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
PIK3CD	5293	hgsc.bcm.edu	hg19	1	9781589	9781589	+	Silent	SNP	G	G	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	PIK3CD	NM_005026	exon15	c.G1899A	p.L633L	ATTCCTGCTGGAC	.	39.0	19.0	54.0	0.0	.	86	.	.	.	none	.	.	PASS	Atlas-SNP
ECM1	1893	hgsc.bcm.edu	hg19	1	150483676	150483676	+	Splice_Site	SNP	T	T	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	ECM1	NM_004425	exon6	c.708+2T>A	.	TTGTGGTAAGGTT	.	31.0	11.0	46.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
OR14C36	127066	hgsc.bcm.edu	hg19	1	248512735	248512735	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	OR14C36	NM_001001918	exon1	c.T659G	p.F220C	ACATCTTTTCGAC	.	68.0	26.0	81.0	0.0	.	113	.	.	.	none	.	.	PASS	Atlas-SNP
HNRPLL	92906	hgsc.bcm.edu	hg19	2	38812955	38812955	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	HNRPLL	NM_138394	exon3	c.A377G	p.E126G	ACACATTCTTTGG	.	47.0	23.0	64.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
OXER1	165140	hgsc.bcm.edu	hg19	2	42990746	42990746	+	Silent	SNP	G	G	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	OXER1	NM_148962	exon1	c.C574T	p.L192L	CCTTCAGGTAGCG	.	48.0	12.0	57.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
ATP6V1E2	90423	hgsc.bcm.edu	hg19	2	46739823	46739823	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	ATP6V1E2	NM_080653	exon2	c.A28C	p.K10Q	TCTGCTTTTTCAC	.	29.0	10.0	43.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
ATP6V1E2	90423	hgsc.bcm.edu	hg19	2	46739824	46739824	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	ATP6V1E2	NM_080653	exon2	c.A27T	p.K9N	CTGCTTTTTCACA	.	29.0	9.0	43.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
CNTNAP5	129684	hgsc.bcm.edu	hg19	2	125204404	125204404	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	CNTNAP5,NS,carcinoma,0,1	CNTNAP5	NM_130773	exon6	c.C808G	p.H270D	CACTGGCACTCGG	.	85.0	29.0	119.0	0.0	.	405	.	.	.	none	.	.	PASS	Atlas-SNP
SF3B1	23451	hgsc.bcm.edu	hg19	2	198272752	198272752	+	Silent	SNP	T	T	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	SF3B1	NM_012433	exon9	c.A1209G	p.E403E	ATCTAATTCCTCA	.	47.0	11.0	55.0	0.0	.	1038	.	.	.	none	.	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	hg19	2	218683236	218683236	+	Silent	SNP	A	A	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	TNS1	NM_022648	exon24	c.T3507C	p.A1169A	GACGCCAGCCACA	.	71.0	22.0	58.0	0.0	.	251	.	.	.	none	.	.	PASS	Atlas-SNP
KIF1A	547	hgsc.bcm.edu	hg19	2	241696843	241696843	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	KIF1A	NM_001244008	exon27	c.G2751T	p.E917D	CTCATCCTCCTCC	.	88.0	4.0	106.0	0.0	.	152	.	.	.	none	.	.	PASS	Atlas-SNP
CRTAP	10491	hgsc.bcm.edu	hg19	3	33155650	33155650	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	CRTAP	NM_006371	exon1	c.A81C	p.Q27H	CGCCCAATACGAA	.	556.0	254.0	580.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
ACAA1	30	hgsc.bcm.edu	hg19	3	38167691	38167691	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	ACAA1	NM_001607	exon9	c.G959C	p.G320A	GCAGGTCCAATGC	.	106.0	49.0	116.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
USP4	7375	hgsc.bcm.edu	hg19	3	49338037	49338037	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	USP4	NM_003363	exon11	c.T1375G	p.L459V	AAACCAAAGTAGA	.	114.0	48.0	123.0	0.0	.	72	.	.	.	none	.	.	PASS	Atlas-SNP
RBM15B	29890	hgsc.bcm.edu	hg19	3	51431290	51431290	+	Silent	SNP	T	T	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	RBM15B	NM_013286	exon1	c.T2460C	p.L820L	GCGGCTTCTCAGG	.	63.0	22.0	64.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
PRR23A	729627	hgsc.bcm.edu	hg19	3	138724832	138724832	+	Silent	SNP	A	A	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	PRR23A	NM_001134659	exon1	c.T279C	p.D93D	GTGTCCATCGAGA	.	142.0	59.0	196.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
SLITRK3	22865	hgsc.bcm.edu	hg19	3	164906764	164906764	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	SLITRK3	NM_014926	exon2	c.C1855A	p.P619T	CAGCTGGTGCAAC	.	59.0	15.0	71.0	0.0	.	263	.	.	.	none	.	.	PASS	Atlas-SNP
ZBBX	79740	hgsc.bcm.edu	hg19	3	167086364	167086364	+	Splice_Site	SNP	T	T	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	ZBBX	NM_024687	exon6	c.69-2A>T	.	CATTTCTGAAGAC	.	37.0	17.0	27.0	0.0	.	299	.	.	.	none	.	.	PASS	Atlas-SNP
SEC62	7095	hgsc.bcm.edu	hg19	3	169701000	169701000	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	SEC62	NM_003262	exon5	c.C508G	p.L170V	TTCAAACTTGAGC	.	261.0	81.0	333.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
DVL3	1857	hgsc.bcm.edu	hg19	3	183887831	183887831	+	Silent	SNP	C	C	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	DVL3	NM_004423	exon14	c.C1536T	p.S512S	TGGCTCCAGTGGC	.	112.0	48.0	121.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
VPS8	23355	hgsc.bcm.edu	hg19	3	184654055	184654055	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	VPS8	NM_001009921	exon34	c.T2920C	p.C974R	AAGCCTTGTAAAG	.	55.0	24.0	66.0	0.0	.	109	.	.	.	none	.	.	PASS	Atlas-SNP
MASP1	5648	hgsc.bcm.edu	hg19	3	186961355	186961355	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	MASP1	NM_139125	exon9	c.C1145T	p.T382I	TTCCTTGTAGAGA	.	69.0	23.0	72.0	0.0	.	240	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC66	339977	hgsc.bcm.edu	hg19	4	52861896	52861896	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	LRRC66	NM_001024611	exon4	c.C1292A	p.A431D	CCCGCAGCTTCCA	.	55.0	26.0	42.0	0.0	.	128	.	.	.	none	.	.	PASS	Atlas-SNP
EPHA5	2044	hgsc.bcm.edu	hg19	4	66230806	66230806	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	EPHA5	NM_004439	exon12	c.T2165A	p.L722Q	TCACCTAGGAAAT	.	81.0	25.0	83.0	0.0	.	315	.	.	.	none	.	.	PASS	Atlas-SNP
SLC9A3	6550	hgsc.bcm.edu	hg19	5	483552	483552	+	Silent	SNP	G	G	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	SLC9A3	NM_004174	exon6	c.C978T	p.N326N	CGAGATGTTGGCC	.	119.0	36.0	147.0	0.0	.	89	.	.	.	none	.	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	hg19	5	37226992	37226992	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	C5orf42	NM_023073	exon12	c.C1705A	p.L569M	AATGCAGTTCTGT	.	102.0	45.0	132.0	0.0	.	422	.	.	.	none	.	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	hg19	5	37226993	37226993	+	Silent	SNP	T	T	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	C5orf42	NM_023073	exon12	c.A1704G	p.E568E	ATGCAGTTCTGTA	.	101.0	44.0	132.0	0.0	.	422	.	.	.	none	.	.	PASS	Atlas-SNP
ANKRD55	79722	hgsc.bcm.edu	hg19	5	55439741	55439741	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	ANKRD55	NM_024669	exon7	c.C499T	p.H167Y	CCCAGTGGAGTGG	.	33.0	14.0	57.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
CDC23	8697	hgsc.bcm.edu	hg19	5	137527594	137527594	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	CDC23	NM_004661	exon12	c.G1319C	p.G440A	CATTCTCCTAAAG	.	111.0	39.0	110.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
PXDC1	221749	hgsc.bcm.edu	hg19	6	3723879	3723879	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	.	NM_183373	exon5	c.C670A	p.P224T	CGAAGGGGACCAG	.	97.0	40.0	80.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
NHLRC1	378884	hgsc.bcm.edu	hg19	6	18121925	18121925	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	NHLRC1	NM_198586	exon1	c.G913A	p.G305S	CTTGGCCGACAAG	.	49.0	21.0	52.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
ABT1	29777	hgsc.bcm.edu	hg19	6	26597296	26597296	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	ABT1	NM_013375	exon1	c.A86C	p.Q29P	AGGAGCAGGAGGA	.	134.0	57.0	148.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
PGC	5225	hgsc.bcm.edu	hg19	6	41704737	41704737	+	Silent	SNP	G	G	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	PGC	NM_002630	exon9	c.C1020T	p.N340N	GTAGCCGTTGTTC	.	65.0	21.0	76.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
HEBP2	23593	hgsc.bcm.edu	hg19	6	138727155	138727155	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	HEBP2,NS,malignant_melanoma,0,1	HEBP2	NM_014320	exon3	c.G286T	p.G96C	GAGCCTGGTTCAG	.	111.0	36.0	124.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
IQCE	23288	hgsc.bcm.edu	hg19	7	2617955	2617955	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	IQCE	NM_152558	exon7	c.A545T	p.D182V	GGAAGGACCGGCA	.	82.0	40.0	65.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1429	25962	hgsc.bcm.edu	hg19	8	95539042	95539042	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	KIAA1429	NM_015496	exon8	c.T1430G	p.L477R	TGTAGCAGTCCTG	.	62.0	22.0	54.0	0.0	.	176	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC171	203238	hgsc.bcm.edu	hg19	9	15666301	15666301	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	.	NM_173550	exon9	c.G1056C	p.E352D	ACAAGAGAGCTTT	.	43.0	18.0	75.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
EGFL7	51162	hgsc.bcm.edu	hg19	9	139566407	139566407	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	EGFL7	NM_016215	exon10	c.C666A	p.H222Q	ACTGCACAGCCTG	.	33.0	7.0	34.0	0.0	.	11	.	.	.	none	.	.	PASS	Atlas-SNP
TBATA	219793	hgsc.bcm.edu	hg19	10	72534001	72534001	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	.	NM_152710	exon9	c.A885C	p.E295D	AGGAGGTTCATGC	.	56.0	23.0	59.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
MINPP1	9562	hgsc.bcm.edu	hg19	10	89311958	89311958	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	MINPP1	NM_004897	exon5	c.A1187G	p.K396R	ATTACAAAAAACA	.	85.0	26.0	104.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
FAM160B1	57700	hgsc.bcm.edu	hg19	10	116615097	116615097	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	FAM160B1	NM_020940	exon14	c.C1945A	p.Q649K	CTTGATCAGGTAA	.	37.0	11.0	53.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
NANOS1	340719	hgsc.bcm.edu	hg19	10	120789990	120789990	+	Missense_Mutation	SNP	T	T	A	rs137998752	alternate_allele	TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	NANOS1	NM_199461	exon1	c.T677A	p.L226H	TGGCGCTCTACAC	.	13.0	10.0	11.0	0.0	.	1	.	.	.	alt	T|1.000;G|0.000	.	PASS	Atlas-SNP
KNDC1	85442	hgsc.bcm.edu	hg19	10	135013101	135013101	+	Silent	SNP	C	C	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	KNDC1	NM_152643	exon15	c.C2898T	p.S966S	ACCCTCCCCAAGG	.	73.0	37.0	63.0	0.0	.	155	.	.	.	none	.	.	PASS	Atlas-SNP
FAM160A2	84067	hgsc.bcm.edu	hg19	11	6238643	6238643	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	FAM160A2	NM_032127	exon9	c.C2215A	p.P739T	GCAAAGGGCTGCT	.	28.0	11.0	32.0	0.0	.	100	.	.	.	none	.	.	PASS	Atlas-SNP
NRXN2	9379	hgsc.bcm.edu	hg19	11	64410176	64410176	+	Silent	SNP	G	G	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	NRXN2	NM_138734	exon1	c.C100T	p.L34L	GCGGCAGCAGAGG	.	29.0	10.0	19.0	0.0	.	247	.	.	.	none	.	.	PASS	Atlas-SNP
C1RL	51279	hgsc.bcm.edu	hg19	12	7261763	7261763	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	C1RL	NM_016546	exon1	c.G14A	p.R5K	CACACTCTGGGTC	.	55.0	9.0	59.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
COL2A1	1280	hgsc.bcm.edu	hg19	12	48379569	48379569	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	COL2A1	NM_001844	exon25	c.C1622G	p.P541R	CCCTTGGGGCCAG	.	78.0	49.0	61.0	0.0	.	368	.	.	.	none	.	.	PASS	Atlas-SNP
CEP290	80184	hgsc.bcm.edu	hg19	12	88512304	88512304	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	CEP290,NS,carcinoma,0,1	CEP290	NM_025114	exon17	c.T1667A	p.I556N	TGACGAATTTTTT	.	83.0	4.0	81.0	0.0	.	195	.	.	.	none	.	.	PASS	Atlas-SNP
FAM71C	196472	hgsc.bcm.edu	hg19	12	100042138	100042138	+	Silent	SNP	G	G	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	FAM71C	NM_153364	exon1	c.G186T	p.V62V	TGACGTGCACAAC	.	99.0	26.0	71.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
IFT88	8100	hgsc.bcm.edu	hg19	13	21217615	21217615	+	Silent	SNP	C	C	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	IFT88	NM_175605	exon21	c.C1731G	p.P577P	AAATCCCAGTCAA	.	57.0	21.0	81.0	0.0	.	83	.	.	.	none	.	.	PASS	Atlas-SNP
PAN3	255967	hgsc.bcm.edu	hg19	13	28830508	28830508	+	Missense_Mutation	SNP	A	A	T	rs372499998		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	PAN3	NM_175854	exon7	c.A1080T	p.R360S	AAGAAGAAGTCAC	.	57.0	22.0	66.0	0.0	.	123	.	.	.	weak	.	.	PASS	Atlas-SNP
ZC3H13	23091	hgsc.bcm.edu	hg19	13	46554017	46554017	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	ZC3H13	NM_015070	exon11	c.G1843T	p.D615Y	CTTGATCTCTGTT	.	70.0	22.0	65.0	0.0	.	197	.	.	.	none	.	.	PASS	Atlas-SNP
TPP2	7174	hgsc.bcm.edu	hg19	13	103301430	103301430	+	Silent	SNP	G	G	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	TPP2	NM_003291	exon22	c.G2802A	p.K934K	GAAGAAGAAATCA	.	49.0	16.0	81.0	0.0	.	124	.	.	.	none	.	.	PASS	Atlas-SNP
FANCM	57697	hgsc.bcm.edu	hg19	14	45628482	45628482	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	FANCM	NM_020937	exon9	c.A1580G	p.E527G	AACTGGAGGTAAT	.	101.0	23.0	90.0	0.0	.	225	.	.	.	none	.	.	PASS	Atlas-SNP
SIX6	4990	hgsc.bcm.edu	hg19	14	60976418	60976418	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	SIX6	NM_007374	exon1	c.A302G	p.K101R	CTGAGAAGCTGCG	.	335.0	120.0	348.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
MYO5A	4644	hgsc.bcm.edu	hg19	15	52699526	52699526	+	Silent	SNP	C	C	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	MYO5A	NM_000259	exon8	c.G909A	p.K303K	CATCTCCTTTGCA	.	69.0	23.0	65.0	0.0	.	145	.	.	.	none	.	.	PASS	Atlas-SNP
PARP16	54956	hgsc.bcm.edu	hg19	15	65563347	65563347	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	PARP16	NM_017851	exon2	c.A238G	p.K80E	CCCGTTTGTGGTT	.	93.0	38.0	96.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	hg19	15	68620582	68620582	+	Silent	SNP	C	C	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	ITGA11	NM_001004439	exon16	c.G1920A	p.Q640Q	ATTGATCTGAACC	.	53.0	25.0	55.0	0.0	.	110	.	.	.	none	.	.	PASS	Atlas-SNP
GRIN2A	2903	hgsc.bcm.edu	hg19	16	10274246	10274246	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	GRIN2A	NM_000833	exon3	c.C23A	p.T8N	AGCAGGGTCCAAT	.	35.0	11.0	28.0	0.0	.	366	.	.	.	none	.	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	hg19	16	57099127	57099127	+	Silent	SNP	G	G	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	NLRC5	NM_032206	exon32	c.G4158A	p.V1386V	CAGGGTGCAGGAG	.	28.0	15.0	30.0	0.0	.	186	.	.	.	none	.	.	PASS	Atlas-SNP
MAP2K4	6416	hgsc.bcm.edu	hg19	17	12028658	12028658	+	Silent	SNP	C	C	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	MAP2K4	NM_003010	exon8	c.C861T	p.R287R	TGTCCGCTCTGAT	.	82.0	42.0	70.0	0.0	.	176	.	.	.	none	.	.	PASS	Atlas-SNP
WSB1	26118	hgsc.bcm.edu	hg19	17	25639388	25639388	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	WSB1	NM_015626	exon9	c.G1259A	p.R420H	CGTATCGTATTTA	.	107.0	5.0	78.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
KRT23	25984	hgsc.bcm.edu	hg19	17	39084730	39084730	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	KRT23	NM_015515	exon5	c.C766T	p.H256Y	CTCGATGCTTCTT	.	50.0	9.0	55.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
TANC2	26115	hgsc.bcm.edu	hg19	17	61498264	61498264	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	TANC2	NM_025185	exon25	c.G4921T	p.A1641S	TCAATGGCCAGTA	.	94.0	16.0	67.0	0.0	.	266	.	.	.	none	.	.	PASS	Atlas-SNP
NOL11	25926	hgsc.bcm.edu	hg19	17	65720229	65720229	+	Nonsense_Mutation	SNP	T	T	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	NOL11	NM_015462	exon6	c.T584G	p.L195X	CACTCTTACTTGG	.	55.0	28.0	27.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
KPNA2	3838	hgsc.bcm.edu	hg19	17	66039316	66039316	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	KPNA2	NM_002266	exon7	c.T767C	p.L256S	CTACCTTAGTTCG	.	86.0	46.0	55.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
NEDD4L	23327	hgsc.bcm.edu	hg19	18	55992364	55992364	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	NEDD4L	NM_015277	exon9	c.G650T	p.R217L	ACAACCGGACCAC	.	48.0	4.0	84.0	0.0	.	126	.	.	.	none	.	.	PASS	Atlas-SNP
CDH20	28316	hgsc.bcm.edu	hg19	18	59221635	59221635	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	CDH20	NM_031891	exon11	c.A2113C	p.I705L	CCCGAGATCGAGA	.	67.0	27.0	65.0	0.0	.	117	.	.	.	none	.	.	PASS	Atlas-SNP
TJP3	27134	hgsc.bcm.edu	hg19	19	3740744	3740744	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	TJP3	NM_001267561	exon14	c.G1853A	p.R618Q	ACGAACGAGTGGT	.	97.0	41.0	113.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
MPND	84954	hgsc.bcm.edu	hg19	19	4343749	4343749	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	MPND	NM_032868	exon2	c.C52A	p.P18T	GAGGCGCCGGAGG	.	27.0	14.0	26.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
SLC5A5	6528	hgsc.bcm.edu	hg19	19	17986910	17986910	+	Silent	SNP	C	C	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	SLC5A5,right_upper_lobe,carcinoma,0,1	SLC5A5	NM_000453	exon5	c.C693A	p.L231L	CAACCTCATGGAG	.	48.0	27.0	41.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
RAB3A	5864	hgsc.bcm.edu	hg19	19	18309591	18309591	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	RAB3A	NM_002866	exon4	c.T416G	p.M139R	TCCTCCATGTCAC	.	40.0	22.0	51.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF726	730087	hgsc.bcm.edu	hg19	19	24115870	24115870	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	.	NM_001244038	exon4	c.T952G	p.C318G	GAAGAATGTGGCA	.	22.0	7.0	20.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
RSPH6A	81492	hgsc.bcm.edu	hg19	19	46308112	46308112	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	RSPH6A	NM_030785	exon3	c.A1051C	p.I351L	GTTTGATTCCCAG	.	44.0	16.0	53.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF470	388566	hgsc.bcm.edu	hg19	19	57088479	57088479	+	Silent	SNP	T	T	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	ZNF470	NM_001001668	exon6	c.T682C	p.L228L	AAACTTTTAAAAT	.	92.0	39.0	116.0	0.0	.	103	.	.	.	none	.	.	PASS	Atlas-SNP
CENPB	1059	hgsc.bcm.edu	hg19	20	3766512	3766512	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	CENPB	NM_001810	exon1	c.C619A	p.Q207K	CGGCCTGGTCGGG	.	109.0	64.0	83.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
RPN2	6185	hgsc.bcm.edu	hg19	20	35864988	35864988	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	RPN2	NM_002951	exon16	c.C1759A	p.L587M	GCTATGCTGGGAC	.	35.0	11.0	42.0	0.0	.	45	.	.	.	none	.	.	PASS	Atlas-SNP
MORC3	23515	hgsc.bcm.edu	hg19	21	37741433	37741433	+	Silent	SNP	A	A	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	MORC3	NM_015358	exon15	c.A1767C	p.A589A	ACCTGCAGTAGAT	.	126.0	62.0	130.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
COMT	1312	hgsc.bcm.edu	hg19	22	19956092	19956092	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	COMT	NM_000754	exon6	c.C649G	p.L217V	GTGCTACTGGCTG	.	59.0	21.0	40.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
PPP1R3F	89801	hgsc.bcm.edu	hg19	X	49126754	49126754	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	PPP1R3F	NM_033215	exon1	c.T422A	p.L141Q	AGGCGCTGCTGCC	.	15.0	10.0	21.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
HUWE1	10075	hgsc.bcm.edu	hg19	X	53619440	53619440	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	HUWE1	NM_031407	exon33	c.G3890A	p.G1297E	CGAGACCCCTCCT	.	15.0	14.0	25.0	0.0	.	724	.	.	.	none	.	.	PASS	Atlas-SNP
ATP1B4	23439	hgsc.bcm.edu	hg19	X	119500447	119500447	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	ATP1B4	NM_001142447	exon2	c.G131C	p.R44P	AGGCTCGGGTGAC	.	145.0	115.0	173.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	hg19	2	218712606	218712607	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	TNS1	NM_022648	exon17	c.2259_2260insT	p.S753fs	.	.	59.0	26.0	67.0	0.0	.	251	.	0.440678	0	none	.	.	PASS	Atlas-Indel,Pindel
KRTAP8-1	337879	hgsc.bcm.edu	hg19	21	32185474	32185474	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	KRTAP8-1	NM_175857	exon1	c.66delG	p.P22fs	.	.	94.0	34.0	96.0	0.0	.	20	.	0.361702	0	none	.	.	PASS	Atlas-Indel,Pindel
TECRL	253017	hgsc.bcm.edu	hg19	4	65274879	65274880	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	TECRL	NM_001010874	exon1	c.191_192insA	p.I64fs	.	.	38.0	15.0	45.0	0.0	.	106	.	0.394737	0	none	.	.	PASS	Atlas-Indel,Pindel
GLUL	2752	hgsc.bcm.edu	hg19	1	182357774	182357774	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	GLUL	NM_001033056	exon2	c.100delG	p.D34fs	.	.	100.0	34.0	91.0	0.0	.	38	.	0.34	0	none	.	.	PASS	Atlas-Indel,Pindel
KDM6A	7403	hgsc.bcm.edu	hg19	X	44950075	44950075	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	KDM6A	NM_021140	exon26	c.3843delC	p.I1281fs	.	.	95.0	67.0	89.0	0.0	.	274	.	0.705263	0	none	.	.	PASS	Atlas-Indel,Pindel
BCL9	607	hgsc.bcm.edu	hg19	1	147086326	147086331	+	In_Frame_Del	DEL	CCATGG	CCATGG	-	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	CCATGG	CCATGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	BCL9	NM_004326	exon6	c.470_475del	p.157_159del	.	.	81.0	27.0	128.0	0.0	.	150	.	0.333333	0	none	.	.	PASS	Atlas-Indel,Pindel
EPHA5	2044	hgsc.bcm.edu	hg19	4	66230803	66230803	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	EPHA5	NM_004439	exon12	c.2169delT	p.G723fs	.	.	80.0	24.0	83.0	0.0	.	315	.	0.3	0	none	.	.	PASS	Atlas-INDEL
GPSM2	29899	hgsc.bcm.edu	hg19	1	109440639	109440645	+	Frame_Shift_Del	DEL	GTTTTGG	GTTTTGG	-	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	GTTTTGG	GTTTTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	GPSM2	NM_013296	exon5	c.472_478del	p.158_160del	.	.	58.0	16.0	113.0	0.0	.	56	.	0.275862	0	none	.	.	PASS	Atlas-Indel,Pindel
SLC38A8	146167	hgsc.bcm.edu	hg19	16	84050195	84050197	+	In_Frame_Del	DEL	AAC	AAC	-	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	SLC38A8	NM_001080442	exon8	c.1090_1092del	p.364_364del	.	.	66.0	28.0	69.0	0.0	.	60	.	0.424242	0	none	.	.	PASS	Atlas-Indel,Pindel
ZNF470	388566	hgsc.bcm.edu	hg19	19	57088481	57088481	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	ZNF470	NM_001001668	exon6	c.683delT	p.L228X	.	.	91.0	37.0	114.0	0.0	.	103	.	0.406593	0	none	.	.	PASS	Atlas-Indel,Pindel
TFRC	7037	hgsc.bcm.edu	hg19	3	195800989	195800990	+	Frame_Shift_Ins	INS	-	-	AT	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	TFRC	NM_001128148	exon4	c.246_247insAT	p.M82fs	.	.	73.0	20.0	83.0	0.0	.	54	.	0.273973	0	none	.	.	PASS	Atlas-Indel,Pindel
FAM184A	79632	hgsc.bcm.edu	hg19	6	119345322	119345322	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	FAM184A	NM_024581	exon2	c.817delA	p.T273fs	.	.	87.0	30.0	70.0	0.0	.	109	.	0.344828	0	none	.	.	PASS	Atlas-Indel,Pindel
TGFB1I1	7041	hgsc.bcm.edu	hg19	16	31486006	31486014	+	In_Frame_Del	DEL	CCTCAGCCG	CCTCAGCCG	-	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	CCTCAGCCG	CCTCAGCCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	TGFB1I1	NM_001042454	exon7	c.641_649del	p.214_217del	.	.	65.0	27.0	40.0	0.0	.	60	.	0.415385	0	none	.	.	PASS	Atlas-Indel,Pindel
RNU6-71	100873774	hgsc.bcm.edu	hg19	6	56564500	56564500	+	RNA	DEL	T	T	-	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	.	.	.	.	.	.	.	30.0	12.0	48.0	0.0	.	.	.	0.4	0	none	.	.	PASS	Atlas-Indel,Pindel
ZNF575	284346	hgsc.bcm.edu	hg19	19	44039436	44039442	+	Frame_Shift_Del	DEL	CGCACAG	CGCACAG	-	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	CGCACAG	CGCACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	ZNF575	NM_174945	exon4	c.334_340del	p.112_114del	.	.	81.0	22.0	110.0	0.0	.	14	.	0.271605	0	none	.	.	PASS	Atlas-Indel,Pindel
EPHA5	2044	hgsc.bcm.edu	hg19	4	66230804	66230806	+	In_Frame_Del	DEL	CTA	CTA	-	novel		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	CTA	CTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	.	EPHA5	NM_004439	exon12	c.2166_2168del	p.722_723del	.	.	81.0	21.0	83.0	0.0	.	315	.	0.259	.	none	.	.	PASS	Pindel