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	32205741	32205741	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	BAI2	NM_001703	exon13	c.A2028C	p.E676D	CTTGTTTTCCGCA	.	148.0	50.0	214.0	0.0	.	128	.	.	.	none	.	.	PASS	Atlas-SNP
PMF1	11243	hgsc.bcm.edu	hg19	1	156209392	156209392	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	PMF1	NM_001199654	exon5	c.A624C	p.X208C	TGAGTGAGGAGAC	.	121.0	42.0	169.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
OR2T3	343173	hgsc.bcm.edu	hg19	1	248637175	248637175	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	OR2T3	NM_001005495	exon1	c.A524C	p.Q175P	TTTGCCAGTCTAG	.	430.0	119.0	467.0	1.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
ERBB4	2066	hgsc.bcm.edu	hg19	2	212248449	212248449	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	ERBB4	NM_005235	exon28	c.G3818A	p.R1273Q	CGGATCCGCCCAT	.	197.0	111.0	178.0	1.0	.	480	.	.	.	none	.	.	PASS	Atlas-SNP
KIF1A	547	hgsc.bcm.edu	hg19	2	241696843	241696843	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	KIF1A	NM_001244008	exon27	c.G2751T	p.E917D	CTCATCCTCCTCC	.	263.0	15.0	138.0	0.0	.	152	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC66	285331	hgsc.bcm.edu	hg19	3	56627039	56627039	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	CCDC66	NM_001141947	exon8	c.A978C	p.Q326H	GAAACAAGAACTG	.	69.0	30.0	123.0	0.0	.	145	.	.	.	none	.	.	PASS	Atlas-SNP
TRIM42	287015	hgsc.bcm.edu	hg19	3	140401754	140401754	+	Silent	SNP	G	G	A	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	TRIM42	NM_152616	exon2	c.G792A	p.K264K	CCTCAAGGCCTTC	.	248.0	102.0	277.0	0.0	.	143	.	.	.	none	.	.	PASS	Atlas-SNP
CDKL2	8999	hgsc.bcm.edu	hg19	4	76532433	76532433	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	CDKL2	NM_003948	exon4	c.C476T	p.T159I	TAATCAGTATAAA	.	125.0	41.0	201.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
SYNPO2	171024	hgsc.bcm.edu	hg19	4	119947961	119947961	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	SYNPO2	NM_001128934	exon3	c.A437C	p.Q146P	AGAACCAAAGAAG	.	162.0	48.0	172.0	0.0	.	353	.	.	.	none	.	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	hg19	4	126240999	126240999	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	FAT4	NM_024582	exon1	c.G3433A	p.D1145N	CAGCCAGATTTTG	.	96.0	30.0	114.0	0.0	.	1752	.	.	.	none	.	.	PASS	Atlas-SNP
ADCY2	108	hgsc.bcm.edu	hg19	5	7816984	7816984	+	Silent	SNP	C	C	T	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	ADCY2	NM_020546	exon23	c.C2889T	p.P963P	GGAGCCCGAGCGG	.	181.0	17.0	234.0	0.0	.	337	.	.	.	none	.	.	PASS	Atlas-SNP
NUP155	9631	hgsc.bcm.edu	hg19	5	37307409	37307409	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	NUP155	NM_153485	exon25	c.T2893C	p.F965L	CTTGGAAGGCCTG	.	165.0	67.0	138.0	0.0	.	116	.	.	.	none	.	.	PASS	Atlas-SNP
PAM	5066	hgsc.bcm.edu	hg19	5	102237063	102237063	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	PAM	NM_138822	exon3	c.G214A	p.D72N	TAGTCCGATACAT	.	63.0	4.0	98.0	0.0	.	180	.	.	.	none	.	.	PASS	Atlas-SNP
RNF14	9604	hgsc.bcm.edu	hg19	5	141357939	141357939	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	RNF14	NM_001201365	exon5	c.G378T	p.W126C	TGCCTGGATGCAA	.	248.0	70.0	306.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
GEMIN5	25929	hgsc.bcm.edu	hg19	5	154278113	154278113	+	Missense_Mutation	SNP	C	C	T	rs144363013	bycluster	TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	GEMIN5	NM_015465	exon23	c.G3232A	p.V1078I	CTCCTACGATGGC	.	244.0	85.0	301.0	0.0	.	120	.	.	.	weak	C|1.000;T|0.000	0.000	PASS	Atlas-SNP
TULP1	7287	hgsc.bcm.edu	hg19	6	35471606	35471606	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	TULP1	NM_003322	exon12	c.C1132G	p.R378G	TGAAGCGGTTCCC	.	44.0	20.0	36.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
CNKSR3	154043	hgsc.bcm.edu	hg19	6	154732110	154732110	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	CNKSR3	NM_173515	exon11	c.A1237G	p.N413D	GAATGTTGGTTTC	.	163.0	60.0	180.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
MET	4233	hgsc.bcm.edu	hg19	7	116397543	116397543	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	MET	NM_000245	exon7	c.A1915C	p.I639L	TCCATAATTATTT	.	86.0	40.0	92.0	0.0	.	412	.	.	.	none	.	.	PASS	Atlas-SNP
MFHAS1	9258	hgsc.bcm.edu	hg19	8	8643536	8643536	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	MFHAS1	NM_004225	exon3	c.A3155G	p.Q1052R	CGTCACTGGTTTC	.	135.0	13.0	165.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
C9orf89	84270	hgsc.bcm.edu	hg19	9	95874554	95874554	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	C9orf89	NM_032310	exon5	c.T419G	p.L140R	TGCTCCTGTACTG	.	57.0	23.0	70.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
C9orf89	84270	hgsc.bcm.edu	hg19	9	95874555	95874555	+	Silent	SNP	G	G	T	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	C9orf89	NM_032310	exon5	c.G420T	p.L140L	GCTCCTGTACTGC	.	56.0	23.0	70.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC3	83643	hgsc.bcm.edu	hg19	10	13043327	13043327	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	CCDC3	NM_031455	exon1	c.C244A	p.L82M	CGCACAGCATCTC	.	70.0	27.0	70.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
C10orf76	79591	hgsc.bcm.edu	hg19	10	103789497	103789497	+	Silent	SNP	C	C	T	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	C10orf76	NM_024541	exon5	c.G312A	p.L104L	TGCGCACAGGGTC	.	46.0	10.0	48.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
PSD	5662	hgsc.bcm.edu	hg19	10	104173630	104173630	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	PSD	NM_001270965	exon6	c.G1449T	p.E483D	CTCCTCCTCCCCT	.	147.0	50.0	209.0	0.0	.	164	.	.	.	none	.	.	PASS	Atlas-SNP
INPPL1	3636	hgsc.bcm.edu	hg19	11	71944164	71944164	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	INPPL1	NM_001567	exon17	c.G1997T	p.G666V	AGCGGGGTTCCCG	.	158.0	66.0	219.0	0.0	.	120	.	.	.	none	.	.	PASS	Atlas-SNP
MMP27	64066	hgsc.bcm.edu	hg19	11	102563689	102563689	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	MMP27	NM_022122	exon9	c.A1277C	p.D426A	GCAGCATCAACAC	.	157.0	48.0	178.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
PAFAH1B2	5049	hgsc.bcm.edu	hg19	11	117038364	117038364	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	PAFAH1B2	NM_002572	exon6	c.C639G	p.I213M	ACTGATCATGCAG	.	330.0	137.0	340.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
RECQL	5965	hgsc.bcm.edu	hg19	12	21623145	21623145	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	RECQL	NM_032941	exon16	c.A1933C	p.K645Q	CGATTTTTCTTTT	.	427.0	263.0	243.0	0.0	.	45	.	.	.	none	.	.	PASS	Atlas-SNP
LRIG3	121227	hgsc.bcm.edu	hg19	12	59308047	59308047	+	Missense_Mutation	SNP	C	C	T	rs373824765		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	LRIG3	NM_153377	exon2	c.G307A	p.V103M	CTCACACTTCTCG	.	88.0	13.0	61.0	0.0	.	120	.	.	.	weak	.	.	PASS	Atlas-SNP
CLMN	79789	hgsc.bcm.edu	hg19	14	95670380	95670380	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	CLMN	NM_024734	exon9	c.C1306T	p.P436S	AGAAAGGATCCTT	.	113.0	68.0	221.0	0.0	.	103	.	.	.	none	.	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	hg19	15	75968209	75968209	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	CSPG4	NM_001897	exon10	c.C6651G	p.F2217L	CTCAAGGAAGCTC	.	56.0	21.0	73.0	0.0	.	175	.	.	.	none	.	.	PASS	Atlas-SNP
RHCG	51458	hgsc.bcm.edu	hg19	15	90030138	90030138	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	RHCG	NM_016321	exon2	c.C263T	p.A88V	CCCACGGCGCTGA	.	357.0	159.0	379.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
STUB1	10273	hgsc.bcm.edu	hg19	16	732019	732019	+	Splice_Site	SNP	G	G	T	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	STUB1,colon,carcinoma,0,1	STUB1	NM_005861	exon5	c.613-1G>T	.	TTCACAGGACAAG	.	276.0	156.0	220.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
GLG1	2734	hgsc.bcm.edu	hg19	16	74505165	74505165	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	GLG1	NM_001145667	exon15	c.T2135G	p.I712R	GAGTCTATCTGGT	.	227.0	60.0	191.0	0.0	.	106	.	.	.	none	.	.	PASS	Atlas-SNP
C16orf46	123775	hgsc.bcm.edu	hg19	16	81094972	81094972	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	C16orf46	NM_001100873	exon3	c.C982T	p.Q328X	GTTTCTGCAGAAG	.	316.0	83.0	250.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
TRPV1	7442	hgsc.bcm.edu	hg19	17	3480482	3480482	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	TRPV1	NM_018727	exon12	c.T1718C	p.I573T	CTCAGGATCATCT	.	257.0	125.0	213.0	0.0	.	99	.	.	.	none	.	.	PASS	Atlas-SNP
NCOR1	9611	hgsc.bcm.edu	hg19	17	15968952	15968952	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	NCOR1	NM_001190440	exon32	c.C4846A	p.Q1616K	GATACTGACTTGG	.	279.0	72.0	222.0	0.0	.	240	.	.	.	none	.	.	PASS	Atlas-SNP
KCNJ18	100134444	hgsc.bcm.edu	hg19	17	21318895	21318895	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	KCNJ12,NS,carcinoma,0,1	.	NM_001194958	exon3	c.C241T	p.R81W	CGCTGGCGGTACA	.	373.0	50.0	300.0	2.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
PPM1E	22843	hgsc.bcm.edu	hg19	17	56833457	56833457	+	Silent	SNP	G	G	C	rs74256772		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	PPM1E,colon,carcinoma,0,1	PPM1E	NM_014906	exon1	c.G99C	p.P33P	GGAGCCGGAACCC	.	83.0	5.0	65.0	0.0	.	97	.	.	.	weak	.	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	hg19	17	76449535	76449535	+	Silent	SNP	G	G	T	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	DNAH17	NM_173628	exon65	c.C10419A	p.V3473V	CTCGATGACATCC	.	238.0	118.0	203.0	0.0	.	347	.	.	.	none	.	.	PASS	Atlas-SNP
PTPRM	5797	hgsc.bcm.edu	hg19	18	8314790	8314790	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	PTPRM	NM_001105244	exon21	c.C2854T	p.R952X	CATTCCCGAGTGA	.	72.0	4.0	100.0	0.0	.	185	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	hg19	19	12187443	12187443	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	ZNF844,bladder,carcinoma,0,11	ZNF844	NM_001136501	exon4	c.C1508G	p.P503R	GAAACCCTATGAG	.	93.0	4.0	88.0	1.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
MZF1	7593	hgsc.bcm.edu	hg19	19	59082699	59082699	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	MZF1	NM_198055	exon2	c.G58A	p.V20I	CCATGACAGGCCC	.	117.0	39.0	127.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	hg19	21	33727865	33727865	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	URB1	NM_014825	exon16	c.G1999T	p.D667Y	CCGTGTCCCGCAG	.	43.0	31.0	77.0	0.0	.	176	.	.	.	none	.	.	PASS	Atlas-SNP
TAB1	10454	hgsc.bcm.edu	hg19	22	39814795	39814795	+	Silent	SNP	G	G	A	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	TAB1	NM_153497	exon6	c.G609A	p.L203L	ACAGCTGAACGTG	.	179.0	68.0	206.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
ND1	10625	hgsc.bcm.edu	hg19	MT	3698	3698	+	Missense_Mutation	SNP	G	G	A	rs199476122		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	.	ENST00000361390	exon1	c.G392A	p.G131D	TGATCGGCGCACT	.	15.0	11.0	16.0	0.0	.	.	.	.	.	weak	.	.	PASS	Atlas-SNP
COX2	5743	hgsc.bcm.edu	hg19	MT	7741	7741	+	Silent	SNP	T	T	C	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	.	ENST00000361739	exon1	c.T156C	p.N52N	AACTAATACTAAC	.	26.0	21.0	24.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
MAP4K1	11184	hgsc.bcm.edu	hg19	19	39101749	39101755	+	Frame_Shift_Del	DEL	ATGAAGT	ATGAAGT	-	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	ATGAAGT	ATGAAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	MAP4K1	NM_007181	exon11	c.747_753del	p.249_251del	.	.	141.0	29.0	190.0	0.0	.	165	.	0.205674	0	none	.	.	PASS	Atlas-Indel,Pindel
VSTM4	196740	hgsc.bcm.edu	hg19	10	50311832	50311835	+	Frame_Shift_Del	DEL	GGGC	GGGC	-	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	GGGC	GGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	VSTM4	NM_144984	exon3	c.529_532del	p.177_178del	.	.	130.0	34.0	201.0	0.0	.	83	.	0.261538	0	none	.	.	PASS	Atlas-Indel,Pindel
PRKCI	5584	hgsc.bcm.edu	hg19	3	170013708	170013708	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	PRKCI	NM_002740	exon15	c.1426delG	p.E476fs	.	.	85.0	42.0	118.0	0.0	.	82	.	0.494118	0	none	.	.	PASS	Atlas-Indel,Pindel
SYNPO2	171024	hgsc.bcm.edu	hg19	4	119947965	119947967	+	In_Frame_Del	DEL	AAG	AAG	-	novel		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	.	SYNPO2	NM_001128933	exon3	c.440_442del	p.147_148del	.	.	165.0	32.0	171.0	0.0	.	353	.	0.194	.	none	.	.	PASS	Pindel
