon8	c.A665T	p.H222L	GCCAGGTGGCAGT	.	70.0	22.0	39.0	0.0	.	224	.	.	Atlas-SNP
SLC17A1	6568	hgsc.bcm.edu	hg19	6	25811931	25811931	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	SLC17A1,NS,carcinoma,0,1	SLC17A1	NM_005074	exon9	c.C965T	p.S322L	AAGTCTGATAACT	.	76.0	17.0	79.0	0.0	.	71	.	.	Atlas-SNP
HIST1H3B	8358	hgsc.bcm.edu	hg19	6	26032209	26032209	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	HIST1H3B	NM_003537	exon1	c.G80A	p.R27H	CTCTTGCGAGCAG	.	29.0	10.0	22.0	0.0	.	59	.	.	Atlas-SNP
GSTA4	2941	hgsc.bcm.edu	hg19	6	52858985	52858985	+	Silent	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	GSTA4	NM_001512	exon2	c.G57T	p.V19V	CCATCTCACGGAC	.	55.0	15.0	42.0	0.0	.	20	.	.	Atlas-SNP
IMPG1	3617	hgsc.bcm.edu	hg19	6	76715138	76715138	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	IMPG1	NM_001563	exon10	c.A1001T	p.E334V	TAGACTTCCTCAC	.	358.0	79.0	344.0	0.0	.	143	.	.	Atlas-SNP
SLC22A16	85413	hgsc.bcm.edu	hg19	6	110763664	110763664	+	Silent	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	SLC22A16	NM_033125	exon4	c.G966A	p.L322L	TTCTGACAGTTTA	.	76.0	17.0	66.0	0.0	.	81	.	.	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	hg19	7	48318705	48318705	+	Silent	SNP	T	T	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	ABCA13	NM_152701	exon18	c.T7914A	p.I2638I	AGAAATTGCTGAA	.	74.0	19.0	65.0	0.0	.	1192	.	.	Atlas-SNP
C7orf72	100130988	hgsc.bcm.edu	hg19	7	50135895	50135895	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	C7orf72	NM_001161834	exon1	c.C214T	p.P72S	TATCCCCCTTCAG	.	285.0	61.0	267.0	0.0	.	26	.	.	Atlas-SNP
SPAM1	6677	hgsc.bcm.edu	hg19	7	123594252	123594252	+	Missense_Mutation	SNP	C	C	T	rs376151172	alternate_allele	TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	SPAM1	NM_153189	exon3	c.C628T	p.L210F	AAATTACTTCGGC	.	115.0	31.0	142.0	0.0	.	195	.	.	Atlas-SNP
JHDM1D	80853	hgsc.bcm.edu	hg19	7	139819020	139819020	+	Splice_Site	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	JHDM1D	NM_030647	exon10	c.1140-1G>T	.	TAACACCTAAATG	.	81.0	23.0	110.0	0.0	.	54	.	.	Atlas-SNP
GPR124	25960	hgsc.bcm.edu	hg19	8	37693203	37693203	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	GPR124	NM_032777	exon13	c.C1965G	p.H655Q	CTTCCACAGCCAC	.	53.0	13.0	21.0	0.0	.	85	.	.	Atlas-SNP
POTEA	340441	hgsc.bcm.edu	hg19	8	43152221	43152221	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	POTEA	NM_001005365	exon2	c.G358A	p.D120N	CTGCTGGACAGAC	.	145.0	24.0	182.0	0.0	.	87	.	.	Atlas-SNP
KIAA0146	23514	hgsc.bcm.edu	hg19	8	48508456	48508456	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	KIAA0146	NM_001080394	exon9	c.C1181G	p.S394X	AAGATTCAGAAAA	.	119.0	31.0	156.0	0.0	.	64	.	.	Atlas-SNP
TRPA1	8989	hgsc.bcm.edu	hg19	8	72975034	72975034	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	TRPA1	NM_007332	exon6	c.G807T	p.E269D	AGTTACCTCCACT	.	243.0	61.0	260.0	0.0	.	256	.	.	Atlas-SNP
TG	7038	hgsc.bcm.edu	hg19	8	133941375	133941375	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	TG	NM_003235	exon23	c.C4754T	p.A1585V	CCAATGCTCCTGT	.	177.0	52.0	144.0	0.0	.	416	.	.	Atlas-SNP
BNC2	54796	hgsc.bcm.edu	hg19	9	16738381	16738381	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	BNC2	NM_017637	exon2	c.G106T	p.G36W	CAACCCCACAACA	.	176.0	59.0	168.0	0.0	.	166	.	.	Atlas-SNP
CDC14B	8555	hgsc.bcm.edu	hg19	9	99285642	99285642	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	CDC14B	NM_033331	exon11	c.G1146C	p.E382D	TCCATTCTCCTGC	.	222.0	57.0	230.0	0.0	.	64	.	.	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	hg19	9	115948581	115948581	+	Silent	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	FKBP15	NM_015258	exon15	c.G1446A	p.Q482Q	AACGGGCTGCAGC	.	89.0	26.0	76.0	0.0	.	128	.	.	Atlas-SNP
SFMBT2	57713	hgsc.bcm.edu	hg19	10	7423775	7423775	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	SFMBT2	NM_001029880	exon2	c.G86A	p.G29E	AGGTCTCCATTTC	.	92.0	24.0	86.0	0.0	.	209	.	.	Atlas-SNP
SUV39H2	79723	hgsc.bcm.edu	hg19	10	14938885	14938885	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	SUV39H2	NM_001193426	exon3	c.A218C	p.D73A	GGCCAGATTCTAC	.	61.0	12.0	68.0	0.0	.	72	.	.	Atlas-SNP
PTCHD3	374308	hgsc.bcm.edu	hg19	10	27702131	27702131	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	PTCHD3	NM_001034842	exon1	c.T1049C	p.F350S	TTGGTAAATTGAT	.	129.0	37.0	109.0	0.0	.	140	.	.	Atlas-SNP
JMJD1C	221037	hgsc.bcm.edu	hg19	10	64967201	64967201	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	JMJD1C	NM_032776	exon10	c.A4228G	p.S1410G	CCCAGCTGGAAAC	.	84.0	21.0	87.0	0.0	.	347	.	.	Atlas-SNP
JMJD1C	221037	hgsc.bcm.edu	hg19	10	64967202	64967202	+	Silent	SNP	G	G	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	JMJD1C	NM_032776	exon10	c.C4227A	p.S1409S	CCAGCTGGAAACA	.	86.0	22.0	89.0	0.0	.	347	.	.	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	hg19	11	1078363	1078363	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	MUC2	NM_002457	exon5	c.C650A	p.S217Y	CCGCATCCTGCTC	.	83.0	29.0	52.0	0.0	.	614	.	.	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	hg19	11	1078364	1078364	+	Silent	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	MUC2	NM_002457	exon5	c.C651T	p.S217S	CGCATCCTGCTCC	.	81.0	28.0	53.0	0.0	.	614	.	.	Atlas-SNP
OR51G1	79324	hgsc.bcm.edu	hg19	11	4944842	4944842	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	OR51G1	NM_001005237	exon1	c.G728T	p.C243F	GAGACACAGGTGT	.	119.0	22.0	118.0	0.0	.	74	.	.	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	hg19	11	57970715	57970715	+	Silent	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	OR1S2	NM_001004459	exon1	c.C939T	p.A313A	TCTCAGGGCACCT	.	101.0	27.0	115.0	0.0	.	119	.	.	Atlas-SNP
GLYAT	10249	hgsc.bcm.edu	hg19	11	58477428	58477428	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	GLYAT,NS,carcinoma,-1,1	GLYAT	NM_201648	exon6	c.G702C	p.L234F	TTCCGGCAAGGTG	.	101.0	20.0	79.0	0.0	.	53	.	.	Atlas-SNP
TRPT1	83707	hgsc.bcm.edu	hg19	11	63992051	63992051	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	TRPT1	NM_001160389	exon5	c.G472T	p.A158S	CTGGGGCCAGGTG	.	69.0	12.0	39.0	0.0	.	14	.	.	Atlas-SNP
PPP2R5B	5526	hgsc.bcm.edu	hg19	11	64695804	64695804	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	PPP2R5B	NM_006244	exon6	c.G629A	p.R210H	GGGAGCGTGAGTA	.	89.0	19.0	75.0	0.0	.	47	.	.	Atlas-SNP
INPPL1	3636	hgsc.bcm.edu	hg19	11	71948271	71948271	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	INPPL1	NM_001567	exon26	c.C2983T	p.Q995X	CCGCACCAGCTGC	.	35.0	10.0	30.0	0.0	.	120	.	.	Atlas-SNP
GRIK4	2900	hgsc.bcm.edu	hg19	11	120831700	120831700	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	GRIK4	NM_014619	exon15	c.A1957T	p.I653F	GTGCCCATTGAGT	.	76.0	22.0	81.0	0.0	.	149	.	.	Atlas-SNP
GUCY2C	2984	hgsc.bcm.edu	hg19	12	14774139	14774139	+	Silent	SNP	G	G	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	GUCY2C,NS,carcinoma,0,1	GUCY2C	NM_004963	exon23	c.C2613A	p.I871I	ATCACCGATGGTT	.	153.0	46.0	127.0	1.0	.	126	.	.	Atlas-SNP
ACVR1B	91	hgsc.bcm.edu	hg19	12	52374782	52374782	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	ACVR1B	NM_020328	exon4	c.G610T	p.A204S	ACAGTGGCCCGAA	.	122.0	34.0	100.0	0.0	.	167	.	.	Atlas-SNP
KRT72	140807	hgsc.bcm.edu	hg19	12	52979897	52979897	+	Missense_Mutation	SNP	C	C	A	rs34119325	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	KRT72,colon,carcinoma,0,1	KRT72	NM_001146225	exon9	c.G1405T	p.A469S	TTGAGGCGCCAAA	.	71.0	10.0	48.0	0.0	.	70	.	C|0.996;T|0.004	Atlas-SNP
KIAA1033	23325	hgsc.bcm.edu	hg19	12	105509006	105509006	+	Silent	SNP	A	A	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	KIAA1033	NM_015275	exon5	c.A366T	p.G122G	AGAAGGAGGTAAG	.	404.0	80.0	562.0	1.0	.	83	.	.	Atlas-SNP
RAD9B	144715	hgsc.bcm.edu	hg19	12	110959986	110959986	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	RAD9B	NM_152442	exon10	c.G895A	p.D299N	AGGTCAGATCTGA	.	141.0	33.0	126.0	0.0	.	50	.	.	Atlas-SNP
PCDH9	5101	hgsc.bcm.edu	hg19	13	66878891	66878891	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	PCDH9	NM_203487	exon5	c.C3610T	p.H1204Y	TGAAATGGCCTTC	.	365.0	82.0	345.0	0.0	.	252	.	.	Atlas-SNP
PCDH9	5101	hgsc.bcm.edu	hg19	13	67800949	67800949	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	PCDH9	NM_203487	exon2	c.G1624A	p.V542I	CAGTTACTGTAAA	.	141.0	39.0	165.0	0.0	.	252	.	.	Atlas-SNP
FBXL3	26224	hgsc.bcm.edu	hg19	13	77581424	77581424	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	FBXL3	NM_012158	exon5	c.G1143T	p.K381N	ACACATCTTCACA	.	103.0	7.0	94.0	0.0	.	46	.	.	Atlas-SNP
SLC10A2	6555	hgsc.bcm.edu	hg19	13	103701772	103701772	+	Silent	SNP	C	C	T	rs201412654		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	SLC10A2	NM_000452	exon5	c.G786A	p.T262T	CATCCCCGTTTCA	.	106.0	28.0	90.0	0.0	.	67	.	.	Atlas-SNP
SLC22A17	51310	hgsc.bcm.edu	hg19	14	23816360	23816360	+	Silent	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	SLC22A17	NM_020372	exon8	c.C1278T	p.A426A	GATGGCGGCAGCT	.	71.0	24.0	70.0	0.0	.	32	.	.	Atlas-SNP
AKAP6	9472	hgsc.bcm.edu	hg19	14	33293092	33293092	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	AKAP6	NM_004274	exon13	c.A6073G	p.N2025D	GAACAAAACGGAA	.	36.0	8.0	32.0	0.0	.	308	.	.	Atlas-SNP
JKAMP	51528	hgsc.bcm.edu	hg19	14	59965466	59965466	+	Nonsense_Mutation	SNP	T	T	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	JKAMP	NM_016475	exon5	c.T480G	p.Y160X	TATCTATTACGCA	.	108.0	29.0	140.0	0.0	.	49	.	.	Atlas-SNP
ELMSAN1	91748	hgsc.bcm.edu	hg19	14	74189521	74189521	+	Silent	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	.	NM_194278	exon10	c.G2604A	p.V868V	GAACTCCACGCAC	.	116.0	36.0	87.0	0.0	.	.	.	.	Atlas-SNP
NRDE2	55051	hgsc.bcm.edu	hg19	14	90764607	90764607	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	.	NM_017970	exon8	c.C1663A	p.P555T	TACCTGGGTTGAT	.	52.0	10.0	29.0	0.0	.	.	.	.	Atlas-SNP
APOPT1	84334	hgsc.bcm.edu	hg19	14	104040498	104040498	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	.	NM_032374	exon3	c.A415G	p.T139A	CTGAGAACTGAAT	.	587.0	149.0	621.0	0.0	.	.	.	.	Atlas-SNP
FMN1	342184	hgsc.bcm.edu	hg19	15	33359250	33359250	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	FMN1	NM_001103184	exon1	c.G836T	p.G279V	CGAAGCCCACTGA	.	125.0	25.0	109.0	0.0	.	174	.	.	Atlas-SNP
IQGAP1	8826	hgsc.bcm.edu	hg19	15	91017734	91017734	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	IQGAP1	NM_003870	exon23	c.C2593T	p.P865S	GATCCTCCTATGG	.	101.0	28.0	92.0	0.0	.	140	.	.	Atlas-SNP
TAT	6898	hgsc.bcm.edu	hg19	16	71606499	71606499	+	Silent	SNP	A	A	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	TAT	NM_000353	exon5	c.T501C	p.P167P	GAAACCAGGTCTT	.	109.0	24.0	122.0	0.0	.	80	.	.	Atlas-SNP
SREBF1	6720	hgsc.bcm.edu	hg19	17	17719659	17719659	+	Silent	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	SREBF1	NM_001005291	exon12	c.C2166T	p.A722A	GTTGGTGGCAGTG	.	20.0	11.0	15.0	0.0	.	47	.	.	Atlas-SNP
PROCA1	147011	hgsc.bcm.edu	hg19	17	27038628	27038628	+	Silent	SNP	G	G	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	PROCA1	NM_152465	exon1	c.C51A	p.T17T	GGGCTCGGTCTTT	.	82.0	18.0	64.0	0.0	.	28	.	.	Atlas-SNP
AKAP1	8165	hgsc.bcm.edu	hg19	17	55187484	55187484	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	AKAP1	NM_001242902	exon4	c.G1813T	p.V605F	AAGAAGGTCGACC	.	60.0	17.0	59.0	0.0	.	73	.	.	Atlas-SNP
CACNG4	27092	hgsc.bcm.edu	hg19	17	65026740	65026740	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	CACNG4	NM_014405	exon4	c.G604T	p.A202S	GTCCTGGCTGTAA	.	77.0	28.0	73.0	0.0	.	44	.	.	Atlas-SNP
ANKRD30B	374860	hgsc.bcm.edu	hg19	18	14850260	14850260	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	ANKRD30B	NM_001145029	exon35	c.T3086C	p.L1029S	ATATATTAAAAGA	.	348.0	80.0	406.0	0.0	.	237	.	.	Atlas-SNP
C19orf77	284422	hgsc.bcm.edu	hg19	19	3474916	3474916	+	Silent	SNP	T	T	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	C19orf77	NM_001136503	exon4	c.A318C	p.G106G	GCTCTCTCCTTCC	.	227.0	68.0	254.0	0.0	.	6	.	.	Atlas-SNP
SAFB	6294	hgsc.bcm.edu	hg19	19	5653399	5653399	+	Silent	SNP	C	C	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	SAFB	NM_002967	exon11	c.C1494T	p.D498D	CAGTGACGGGAAA	.	189.0	53.0	142.0	0.0	.	74	.	.	Atlas-SNP
TNFSF14	8740	hgsc.bcm.edu	hg19	19	6670048	6670048	+	Silent	SNP	A	A	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	TNFSF14	NM_003807	exon2	c.T33C	p.F11F	CACCACAAACACT	.	86.0	25.0	93.0	0.0	.	40	.	.	Atlas-SNP
ELAVL1	1994	hgsc.bcm.edu	hg19	19	8038704	8038704	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	ELAVL1	NM_001419	exon4	c.G335T	p.G112V	GGGAGCCCGCTGA	.	125.0	38.0	120.0	0.0	.	44	.	.	Atlas-SNP
ZNF812	729648	hgsc.bcm.edu	hg19	19	9801514	9801514	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	ZNF812	NM_001199814	exon6	c.A665G	p.K222R	TTAGTCTTTTTAG	.	84.0	23.0	98.0	0.0	.	27	.	.	Atlas-SNP
MAN2B1	4125	hgsc.bcm.edu	hg19	19	12776599	12776599	+	Silent	SNP	C	C	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	MAN2B1,colon,carcinoma,0,1	MAN2B1	NM_001173498	exon2	c.G180C	p.P60P	CATGTTCGGCTGC	.	100.0	33.0	67.0	1.0	.	91	.	.	Atlas-SNP
FPR3	2359	hgsc.bcm.edu	hg19	19	52327451	52327451	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	FPR3	NM_002030	exon2	c.G450C	p.W150C	ACTCTGGATTTTC	.	162.0	11.0	141.0	0.0	.	66	.	.	Atlas-SNP
ZNF28	7576	hgsc.bcm.edu	hg19	19	53304147	53304147	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	ZNF28	NM_006969	exon4	c.T951A	p.H317Q	TATCTTATGTGTT	.	116.0	27.0	112.0	0.0	.	191	.	.	Atlas-SNP
PXMP4	11264	hgsc.bcm.edu	hg19	20	32298387	32298387	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	PXMP4	NM_007238	exon3	c.G349T	p.G117X	TTTCTCCAAACAC	.	163.0	40.0	161.0	0.0	.	20	.	.	Atlas-SNP
NFATC2	4773	hgsc.bcm.edu	hg19	20	50092056	50092056	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	NFATC2	NM_012340	exon4	c.A1474C	p.I492L	CCACTATCTTCTC	.	329.0	83.0	308.0	0.0	.	112	.	.	Atlas-SNP
ITSN1	6453	hgsc.bcm.edu	hg19	21	35172168	35172168	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	ITSN1	NM_001001132	exon19	c.G2239A	p.A747T	TACCGGGCACTGT	.	31.0	8.0	44.0	0.0	.	166	.	.	Atlas-SNP
YBEY	54059	hgsc.bcm.edu	hg19	21	47711386	47711386	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	YBEY	NM_001006114	exon3	c.G349C	p.D117H	AGCGGGGATGCTG	.	147.0	50.0	164.0	0.0	.	23	.	.	Atlas-SNP
KCNJ4	3761	hgsc.bcm.edu	hg19	22	38823337	38823337	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	KCNJ4	NM_004981	exon2	c.G801T	p.E267D	GCTGTCCTCGTCG	.	62.0	24.0	39.0	0.0	.	74	.	.	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	hg19	22	46829366	46829366	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	CELSR1	NM_014246	exon5	c.C4535T	p.T1512M	ACGGTCGTTGTTG	.	33.0	9.0	33.0	0.0	.	242	.	.	Atlas-SNP
HCCS	3052	hgsc.bcm.edu	hg19	X	11139892	11139892	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	HCCS	NM_001122608	exon7	c.G769C	p.D257H	GTATGGGACAGAA	.	32.0	15.0	33.0	0.0	.	17	.	.	Atlas-SNP
PRPS2	5634	hgsc.bcm.edu	hg19	X	12838904	12838904	+	Silent	SNP	A	A	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	PRPS2	NM_001039091	exon6	c.A855G	p.K285K	AATGAAACACTGC	.	42.0	23.0	35.0	0.0	.	41	.	.	Atlas-SNP
SLC9A7	84679	hgsc.bcm.edu	hg19	X	46541903	46541903	+	Silent	SNP	G	G	A	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	SLC9A7	NM_001257291	exon2	c.C393T	p.S131S	AGTGCAGCTGAGT	.	49.0	26.0	51.0	0.0	.	73	.	.	Atlas-SNP
CBWD5	220869	hgsc.bcm.edu	hg19	9	70484455	70484455	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	CBWD5	NM_001024916	exon3	c.259delT	p.S87fs	.	.	3127.0	257.0	3248.0	0.0	.	1	.	.	Atlas-Indel,Pindel
MYOM1	8736	hgsc.bcm.edu	hg19	18	3116449	3116450	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	MYOM1	NM_003803	exon21	c.3183_3184insC	p.P1061fs	.	.	90.0	10.0	77.0	0.0	.	192	.	.	Atlas-INDEL
CDC42BPA	8476	hgsc.bcm.edu	hg19	1	227316906	227316908	+	In_Frame_Del	DEL	GCA	GCA	-	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	CDC42BPA	NM_003607	exon11	c.1416_1418del	p.472_473del	.	.	421.0	107.0	580.0	0.0	.	528	.	.	Atlas-Indel,Pindel
RNF133	168433	hgsc.bcm.edu	hg19	7	122338762	122338763	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	RNF133	NM_139175	exon1	c.211_212del	p.71_71del	.	.	84.0	28.0	90.0	0.0	.	41	.	.	Atlas-Indel,Pindel
CDC27	996	hgsc.bcm.edu	hg19	17	45234594	45234729	+	Frame_Shift_Del	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-	novel		TCGA-BC-4073-01B-02D-A12Z-10	TCGA-BC-4073-10A-01D-A12Z-10	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fcc3deff-4d29-489d-834f-f2c98fd750d8	4af05379-ed6d-488f-932c-43921f43e40b	.	CDC27	NM_001114091	exon6	c.601_631del	p.201_211del	.	.	153.0	12.0	140.0	0.0	.	337	.	.	Pindel