Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	TVarRat	NVarRat	dbSNP_Strength	dbSNP_AF	dbSNP_PopFreq	Confidence	Algorithm
BAI2	576	hgsc.bcm.edu	hg19	1	32207416	32207416	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	BAI2	NM_001703	exon9	c.G1570T	p.E524X	TCTTCTCACTACA	.	110.0	17.0	109.0	0.0	.	128	.	.	.	none	.	.	PASS	Atlas-SNP
TOE1	114034	hgsc.bcm.edu	hg19	1	45808095	45808095	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	TOE1	NM_025077	exon6	c.C532G	p.L178V	CTATTCCTGGAGC	.	168.0	29.0	168.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
LPHN2	23266	hgsc.bcm.edu	hg19	1	82456455	82456455	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	LPHN2	NM_012302	exon20	c.C3838G	p.L1280V	TCCCTTCTGTACC	.	165.0	44.0	142.0	0.0	.	464	.	.	.	none	.	.	PASS	Atlas-SNP
C1orf51	148523	hgsc.bcm.edu	hg19	1	150259000	150259000	+	Silent	SNP	T	T	A	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	C1orf51	NM_144697	exon5	c.T792A	p.T264T	CACCACTCCAATT	.	183.0	35.0	161.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
CRTC2	200186	hgsc.bcm.edu	hg19	1	153924520	153924520	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	CRTC2	NM_181715	exon10	c.G971T	p.G324V	CCCAGGCCCATGC	.	108.0	14.0	95.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
FAM5C	339479	hgsc.bcm.edu	hg19	1	190067269	190067269	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	FAM5C	NM_199051	exon8	c.T2180A	p.L727X	CGAAGCAAGCAAG	.	129.0	14.0	146.0	0.0	.	343	.	.	.	none	.	.	PASS	Atlas-SNP
TAF1B	9014	hgsc.bcm.edu	hg19	2	10016047	10016047	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	TAF1B	NM_005680	exon7	c.G607C	p.E203Q	CGAAAGGAGAAGG	.	200.0	40.0	210.0	0.0	.	62	.	.	.	none	.	.	PASS	Atlas-SNP
CAD	790	hgsc.bcm.edu	hg19	2	27460276	27460276	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	CAD	NM_004341	exon28	c.G4426A	p.E1476K	CTGCGGGAACCAG	.	120.0	20.0	119.0	0.0	.	199	.	.	.	none	.	.	PASS	Atlas-SNP
TSGA10	80705	hgsc.bcm.edu	hg19	2	99720473	99720473	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	TSGA10	NM_182911	exon9	c.G568T	p.E190X	CACTTTCGGTATC	.	113.0	12.0	86.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
DARS	1615	hgsc.bcm.edu	hg19	2	136736937	136736937	+	Splice_Site	SNP	C	C	A	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	DARS	NM_001349	exon4	c.125-1G>T	.	CTCGATCTGTAAT	.	124.0	25.0	93.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
KIF5C	3800	hgsc.bcm.edu	hg19	2	149835496	149835496	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	KIF5C	NM_004522	exon13	c.C1354T	p.Q452X	TTGGATCAGGATG	.	61.0	17.0	44.0	0.0	.	166	.	.	.	none	.	.	PASS	Atlas-SNP
USP37	57695	hgsc.bcm.edu	hg19	2	219328058	219328058	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	USP37	NM_020935	exon22	c.T2498C	p.L833P	CTTTTGAGGTCAT	.	87.0	5.0	99.0	0.0	.	76	.	.	.	none	.	.	PASS	Atlas-SNP
PTPRN	5798	hgsc.bcm.edu	hg19	2	220161767	220161767	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	PTPRN	NM_002846	exon15	c.T2176G	p.C726G	TGGCACAGGTGTT	.	75.0	21.0	80.0	0.0	.	138	.	.	.	none	.	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	hg19	2	238275884	238275884	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	COL6A3	NM_004369	exon11	c.A4946G	p.N1649S	CTGAAGTTGATGG	.	52.0	9.0	60.0	0.0	.	608	.	.	.	none	.	.	PASS	Atlas-SNP
SETD5	55209	hgsc.bcm.edu	hg19	3	9512542	9512542	+	Silent	SNP	T	T	C	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	SETD5	NM_001080517	exon19	c.T3124C	p.L1042L	GGATCCTTGTCAC	.	25.0	4.0	24.0	0.0	.	210	.	.	.	none	.	.	PASS	Atlas-SNP
CAPN7	23473	hgsc.bcm.edu	hg19	3	15262464	15262464	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	CAPN7	NM_014296	exon5	c.C614T	p.T205I	GATACACAGCAGA	.	65.0	16.0	51.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
EXOSC7	23016	hgsc.bcm.edu	hg19	3	45048921	45048921	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	EXOSC7	NM_015004	exon7	c.C625T	p.R209W	GGCTATCGGCATG	.	31.0	10.0	57.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
TREX1	11277	hgsc.bcm.edu	hg19	3	48508760	48508760	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	TREX1	NM_016381	exon1	c.A871T	p.T291S	GGGGTCACAGCCT	.	93.0	12.0	101.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
VPS8	23355	hgsc.bcm.edu	hg19	3	184700420	184700420	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	VPS8	NM_001009921	exon40	c.C3487T	p.H1163Y	ATTCCTCATCTAC	.	71.0	13.0	65.0	0.0	.	109	.	.	.	none	.	.	PASS	Atlas-SNP
ABCG2	9429	hgsc.bcm.edu	hg19	4	89042889	89042889	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	ABCG2	NM_004827	exon6	c.T587G	p.I196R	ATTCCTATACTAG	.	75.0	13.0	70.0	0.0	.	151	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1109	84162	hgsc.bcm.edu	hg19	4	123156097	123156097	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	KIAA1109	NM_015312	exon25	c.G3493T	p.E1165X	AGTGCAGAGTCTG	.	107.0	25.0	102.0	0.0	.	424	.	.	.	none	.	.	PASS	Atlas-SNP
FASTKD3	79072	hgsc.bcm.edu	hg19	5	7867621	7867621	+	Silent	SNP	A	A	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	FASTKD3	NM_024091	exon2	c.T576C	p.P192P	ACTTTGAGGATCC	.	180.0	23.0	130.0	0.0	.	88	.	.	.	none	.	.	PASS	Atlas-SNP
ADAMTS6	11174	hgsc.bcm.edu	hg19	5	64537954	64537954	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	ADAMTS6	NM_197941	exon15	c.A1910C	p.Y637S	CAGTTATAATACT	.	79.0	4.0	67.0	0.0	.	174	.	.	.	none	.	.	PASS	Atlas-SNP
SPATA9	83890	hgsc.bcm.edu	hg19	5	94994451	94994451	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	SPATA9	NM_031952	exon5	c.G641C	p.R214T	AATGACCTATAAG	.	62.0	10.0	51.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
SLC36A2	153201	hgsc.bcm.edu	hg19	5	150701645	150701645	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	SLC36A2	NM_181776	exon9	c.T1142A	p.L381Q	AGATCCAGAGGCA	.	147.0	31.0	130.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	hg19	5	169463529	169463529	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	DOCK2	NM_004946	exon36	c.A3635G	p.K1212R	TCTACAAAGATAA	.	85.0	23.0	74.0	0.0	.	389	.	.	.	none	.	.	PASS	Atlas-SNP
NSD1	64324	hgsc.bcm.edu	hg19	5	176696648	176696648	+	Silent	SNP	C	C	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	NSD1	NM_022455	exon16	c.C5349T	p.N1783N	TTCCAACATTGAT	.	89.0	14.0	73.0	0.0	.	416	.	.	.	none	.	.	PASS	Atlas-SNP
CLPS	1208	hgsc.bcm.edu	hg19	6	35765001	35765001	+	Missense_Mutation	SNP	C	C	G	rs140966197	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	CLPS,NS,carcinoma,+1,1	CLPS	NM_001252598	exon1	c.G65C	p.R22P	ATCCCCCGGGGGC	.	153.0	13.0	118.0	0.0	.	15	.	.	.	alt	C|0.999;T|0.001	.	PASS	Atlas-SNP
GLTSCR1L	23506	hgsc.bcm.edu	hg19	6	42796705	42796705	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	KIAA0240,NS,carcinoma,0,1	.	NM_015349	exon5	c.C634G	p.Q212E	TCTGGTCAAATAC	.	221.0	35.0	215.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
MRPL2	51069	hgsc.bcm.edu	hg19	6	43023646	43023646	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	MRPL2	NM_015950	exon5	c.T620G	p.I207S	GCTCGGATATATT	.	41.0	10.0	44.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
SENP6	26054	hgsc.bcm.edu	hg19	6	76412443	76412443	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	SENP6	NM_015571	exon19	c.G2371A	p.A791T	GAAAATGCTGTCA	.	62.0	11.0	58.0	0.0	.	189	.	.	.	none	.	.	PASS	Atlas-SNP
SHPRH	257218	hgsc.bcm.edu	hg19	6	146234630	146234630	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	SHPRH	NM_173082	exon24	c.G4322C	p.R1441P	AGCTGTCGAGCAC	.	95.0	18.0	80.0	0.0	.	169	.	.	.	none	.	.	PASS	Atlas-SNP
LPA	4018	hgsc.bcm.edu	hg19	6	161027563	161027563	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	LPA,colon,carcinoma,0,1	LPA	NM_005577	exon18	c.G2731A	p.V911I	GCGCGACGGCAGT	.	197.0	8.0	214.0	0.0	.	237	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA0895	23366	hgsc.bcm.edu	hg19	7	36396613	36396613	+	Silent	SNP	G	G	A	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	KIAA0895	NM_001100425	exon3	c.C765T	p.F255F	AGATTTGAAGAAT	.	79.0	11.0	85.0	0.0	.	89	.	.	.	none	.	.	PASS	Atlas-SNP
URGCP	55665	hgsc.bcm.edu	hg19	7	43918082	43918082	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	URGCP	NM_001077663	exon6	c.T980G	p.I327S	GGGAAAATGTCCA	.	109.0	24.0	76.0	0.0	.	170	.	.	.	none	.	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	hg19	7	103629656	103629656	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	RELN	NM_173054	exon1	c.G148A	p.G50R	GCTCCCCATCCCC	.	112.0	20.0	90.0	0.0	.	593	.	.	.	none	.	.	PASS	Atlas-SNP
HAS2	3037	hgsc.bcm.edu	hg19	8	122641473	122641473	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	HAS2	NM_005328	exon2	c.T108A	p.F36L	TTGGATAAACTGG	.	90.0	16.0	95.0	0.0	.	87	.	.	.	none	.	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	hg19	9	137734002	137734002	+	Splice_Site	SNP	G	G	C	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	COL5A1	NM_000093	exon66	c.5371-1G>C	.	TCCCCAGACCAAG	.	100.0	12.0	82.0	0.0	.	323	.	.	.	none	.	.	PASS	Atlas-SNP
HTRA1	5654	hgsc.bcm.edu	hg19	10	124273843	124273843	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	HTRA1	NM_002775	exon9	c.A1411T	p.I471F	ATCATGATCACAG	.	99.0	20.0	100.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
CNTN1	1272	hgsc.bcm.edu	hg19	12	41327590	41327590	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	CNTN1	NM_001256063	exon9	c.A895C	p.N299H	ATCTTCAATATTC	.	76.0	14.0	84.0	0.0	.	207	.	.	.	none	.	.	PASS	Atlas-SNP
KRT77	374454	hgsc.bcm.edu	hg19	12	53097170	53097170	+	Silent	SNP	G	G	T	rs375217197	alternate_allele	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	KRT77	NM_175078	exon1	c.C49A	p.R17R	AAACCCGCCTGCT	.	70.0	19.0	78.0	0.0	.	58	.	.	.	alt	.	.	PASS	Atlas-SNP
GCN1L1	10985	hgsc.bcm.edu	hg19	12	120599294	120599294	+	Silent	SNP	C	C	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	GCN1L1	NM_006836	exon22	c.G2436A	p.E812E	ACTCACCTCCTTC	.	119.0	10.0	120.0	0.0	.	207	.	.	.	none	.	.	PASS	Atlas-SNP
NFKBIA	4792	hgsc.bcm.edu	hg19	14	35871629	35871629	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	NFKBIA	NM_020529	exon5	c.T877A	p.S293T	ACTCTGACTCTGT	.	145.0	24.0	144.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
SLC39A9	55334	hgsc.bcm.edu	hg19	14	69866098	69866098	+	Silent	SNP	C	C	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	SLC39A9,NS,carcinoma,0,1	SLC39A9	NM_001252150	exon1	c.C12T	p.F4F	TGATTTCATCTCC	.	47.0	13.0	39.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
SLC28A2	9153	hgsc.bcm.edu	hg19	15	45561728	45561728	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	SLC28A2	NM_004212	exon14	c.A1561C	p.I521L	CAGTGGATTTCTG	.	37.0	6.0	38.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
MTFMT	123263	hgsc.bcm.edu	hg19	15	65295424	65295424	+	Silent	SNP	A	A	C	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	MTFMT	NM_139242	exon9	c.T1146G	p.V382V	CATAGCAACAGTT	.	56.0	9.0	38.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
C15orf27	123591	hgsc.bcm.edu	hg19	15	76484312	76484312	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	C15orf27	NM_152335	exon9	c.G772A	p.E258K	CAGTTTGAGATCC	.	49.0	9.0	43.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	hg19	16	10992818	10992818	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	CIITA	NM_000246	exon5	c.T395C	p.M132T	AGAGTATGGAGAT	.	137.0	15.0	141.0	0.0	.	92	.	.	.	none	.	.	PASS	Atlas-SNP
ZFHX3	463	hgsc.bcm.edu	hg19	16	72821615	72821615	+	Silent	SNP	G	G	A	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	ZFHX3,NS,carcinoma,0,1	ZFHX3	NM_006885	exon10	c.C10560T	p.G3520G	GCCGCCGCCACCG	.	81.0	4.0	56.0	0.0	.	404	.	.	.	none	.	.	PASS	Atlas-SNP
GAN	8139	hgsc.bcm.edu	hg19	16	81411103	81411103	+	Missense_Mutation	SNP	C	C	T	rs368372086		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	GAN	NM_022041	exon11	c.C1696T	p.R566C	GACCTTCGCCGTA	.	359.0	54.0	261.0	0.0	.	59	.	.	.	weak	.	.	PASS	Atlas-SNP
KRT9	3857	hgsc.bcm.edu	hg19	17	39726126	39726126	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	KRT9,NS,carcinoma,0,1	KRT9	NM_000226	exon3	c.G867T	p.K289N	ATTCTTCTTGAGG	.	277.0	60.0	264.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
PPM1D	8493	hgsc.bcm.edu	hg19	17	58740446	58740446	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	PPM1D	NM_003620	exon6	c.G1351T	p.E451X	TTTTTAGAGGTTT	.	142.0	42.0	101.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
TANC2	26115	hgsc.bcm.edu	hg19	17	61490920	61490920	+	Silent	SNP	G	G	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	TANC2_ENST00000389520,NS,carcinoma,0,2	TANC2	NM_025185	exon22	c.G3693T	p.A1231A	ATGGGCGATGGCC	.	28.0	4.0	14.0	0.0	.	266	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA8	10351	hgsc.bcm.edu	hg19	17	66928478	66928478	+	Missense_Mutation	SNP	T	T	C	rs149928780		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	ABCA8	NM_007168	exon6	c.A748G	p.R250G	TCATCCTTTTCCT	.	76.0	5.0	47.0	0.0	.	213	.	.	.	weak	T|1.000;C|0.000	0.000	PASS	Atlas-SNP
ABCA5	23461	hgsc.bcm.edu	hg19	17	67304486	67304486	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	ABCA5	NM_018672	exon4	c.G493C	p.A165P	GAGCAGCCTCACA	.	174.0	23.0	170.0	0.0	.	162	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF681	148213	hgsc.bcm.edu	hg19	19	23926507	23926507	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	ZNF681,colon,carcinoma,0,2	ZNF681	NM_138286	exon4	c.G1845C	p.E615D	GAGTTTCTCACCA	.	27.0	4.0	16.0	0.0	.	76	.	.	.	none	.	.	PASS	Atlas-SNP
SLC23A2	9962	hgsc.bcm.edu	hg19	20	4855238	4855238	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	SLC23A2	NM_203327	exon10	c.T929A	p.L310Q	TTGAACAGCTGTA	.	181.0	28.0	213.0	0.0	.	62	.	.	.	none	.	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	hg19	22	26423002	26423002	+	Silent	SNP	C	C	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	MYO18B,right_upper_lobe,carcinoma,0,1	MYO18B	NM_032608	exon43	c.C7062G	p.L2354L	GTCCCTCTTAGAA	.	200.0	48.0	185.0	0.0	.	322	.	.	.	none	.	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	hg19	22	46653660	46653660	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	PKDREJ	NM_006071	exon1	c.A5560C	p.N1854H	ATCCATTGGTACT	.	137.0	34.0	134.0	0.0	.	195	.	.	.	none	.	.	PASS	Atlas-SNP
PPP6R2	9701	hgsc.bcm.edu	hg19	22	50878437	50878437	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	PPP6R2	NM_001242898	exon21	c.G2333T	p.S778I	AATGCAGCCATGC	.	69.0	13.0	86.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
FMR1	2332	hgsc.bcm.edu	hg19	X	147011651	147011651	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	FMR1	NM_002024	exon7	c.T518A	p.I173N	AGTCCATCAATGA	.	47.0	4.0	69.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
SEC24A	10802	hgsc.bcm.edu	hg19	5	133997149	133997160	+	In_Frame_Del	DEL	CTCACAAACAAA	CTCACAAACAAA	-	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	CTCACAAACAAA	CTCACAAACAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	SEC24A	NM_021982	exon2	c.437_448del	p.146_150del	.	.	104.0	12.0	108.0	0.0	.	77	.	0.115385	0	none	.	.	PASS	Atlas-INDEL
PCDH18	54510	hgsc.bcm.edu	hg19	4	138452043	138452043	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	PCDH18	NM_019035	exon1	c.1201delG	p.G401fs	.	.	88.0	13.0	80.0	0.0	.	229	.	0.147727	0	none	.	.	PASS	Atlas-INDEL
GAA	2548	hgsc.bcm.edu	hg19	17	78085893	78085894	+	Frame_Shift_Del	DEL	CC	CC	-	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	GAA	NM_001079803	exon13	c.1747_1748del	p.583_583del	.	.	107.0	20.0	108.0	0.0	.	66	.	0.186916	0	none	.	.	PASS	Atlas-INDEL
TECTA	7007	hgsc.bcm.edu	hg19	11	120980039	120980039	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	TECTA	NM_005422	exon3	c.317delG	p.G106fs	.	.	76.0	19.0	72.0	0.0	.	329	.	0.25	0	none	.	.	PASS	Atlas-INDEL
PPRC1	23082	hgsc.bcm.edu	hg19	10	103898442	103898442	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	PPRC1	NM_015062	exon3	c.408delC	p.D136fs	.	.	90.0	15.0	87.0	0.0	.	151	.	0.166667	0	none	.	.	PASS	Atlas-INDEL
CACNA1G	8913	hgsc.bcm.edu	hg19	17	48692731	48692732	+	Frame_Shift_Del	DEL	GC	GC	-	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	CACNA1G	NM_001256325	exon27	c.4789_4790del	p.1597_1597del	.	.	75.0	13.0	50.0	0.0	.	659	.	0.173333	0	none	.	.	PASS	Atlas-INDEL
PTCHD1	139411	hgsc.bcm.edu	hg19	X	23411958	23411959	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	PTCHD1	NM_173495	exon3	c.2323_2324insG	p.F775fs	.	.	44.0	19.0	55.0	0.0	.	213	.	0.431818	0	none	.	.	PASS	Atlas-INDEL
LCT	3938	hgsc.bcm.edu	hg19	2	136566494	136566494	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	.	LCT	NM_002299	exon8	c.3424delG	p.A1142fs	.	.	159.0	21.0	128.0	0.0	.	309	.	0.132075	0	none	.	.	PASS	Atlas-INDEL