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
CSMD2	114784	hgsc.bcm.edu	hg19	1	34174693	34174693	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	CSMD2	NM_052896	exon22	c.T3452A	p.L1151H	ACCTTGAGGACAT	.	190.0	60.0	61.0	0.0	.	946	.	.	Atlas-SNP
CYP4A22	284541	hgsc.bcm.edu	hg19	1	47603268	47603268	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	CYP4A22	NM_001010969	exon1	c.C111A	p.L37L	TCAGCTCTACCTG	.	200.0	54.0	66.0	0.0	.	60	.	.	Atlas-SNP
FGGY	55277	hgsc.bcm.edu	hg19	1	60223658	60223658	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	FGGY	NM_001113411	exon16	c.A1640G	p.D547G	TACAGGATAAAAA	.	97.0	39.0	45.0	0.0	.	99	.	.	Atlas-SNP
ELTD1	64123	hgsc.bcm.edu	hg19	1	79385992	79385992	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ELTD1	NM_022159	exon10	c.T1337C	p.I446T	GTAAAAATGCATA	.	125.0	50.0	40.0	0.0	.	143	.	.	Atlas-SNP
ZNHIT6	54680	hgsc.bcm.edu	hg19	1	86173940	86173940	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ZNHIT6	NM_017953	exon1	c.A28C	p.K10Q	CAGACTTCCCTTC	.	56.0	16.0	39.0	0.0	.	42	.	.	Atlas-SNP
CDC7	8317	hgsc.bcm.edu	hg19	1	91977431	91977431	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	CDC7	NM_001134419	exon6	c.C523A	p.H175N	ATTGTTCACCGTG	.	465.0	156.0	228.0	0.0	.	74	.	.	Atlas-SNP
ADAMTSL4	54507	hgsc.bcm.edu	hg19	1	150532349	150532349	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ADAMTSL4	NM_019032	exon18	c.C3056T	p.P1019L	AGCGCCCCTGTAA	.	50.0	22.0	22.0	0.0	.	101	.	.	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	hg19	1	228462084	228462084	+	Silent	SNP	C	C	T	rs202200633	bycluster	TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	OBSCN	NM_001271223	exon23	c.C6747T	p.D2249D	AGAGGACGCAGGG	.	127.0	56.0	86.0	0.0	.	2142	.	C|0.996;T|0.004	Atlas-SNP
MFSD2B	388931	hgsc.bcm.edu	hg19	2	24240356	24240356	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	MFSD2B	NM_001080473	exon6	c.G579A	p.L193L	AACACTGATGGGG	.	127.0	26.0	59.0	0.0	.	45	.	.	Atlas-SNP
SLC8A1	6546	hgsc.bcm.edu	hg19	2	40656836	40656836	+	Silent	SNP	T	T	G	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	SLC8A1	NM_001252624	exon1	c.A585C	p.T195T	CTTCCTTGTCTCT	.	189.0	94.0	71.0	0.0	.	221	.	.	Atlas-SNP
THADA	63892	hgsc.bcm.edu	hg19	2	43819171	43819171	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	THADA	NM_001083953	exon3	c.G91T	p.E31X	TCCCTTCCACATC	.	297.0	179.0	101.0	0.0	.	131	.	.	Atlas-SNP
USP34	9736	hgsc.bcm.edu	hg19	2	61415443	61415443	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	USP34	NM_014709	exon80	c.G10435C	p.D3479H	CTAAGTCAGACAG	.	149.0	83.0	55.0	0.0	.	334	.	.	Atlas-SNP
ADD2	119	hgsc.bcm.edu	hg19	2	70923474	70923474	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ADD2	NM_001185055	exon4	c.T425A	p.L142Q	TTGGCCAGGTTCA	.	412.0	111.0	56.0	0.0	.	261	.	.	Atlas-SNP
EXOC6B	23233	hgsc.bcm.edu	hg19	2	72727062	72727062	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	EXOC6B	NM_015189	exon12	c.A1207T	p.N403Y	TGAGGTTCTTCAA	.	435.0	128.0	223.0	0.0	.	93	.	.	Atlas-SNP
TMEM127	55654	hgsc.bcm.edu	hg19	2	96919804	96919804	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	TMEM127	NM_001193304	exon4	c.C459T	p.L153L	CAAGATGAGTTCA	.	129.0	11.0	55.0	0.0	.	13	.	.	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	hg19	2	141260598	141260598	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	LRP1B	NM_018557	exon54	c.G8596A	p.D2866N	CTCCATCACACTG	.	289.0	96.0	111.0	0.0	.	1315	.	.	Atlas-SNP
PAX3	5077	hgsc.bcm.edu	hg19	2	223163313	223163313	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	PAX3	NM_181457	exon1	c.G22T	p.V8L	TGGGCACAGCGCC	.	96.0	30.0	44.0	0.0	.	106	.	.	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	hg19	2	238263564	238263564	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	COL6A3,face,carcinoma,0,1	COL6A3	NM_004369	exon24	c.G6605A	p.R2202Q	CCCCTTCGGCCAA	.	66.0	23.0	15.0	0.0	.	608	.	.	Atlas-SNP
EPHA6	285220	hgsc.bcm.edu	hg19	3	96706230	96706230	+	Silent	SNP	A	A	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	EPHA6	NM_001080448	exon3	c.A507T	p.V169V	CCAGGTATGTAAT	.	170.0	59.0	60.0	0.0	.	439	.	.	Atlas-SNP
TM4SF18	116441	hgsc.bcm.edu	hg19	3	149051080	149051080	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	TM4SF18	NM_001184723	exon1	c.C90T	p.F30F	ATTCGGGAAATAC	.	375.0	107.0	87.0	0.0	.	12	.	.	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	hg19	3	195518119	195518119	+	Missense_Mutation	SNP	A	A	T	rs201789760	bycluster	TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	MUC4	NM_018406	exon2	c.T332A	p.M111K	GTCTCCATCACAT	.	496.0	38.0	155.0	0.0	.	1505	.	.	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	hg19	3	195518120	195518120	+	Missense_Mutation	SNP	T	T	G	rs200332113	bycluster	TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	MUC4	NM_018406	exon2	c.A331C	p.M111L	TCTCCATCACATT	.	500.0	31.0	154.0	0.0	.	1505	.	.	Atlas-SNP
SEC24B	10427	hgsc.bcm.edu	hg19	4	110447421	110447421	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	SEC24B_ENST00000265175,NS,carcinoma,0,2	SEC24B	NM_006323	exon17	c.G2831A	p.R944H	TTGTCCGTTCTAC	.	276.0	19.0	162.0	0.0	.	186	.	.	Atlas-SNP
IL6ST	3572	hgsc.bcm.edu	hg19	5	55247872	55247872	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	IL6ST	NM_002184	exon13	c.A1584G	p.K528K	TACTTTTTTTGTC	.	389.0	122.0	123.0	0.0	.	75	.	.	Atlas-SNP
ADAMTS19	171019	hgsc.bcm.edu	hg19	5	128977592	128977592	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ADAMTS19	NM_133638	exon11	c.A1793T	p.E598V	AAGGTGAGAAAGA	.	324.0	94.0	110.0	0.0	.	216	.	.	Atlas-SNP
ADGB	79747	hgsc.bcm.edu	hg19	6	146977910	146977910	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ADGB	NM_024694	exon5	c.A406C	p.M136L	TAGCTGATGAGAT	.	231.0	78.0	130.0	0.0	.	93	.	.	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	hg19	6	152676100	152676100	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	SYNE1	NM_033071	exon67	c.A10641G	p.V3547V	ACAGTGTACCTGT	.	73.0	31.0	26.0	0.0	.	3227	.	.	Atlas-SNP
OPRM1	4988	hgsc.bcm.edu	hg19	6	154331688	154331688	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	OPRM1	NM_001145281	exon1	c.C41T	p.P14L	GGAAGCCCTCCAG	.	115.0	31.0	47.0	0.0	.	241	.	.	Atlas-SNP
BRAT1	221927	hgsc.bcm.edu	hg19	7	2579479	2579479	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	BRAT1	NM_152743	exon11	c.G1439A	p.S480N	GGTGAGCTCAGGA	.	90.0	33.0	17.0	0.0	.	57	.	.	Atlas-SNP
SDK1	221935	hgsc.bcm.edu	hg19	7	4009044	4009044	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	SDK1	NM_152744	exon11	c.C1702T	p.L568F	GCCACGCTCACTG	.	74.0	31.0	30.0	0.0	.	361	.	.	Atlas-SNP
ABCB1	5243	hgsc.bcm.edu	hg19	7	87179344	87179344	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ABCB1	NM_000927	exon14	c.G1377A	p.R459R	TATGGTCCTAATA	.	193.0	44.0	46.0	0.0	.	263	.	.	Atlas-SNP
C7orf63	79846	hgsc.bcm.edu	hg19	7	89938655	89938655	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	C7orf63	NM_001039706	exon22	c.A2629G	p.T877A	CACCAAACACATA	.	440.0	167.0	290.0	0.0	.	158	.	.	Atlas-SNP
NAA38	51691	hgsc.bcm.edu	hg19	7	117828373	117828373	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	NAA38	NM_016200	exon3	c.G114T	p.L38F	GATTTTGGATGAA	.	161.0	53.0	99.0	0.0	.	16	.	.	Atlas-SNP
C7orf49	78996	hgsc.bcm.edu	hg19	7	134852549	134852549	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	C7orf49	NM_001243749	exon3	c.A185T	p.D62V	TCCTTGTCGCAGG	.	125.0	47.0	66.0	0.0	.	24	.	.	Atlas-SNP
C7orf49	78996	hgsc.bcm.edu	hg19	7	134852550	134852550	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	C7orf49	NM_001243749	exon3	c.G184T	p.D62Y	CCTTGTCGCAGGG	.	122.0	45.0	67.0	0.0	.	24	.	.	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	hg19	7	151833918	151833918	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	MLL3	NM_170606	exon59	c.G14735T	p.X4912L	GCATTTCAGTTCA	.	55.0	15.0	13.0	0.0	.	1564	.	.	Atlas-SNP
CHRNB3	1142	hgsc.bcm.edu	hg19	8	42587132	42587132	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	CHRNB3,right_upper_lobe,carcinoma,0,2	CHRNB3	NM_000749	exon5	c.G682A	p.V228I	TCCTTCGTCCTGA	.	211.0	73.0	131.0	0.0	.	74	.	.	Atlas-SNP
ZNF572	137209	hgsc.bcm.edu	hg19	8	125987939	125987939	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ZNF572	NM_152412	exon2	c.G57A	p.E19E	GAGGGAGAGTTTG	.	278.0	64.0	108.0	0.0	.	82	.	.	Atlas-SNP
MELK	9833	hgsc.bcm.edu	hg19	9	36630338	36630338	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	MELK	NM_014791	exon9	c.A709G	p.I237V	AGTAGCATTCTGC	.	118.0	41.0	56.0	0.0	.	74	.	.	Atlas-SNP
SPATA31A6	389730	hgsc.bcm.edu	hg19	9	43630592	43630592	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	FAM75A6,NS,carcinoma,0,1	.	NM_001145196	exon1	c.G110A	p.G37E	AAGAACCCCAGGG	.	30.0	11.0	17.0	0.0	.	.	.	.	Atlas-SNP
MPP7	143098	hgsc.bcm.edu	hg19	10	28420525	28420525	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	MPP7	NM_173496	exon8	c.A411G	p.V137V	TATTTTTACTGAG	.	225.0	82.0	73.0	0.0	.	60	.	.	Atlas-SNP
OPALIN	93377	hgsc.bcm.edu	hg19	10	98108095	98108095	+	Missense_Mutation	SNP	T	T	C	rs113141694		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	OPALIN	NM_033207	exon5	c.A200G	p.D67G	GGTCTGTCACTTT	.	93.0	23.0	37.0	0.0	.	31	.	T|0.500;C|0.500	Atlas-SNP
HPS6	79803	hgsc.bcm.edu	hg19	10	103825804	103825804	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	HPS6	NM_024747	exon1	c.C573T	p.F191F	TGCCTTCGGGCTG	.	28.0	9.0	18.0	0.0	.	38	.	.	Atlas-SNP
OR8I2	120586	hgsc.bcm.edu	hg19	11	55861148	55861148	+	Missense_Mutation	SNP	G	G	T	rs148027692	bycluster;alternate_allele	TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	OR8I2,NS,malignant_melanoma,+1,1	OR8I2	NM_001003750	exon1	c.G365T	p.R122L	ACAATCGCTACAT	.	175.0	58.0	80.0	1.0	.	119	.	G|1.000;A|0.000	Atlas-SNP
MRPL11	65003	hgsc.bcm.edu	hg19	11	66206166	66206166	+	Silent	SNP	G	G	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	MRPL11	NM_170739	exon1	c.C60A	p.I20I	CGCCCGGATCACA	.	81.0	24.0	67.0	0.0	.	25	.	.	Atlas-SNP
CABP4	57010	hgsc.bcm.edu	hg19	11	67223230	67223230	+	Silent	SNP	C	C	T	rs369080675		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	CABP4	NM_145200	exon1	c.C336T	p.Y112Y	GACATACGGGCCC	.	75.0	33.0	38.0	0.0	.	33	.	.	Atlas-SNP
MAML2	84441	hgsc.bcm.edu	hg19	11	95825206	95825206	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	MAML2	NM_032427	exon2	c.G1989A	p.Q663Q	TTGTTGCTGCTGC	.	328.0	34.0	103.0	0.0	.	94	.	.	Atlas-SNP
PDGFD	80310	hgsc.bcm.edu	hg19	11	103797732	103797732	+	Missense_Mutation	SNP	C	C	T	rs371743652	alternate_allele	TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	PDGFD	NM_025208	exon6	c.G895A	p.V299M	GCTGCACGAGGAG	.	137.0	51.0	61.0	0.0	.	125	.	.	Atlas-SNP
PKNOX2	63876	hgsc.bcm.edu	hg19	11	125237753	125237753	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	PKNOX2	NM_022062	exon5	c.C99T	p.T33T	GGCAACCGCCCAG	.	156.0	53.0	73.0	0.0	.	60	.	.	Atlas-SNP
A2M	2	hgsc.bcm.edu	hg19	12	9244021	9244021	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	A2M	NM_000014	exon19	c.G2245T	p.A749S	CACCTGCTGAGCT	.	161.0	9.0	44.0	0.0	.	180	.	.	Atlas-SNP
PDE3A	5139	hgsc.bcm.edu	hg19	12	20833113	20833113	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	PDE3A	NM_000921	exon16	c.T3334A	p.S1112T	TCGCACTCTTCAG	.	402.0	87.0	203.0	0.0	.	184	.	.	Atlas-SNP
ITGA7	3679	hgsc.bcm.edu	hg19	12	56087102	56087102	+	Splice_Site	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ITGA7	NM_001144996	exon21	c.2548-1G>A	.	GGAAACCTGTGGG	.	101.0	24.0	29.0	0.0	.	194	.	.	Atlas-SNP
DGKA	1606	hgsc.bcm.edu	hg19	12	56332338	56332338	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	DGKA	NM_201554	exon6	c.C393T	p.D131D	CCTGGACAGCTCA	.	413.0	106.0	133.0	0.0	.	70	.	.	Atlas-SNP
C12orf50	160419	hgsc.bcm.edu	hg19	12	88420359	88420359	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	C12orf50	NM_152589	exon3	c.G39T	p.W13C	AGTTTCCCAGAAG	.	177.0	10.0	51.0	0.0	.	70	.	.	Atlas-SNP
CCDC41	51134	hgsc.bcm.edu	hg19	12	94706794	94706794	+	Splice_Site	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	CCDC41	NM_016122	exon16	c.1708-1G>A	.	TTTTCTCTAAAAA	.	289.0	151.0	104.0	0.0	.	59	.	.	Atlas-SNP
NT5DC3	51559	hgsc.bcm.edu	hg19	12	104208729	104208729	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	NT5DC3	NM_001031701	exon2	c.A379G	p.I127V	CATTGATGAGAAG	.	530.0	288.0	158.0	0.0	.	113	.	.	Atlas-SNP
UNG	7374	hgsc.bcm.edu	hg19	12	109540669	109540669	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	UNG	NM_080911	exon5	c.T559C	p.S187P	GAGTTGTCTACAG	.	188.0	49.0	59.0	0.0	.	30	.	.	Atlas-SNP
SUPT20H	55578	hgsc.bcm.edu	hg19	13	37599542	37599542	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	.	NM_017569	exon17	c.A1247G	p.N416S	GCTTCATTCTGGA	.	265.0	83.0	121.0	0.0	.	.	.	.	Atlas-SNP
SEMA6D	80031	hgsc.bcm.edu	hg19	15	48057214	48057214	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	SEMA6D	NM_153617	exon13	c.G1388T	p.S463I	ACGACAGCGTATT	.	109.0	30.0	46.0	0.0	.	322	.	.	Atlas-SNP
MAPK6	5597	hgsc.bcm.edu	hg19	15	52357196	52357196	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	MAPK6	NM_002748	exon6	c.A2165G	p.X722X	TGAACTAAAACAC	.	279.0	110.0	170.0	0.0	.	70	.	.	Atlas-SNP
UNC13C	440279	hgsc.bcm.edu	hg19	15	54435882	54435882	+	Splice_Site	SNP	G	G	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	UNC13C	NM_001080534	exon3	c.3071+1G>A	.	TGGTGGGTAAGTA	.	224.0	67.0	72.0	0.0	.	674	.	.	Atlas-SNP
SCAPER	49855	hgsc.bcm.edu	hg19	15	77087747	77087747	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	SCAPER	NM_020843	exon7	c.G646A	p.A216T	TGGGAGCCAGACG	.	113.0	34.0	87.0	0.0	.	160	.	.	Atlas-SNP
MFGE8	4240	hgsc.bcm.edu	hg19	15	89450543	89450543	+	Silent	SNP	A	A	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	MFGE8	NM_001114614	exon3	c.T270G	p.S90S	ACGCACAGACGAG	.	186.0	56.0	93.0	0.0	.	60	.	.	Atlas-SNP
LRRK1	79705	hgsc.bcm.edu	hg19	15	101592005	101592005	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	LRRK1	NM_024652	exon24	c.G3529A	p.D1177N	CACACGGACCCCA	.	200.0	12.0	74.0	0.0	.	310	.	.	Atlas-SNP
MINK1	50488	hgsc.bcm.edu	hg19	17	4796728	4796728	+	Splice_Site	SNP	G	G	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	MINK1	NM_153827	exon21	c.2401-1G>A	.	CCTGCAGGACTTT	.	125.0	8.0	70.0	0.0	.	110	.	.	Atlas-SNP
PHF23	79142	hgsc.bcm.edu	hg19	17	7139869	7139869	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	PHF23	NM_024297	exon4	c.C377G	p.T126S	AGCAAGGTAGCAC	.	137.0	37.0	66.0	0.0	.	38	.	.	Atlas-SNP
APPBP2	10513	hgsc.bcm.edu	hg19	17	58539193	58539193	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	APPBP2	NM_006380	exon8	c.G914T	p.C305F	GACTGACAGATAT	.	312.0	124.0	162.0	0.0	.	48	.	.	Atlas-SNP
BPTF	2186	hgsc.bcm.edu	hg19	17	65889635	65889635	+	Silent	SNP	T	T	G	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	BPTF	NM_004459	exon8	c.T2583G	p.A861A	ATTTGCTTTGAAT	.	852.0	331.0	454.0	0.0	.	415	.	.	Atlas-SNP
UBE2O	63893	hgsc.bcm.edu	hg19	17	74387574	74387574	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	UBE2O	NM_022066	exon18	c.A3329T	p.Q1110L	ATGGACTGCACCA	.	178.0	40.0	82.0	0.0	.	207	.	.	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	hg19	17	78328292	78328292	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	RNF213	NM_001256071	exon36	c.A10778G	p.Q3593R	AGAAGCAAGAAGA	.	90.0	22.0	27.0	0.0	.	766	.	.	Atlas-SNP
ZNF532	55205	hgsc.bcm.edu	hg19	18	56651549	56651549	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ZNF532	NM_018181	exon11	c.G3757A	p.E1253K	AGCCACGAGGATG	.	232.0	84.0	125.0	0.0	.	108	.	.	Atlas-SNP
CDH7	1005	hgsc.bcm.edu	hg19	18	63511096	63511096	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	CDH7	NM_004361	exon7	c.G1030T	p.A344S	GAAGCTGCAAATA	.	249.0	97.0	99.0	0.0	.	362	.	.	Atlas-SNP
ZNF799	90576	hgsc.bcm.edu	hg19	19	12502155	12502155	+	Missense_Mutation	SNP	T	T	G	rs201335235		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ZNF799	NM_001080821	exon4	c.A1057C	p.K353Q	GACTTTTCAGTGA	.	226.0	11.0	90.0	0.0	.	111	.	.	Atlas-SNP
TARM1	441864	hgsc.bcm.edu	hg19	19	54573335	54573335	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	TARM1	NM_001135686	exon5	c.C738G	p.I246M	TCCCATGATAACC	.	97.0	24.0	40.0	0.0	.	10	.	.	Atlas-SNP
ELMO2	63916	hgsc.bcm.edu	hg19	20	44997586	44997586	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ELMO2	NM_182764	exon20	c.T1906A	p.S636T	GGATGGAGAAGGC	.	149.0	49.0	63.0	0.0	.	51	.	.	Atlas-SNP
NELFCD	51497	hgsc.bcm.edu	hg19	20	57561177	57561177	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	.	NM_198976	exon2	c.T144A	p.D48E	AGAGGATGATGCG	.	135.0	63.0	78.0	0.0	.	.	.	.	Atlas-SNP
SRMS	6725	hgsc.bcm.edu	hg19	20	62178615	62178615	+	Missense_Mutation	SNP	C	C	T	rs149894938		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	SRMS	NM_080823	exon1	c.G202A	p.G68R	GCTCCCCGCCACA	.	49.0	18.0	34.0	0.0	.	48	.	C|1.000;T|0.000	Atlas-SNP
HUNK	30811	hgsc.bcm.edu	hg19	21	33340695	33340695	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	HUNK	NM_014586	exon6	c.C1008A	p.N336K	TCCCAACAGGTAA	.	90.0	28.0	56.0	0.0	.	74	.	.	Atlas-SNP
POFUT2	23275	hgsc.bcm.edu	hg19	21	46707671	46707671	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	POFUT2	NM_015227	exon1	c.C116T	p.A39V	GAAGCCGCCCCCG	.	54.0	21.0	30.0	0.0	.	77	.	.	Atlas-SNP
DEPDC5	9681	hgsc.bcm.edu	hg19	22	32188763	32188763	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	DEPDC5_ENST00000535622,colon,carcinoma,0,3	DEPDC5	NM_001242897	exon12	c.C727T	p.R243X	TCAATTCGACAGG	.	125.0	64.0	81.0	0.0	.	266	.	.	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	hg19	22	46931320	46931320	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	CELSR1	NM_014246	exon1	c.C1748A	p.P583H	ACCACGGGGTAGC	.	21.0	14.0	35.0	0.0	.	242	.	.	Atlas-SNP
ARMCX6	54470	hgsc.bcm.edu	hg19	X	100871412	100871412	+	Silent	SNP	G	G	T	rs138992392	alternate_allele	TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ARMCX6	NM_001184768	exon4	c.C199A	p.R67R	AGGGCCGAGCCAT	.	124.0	102.0	61.0	0.0	.	21	.	G|1.000;A|0.000	Atlas-SNP
ND4	0	hgsc.bcm.edu	hg19	MT	11420	11420	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	.	ENST00000361381	exon1	c.G661A	p.V221I	GCCCATGTCGAAG	.	549.0	504.0	476.0	0.0	.	.	.	.	Atlas-SNP
AWAT1	158833	hgsc.bcm.edu	hg19	X	69459750	69459751	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	AWAT1	NM_001013579	exon6	c.798_799insC	p.G266fs	.	.	149.0	11.0	64.0	0.0	.	74	.	.	Atlas-INDEL
TDRD9	122402	hgsc.bcm.edu	hg19	14	104472995	104472996	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	TDRD9	NM_153046	exon17	c.1892_1893insT	p.S631fs	.	.	240.0	15.0	177.0	0.0	.	175	.	.	Atlas-INDEL
DFNB31	25861	hgsc.bcm.edu	hg19	9	117168768	117168769	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	DFNB31	NM_001173425	exon9	c.2103_2104insG	p.G701fs	.	.	108.0	10.0	55.0	0.0	.	100	.	.	Atlas-INDEL
MYCT1	80177	hgsc.bcm.edu	hg19	6	153043057	153043058	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	MYCT1	NM_025107	exon2	c.377_378insC	p.Y126fs	.	.	342.0	21.0	131.0	0.0	.	48	.	.	Atlas-INDEL
CAMSAP2	23271	hgsc.bcm.edu	hg19	1	200817808	200817808	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	.	NM_203459	exon11	c.1910delA	p.D637fs	.	.	253.0	91.0	75.0	0.0	.	.	.	.	Atlas-Indel,Pindel
BARHL2	343472	hgsc.bcm.edu	hg19	1	91178035	91178036	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	BARHL2	NM_020063	exon3	c.998_999insG	p.A333fs	.	.	106.0	10.0	62.0	0.0	.	62	.	.	Atlas-INDEL
MAGEC1	9947	hgsc.bcm.edu	hg19	X	140993903	140993905	+	In_Frame_Del	DEL	GCC	GCC	-	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	GCC	GCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	MAGEC1	NM_005462	exon4	c.712_714del	p.238_238del	.	.	236.0	24.0	110.0	0.0	.	317	.	.	Atlas-INDEL
COL22A1	169044	hgsc.bcm.edu	hg19	8	139895383	139895384	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	COL22A1	NM_152888	exon2	c.33_34insG	p.G11fs	.	.	88.0	10.0	38.0	0.0	.	390	.	.	Atlas-INDEL
OR2B11	127623	hgsc.bcm.edu	hg19	1	247615077	247615077	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	OR2B11	NM_001004492	exon1	c.209delT	p.L70fs	.	.	215.0	46.0	74.0	0.0	.	102	.	.	Atlas-Indel,Pindel
FAT2	2196	hgsc.bcm.edu	hg19	5	150886943	150886944	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	FAT2	NM_001447	exon22	c.12289_12290insA	p.A4097fs	.	.	361.0	25.0	110.0	0.0	.	465	.	.	Atlas-INDEL
ADCY4	196883	hgsc.bcm.edu	hg19	14	24787938	24787939	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	ADCY4	NM_139247	exon25	c.3003_3004insA	p.K1001fs	.	.	273.0	17.0	81.0	0.0	.	86	.	.	Atlas-INDEL
EIF2AK3	9451	hgsc.bcm.edu	hg19	2	88874831	88874857	+	In_Frame_Del	DEL	CTGAAAAAGACCTGCTTCTTTGTGGTG	CTGAAAAAGACCTGCTTCTTTGTGGTG	-	novel		TCGA-BC-A10T-01A-11D-A12Z-10	TCGA-BC-A10T-11A-11D-A12Z-10	CTGAAAAAGACCTGCTTCTTTGTGGTG	CTGAAAAAGACCTGCTTCTTTGTGGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f755c284-603b-4eac-93b5-5d67fbd723da	47347db4-6417-4a5b-b1a3-5c95691ca78c	.	EIF2AK3	NM_004836	exon13	c.2145_2171del	p.715_724del	.	.	189.0	13.0	76.0	0.0	.	160	.	.	Pindel