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
AADACL4	343066	hgsc.bcm.edu	hg19	1	12711237	12711237	+	Silent	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	AADACL4	NM_001013630	exon2	c.G264T	p.V88V	ACTTGTGGTGACC	.	120.0	66.0	121.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
RHD	6007	hgsc.bcm.edu	hg19	1	25628090	25628090	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	RHD	NM_001127691	exon5	c.G714A	p.V238V	TGCCGTGTTCAAC	.	134.0	123.0	87.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
CSMD2	114784	hgsc.bcm.edu	hg19	1	34015918	34015918	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	CSMD2	NM_052896	exon55	c.C8344A	p.H2782N	GGGAGTGAGGCGG	.	186.0	106.0	109.0	0.0	.	946	.	.	.	none	.	.	PASS	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	hg19	1	39853737	39853737	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	MACF1	NM_012090	exon54	c.G9037C	p.G3013R	ACTCAGGGTCTGG	.	138.0	42.0	139.0	0.0	.	909	.	.	.	none	.	.	PASS	Atlas-SNP
ITGB3BP	23421	hgsc.bcm.edu	hg19	1	63974218	63974218	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	ITGB3BP,larynx,carcinoma,0,1	ITGB3BP	NM_001206739	exon3	c.A146C	p.D49A	AGACCATCCAACT	.	201.0	53.0	292.0	2.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
GNG12	55970	hgsc.bcm.edu	hg19	1	68171150	68171150	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.,1	GNG12	NM_018841	exon4	c.C203G	p.T68S	ATGCAAGTTTTTT	.	89.0	43.0	73.0	0.0	.	11	.	.	.	none	.	.	PASS	Atlas-SNP
ZBTB7B	51043	hgsc.bcm.edu	hg19	1	154987232	154987232	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	ZBTB7B	NM_001252406	exon4	c.C198G	p.H66Q	GGGCCACCTATGT	.	80.0	26.0	77.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
RCOR3	55758	hgsc.bcm.edu	hg19	1	211462545	211462545	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	RCOR3,caecum,carcinoma,0,1	RCOR3	NM_001136223	exon8	c.C746A	p.T249N	TCCAAACTAGCAA	.	244.0	26.0	181.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
AKT3	10000	hgsc.bcm.edu	hg19	1	243800913	243800913	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	AKT3	NM_001206729	exon6	c.G561A	p.K187K	AGTTACCTTTGCA	.	42.0	6.0	75.0	0.0	.	177	.	.	.	none	.	.	PASS	Atlas-SNP
KCNS3	3790	hgsc.bcm.edu	hg19	2	18113163	18113163	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	KCNS3	NM_002252	exon3	c.G888C	p.R296S	TATGAGGATTTTC	.	220.0	83.0	161.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
KHK	3795	hgsc.bcm.edu	hg19	2	27315218	27315218	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	KHK	NM_006488	exon2	c.G111T	p.W37C	GAGATGGCAGCGC	.	65.0	31.0	32.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
ERLEC1	27248	hgsc.bcm.edu	hg19	2	54028861	54028861	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	ERLEC1	NM_015701	exon8	c.C761A	p.S254Y	GAGCATCTCCTGT	.	128.0	61.0	122.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
NAGK	55577	hgsc.bcm.edu	hg19	2	71304704	71304704	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	NAGK	NM_017567	exon9	c.A920G	p.K307R	AGGGCAAGATTGG	.	99.0	38.0	59.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
UGGT1	56886	hgsc.bcm.edu	hg19	2	128941262	128941262	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	UGGT1	NM_020120	exon38	c.G4258T	p.V1420L	TATGTTGTGGATC	.	141.0	59.0	140.0	0.0	.	126	.	.	.	none	.	.	PASS	Atlas-SNP
MAP3K19	80122	hgsc.bcm.edu	hg19	2	135744072	135744072	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	.	NM_025052	exon7	c.G2370C	p.Q790H	AGGTGTCTGAGCC	.	112.0	40.0	80.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
GCA	25801	hgsc.bcm.edu	hg19	2	163208899	163208899	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	GCA	NM_012198	exon3	c.A244C	p.I82L	TCTGGAATTAATG	.	119.0	58.0	111.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
SPC25	57405	hgsc.bcm.edu	hg19	2	169746011	169746011	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	SPC25,NS,carcinoma,0,1	SPC25	NM_020675	exon2	c.G19C	p.A7P	AAAGTGCCAGTTC	.	44.0	18.0	59.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
METTL5	29081	hgsc.bcm.edu	hg19	2	170677784	170677784	+	Splice_Site	SNP	C	C	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	METTL5	NM_014168	exon4	c.225-1G>T	.	CACAACCTATAAA	.	114.0	39.0	82.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
NHEJ1	79840	hgsc.bcm.edu	hg19	2	220022946	220022946	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	NHEJ1	NM_024782	exon2	c.G139A	p.E47K	CCTGTTCATGCCA	.	112.0	47.0	76.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
SETD5	55209	hgsc.bcm.edu	hg19	3	9475587	9475587	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	SETD5	NM_001080517	exon4	c.A130G	p.N44D	ACTCATAATTATG	.	155.0	41.0	168.0	0.0	.	210	.	.	.	none	.	.	PASS	Atlas-SNP
DNAH1	25981	hgsc.bcm.edu	hg19	3	52428521	52428521	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	DNAH1	NM_015512	exon67	c.T10667C	p.I3556T	TCTCGATCATGAC	.	115.0	58.0	109.0	0.0	.	534	.	.	.	none	.	.	PASS	Atlas-SNP
ABHD6	57406	hgsc.bcm.edu	hg19	3	58242370	58242370	+	Silent	SNP	A	A	T	rs11544005	alternate_allele	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	ABHD6	NM_020676	exon2	c.A57T	p.P19P	CATCCCAATCCTG	.	103.0	23.0	106.0	0.0	.	28	.	.	.	alt	.	.	PASS	Atlas-SNP
CBLB	868	hgsc.bcm.edu	hg19	3	105572285	105572285	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	CBLB	NM_170662	exon3	c.G392T	p.R131I	TACATTCTCTCCT	.	135.0	33.0	145.0	0.0	.	118	.	.	.	none	.	.	PASS	Atlas-SNP
EAF2	55840	hgsc.bcm.edu	hg19	3	121554190	121554190	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	EAF2	NM_018456	exon1	c.G58A	p.G20R	AAGTTAGGGGAGA	.	97.0	9.0	75.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
PARP14	54625	hgsc.bcm.edu	hg19	3	122436993	122436993	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	PARP14	NM_017554	exon13	c.C4076G	p.S1359X	AAGGATCAGCCCA	.	185.0	102.0	165.0	0.0	.	242	.	.	.	none	.	.	PASS	Atlas-SNP
RBP2	5948	hgsc.bcm.edu	hg19	3	139195286	139195286	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	RBP2	NM_004164	exon1	c.A16T	p.N6Y	TTCCATTCTGGTC	.	74.0	11.0	76.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
PLD1	5337	hgsc.bcm.edu	hg19	3	171395429	171395429	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	PLD1	NM_002662	exon17	c.C1923T	p.T641T	GAATCTGGTTTCC	.	118.0	31.0	141.0	0.0	.	134	.	.	.	none	.	.	PASS	Atlas-SNP
RFC4	5984	hgsc.bcm.edu	hg19	3	186508173	186508173	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	RFC4,NS,carcinoma,0,1	RFC4	NM_181573	exon9	c.A824T	p.D275V	ACTCCATCAATTT	.	144.0	36.0	182.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	hg19	4	3162057	3162057	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	HTT	NM_002111	exon29	c.C3802T	p.R1268C	TTTCTCCGCTCAG	.	181.0	67.0	173.0	0.0	.	221	.	.	.	none	.	.	PASS	Atlas-SNP
PI4K2B	55300	hgsc.bcm.edu	hg19	4	25235821	25235821	+	Silent	SNP	C	C	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	PI4K2B	NM_018323	exon1	c.C36A	p.S12S	GGCGTCCGCGGAC	.	44.0	13.0	7.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
ARAP2	116984	hgsc.bcm.edu	hg19	4	36152575	36152575	+	Silent	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	ARAP2,NS,carcinoma,0,1	ARAP2	NM_015230	exon16	c.C2844A	p.I948I	TTCATTGATATTA	.	115.0	36.0	121.0	1.0	.	210	.	.	.	none	.	.	PASS	Atlas-SNP
SYNPO2	171024	hgsc.bcm.edu	hg19	4	119952707	119952707	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	SYNPO2	NM_001128934	exon4	c.A2777T	p.N926I	CCTATAATCCTAT	.	78.0	11.0	58.0	0.0	.	353	.	.	.	none	.	.	PASS	Atlas-SNP
SMAD1	4086	hgsc.bcm.edu	hg19	4	146463798	146463798	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	SMAD1	NM_005900	exon4	c.G723A	p.P241P	TCAGCCGATGGAC	.	88.0	4.0	89.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
IQGAP2	10788	hgsc.bcm.edu	hg19	5	75888702	75888702	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	IQGAP2	NM_006633	exon9	c.G859A	p.E287K	TATGAAGAACTGC	.	466.0	78.0	316.0	0.0	.	186	.	.	.	none	.	.	PASS	Atlas-SNP
IQGAP2	10788	hgsc.bcm.edu	hg19	5	75888710	75888710	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	IQGAP2	NM_006633	exon9	c.G867A	p.L289L	ACTGCTGACACAA	.	484.0	78.0	344.0	0.0	.	186	.	.	.	none	.	.	PASS	Atlas-SNP
IQGAP2	10788	hgsc.bcm.edu	hg19	5	75973147	75973147	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	IQGAP2	NM_006633	exon28	c.C3632T	p.S1211L	ATATTTCAATTGA	.	95.0	11.0	88.0	0.0	.	186	.	.	.	none	.	.	PASS	Atlas-SNP
FNIP1	96459	hgsc.bcm.edu	hg19	5	131007961	131007961	+	Missense_Mutation	SNP	C	C	T	rs367969091		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	FNIP1	NM_133372	exon14	c.G2176A	p.G726R	CCATTCCTGTGGA	.	109.0	63.0	82.0	0.0	.	104	.	.	.	weak	.	.	PASS	Atlas-SNP
NSD1	64324	hgsc.bcm.edu	hg19	5	176721020	176721020	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	NSD1	NM_022455	exon23	c.G6651T	p.E2217D	TGGGGAGATCCGT	.	120.0	46.0	91.0	0.0	.	416	.	.	.	none	.	.	PASS	Atlas-SNP
CLK4	57396	hgsc.bcm.edu	hg19	5	178050363	178050363	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	CLK4	NM_020666	exon2	c.G55T	p.G19X	CATGTCCCCAGCT	.	135.0	60.0	83.0	0.0	.	103	.	.	.	none	.	.	PASS	Atlas-SNP
ZSCAN23	222696	hgsc.bcm.edu	hg19	6	28402345	28402345	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	ZSCAN23	NM_001012455	exon4	c.C1067T	p.T356I	TCTCCAGTGTGAA	.	110.0	61.0	99.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
DPCR1	135656	hgsc.bcm.edu	hg19	6	30918494	30918494	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	DPCR1	NM_080870	exon2	c.C2253G	p.N751K	TGAGAACACCACA	.	113.0	5.0	117.0	0.0	.	99	.	.	.	none	.	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	hg19	6	32016288	32016288	+	Silent	SNP	C	C	T	rs373655652		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	TNXB	NM_019105	exon29	c.G9891A	p.A3297A	CCCCTGCGCGTCC	.	173.0	105.0	97.0	0.0	.	553	.	.	.	weak	.	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	hg19	6	32063589	32063589	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	TNXB	NM_019105	exon3	c.G2041C	p.E681Q	GCTCTTCCTGCCC	.	291.0	13.0	109.0	0.0	.	553	.	.	.	none	.	.	PASS	Atlas-SNP
CUL9	23113	hgsc.bcm.edu	hg19	6	43155541	43155541	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	CUL9	NM_015089	exon7	c.A1672G	p.S558G	GAGGGCAGCACTC	.	84.0	19.0	84.0	0.0	.	248	.	.	.	none	.	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	hg19	6	51586795	51586795	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	PKHD1	NM_170724	exon61	c.A10180C	p.I3394L	CTGAAATCTTCAA	.	76.0	32.0	92.0	0.0	.	927	.	.	.	none	.	.	PASS	Atlas-SNP
COL21A1	81578	hgsc.bcm.edu	hg19	6	55933890	55933890	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	COL21A1	NM_030820	exon22	c.C2045A	p.P682Q	TCTCCTGGGGAAC	.	95.0	5.0	84.0	0.0	.	201	.	.	.	none	.	.	PASS	Atlas-SNP
UBE3D	90025	hgsc.bcm.edu	hg19	6	83767555	83767555	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	.	NM_198920	exon2	c.A264C	p.K88N	GCCTAATTTTGCT	.	78.0	39.0	83.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
COQ3	51805	hgsc.bcm.edu	hg19	6	99823846	99823846	+	Silent	SNP	T	T	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	COQ3	NM_017421	exon5	c.A699T	p.T233T	TAAAAATGTTTCT	.	79.0	26.0	114.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
LATS1	9113	hgsc.bcm.edu	hg19	6	149997827	149997827	+	Silent	SNP	C	C	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	LATS1	NM_004690	exon6	c.G2640C	p.G880G	GGGATCCCCCCAT	.	71.0	20.0	59.0	0.0	.	241	.	.	.	none	.	.	PASS	Atlas-SNP
RNF216	54476	hgsc.bcm.edu	hg19	7	5781127	5781127	+	Nonsense_Mutation	SNP	G	G	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	RNF216	NM_207111	exon4	c.C521G	p.S174X	TGCTCTGATCTGG	.	147.0	74.0	139.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF655	79027	hgsc.bcm.edu	hg19	7	99158261	99158261	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	ZNF655	NM_024061	exon2	c.C79T	p.L27L	GAGTGTCTGTCCC	.	79.0	21.0	69.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
SSMEM1	0	hgsc.bcm.edu	hg19	7	129856036	129856036	+	Missense_Mutation	SNP	A	A	T	rs144099660	alternate_allele	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	.	NM_145268	exon3	c.A461T	p.E154V	GTGAAGAGTCTAA	.	185.0	48.0	171.0	0.0	.	.	.	.	.	alt	A|1.000;C|0.000	.	PASS	Atlas-SNP
HIPK2	28996	hgsc.bcm.edu	hg19	7	139258060	139258060	+	Silent	SNP	C	C	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	HIPK2	NM_022740	exon15	c.G3210T	p.P1070P	GGAGTACGGAGCC	.	37.0	12.0	12.0	0.0	.	192	.	.	.	none	.	.	PASS	Atlas-SNP
LRRCC1	85444	hgsc.bcm.edu	hg19	8	86057651	86057651	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	LRRCC1	NM_033402	exon19	c.G3004T	p.E1002X	ATGCGTGAACTTT	.	275.0	71.0	335.0	0.0	.	212	.	.	.	none	.	.	PASS	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	hg19	8	113678545	113678545	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	CSMD3	NM_198123	exon17	c.A2777C	p.E926A	TCAGCTTCAATCA	.	141.0	90.0	145.0	0.0	.	2325	.	.	.	none	.	.	PASS	Atlas-SNP
PLAA	9373	hgsc.bcm.edu	hg19	9	26925951	26925951	+	Silent	SNP	C	C	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	PLAA	NM_001031689	exon6	c.G741T	p.V247V	TGTTGTCACAAAG	.	81.0	48.0	92.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
TLN1	7094	hgsc.bcm.edu	hg19	9	35711276	35711276	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	TLN1	NM_006289	exon30	c.A3995T	p.K1332M	TGACTCTTGAGGT	.	57.0	21.0	61.0	0.0	.	185	.	.	.	none	.	.	PASS	Atlas-SNP
RNF20	56254	hgsc.bcm.edu	hg19	9	104302538	104302538	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	RNF20	NM_019592	exon3	c.G183C	p.M61I	AGAAATGTTGGAT	.	76.0	48.0	92.0	0.0	.	110	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA1	19	hgsc.bcm.edu	hg19	9	107573100	107573100	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	ABCA1	NM_005502	exon29	c.G4156C	p.E1386Q	ACTGTTCGTTGTA	.	146.0	24.0	103.0	0.0	.	244	.	.	.	none	.	.	PASS	Atlas-SNP
RPL7A	6130	hgsc.bcm.edu	hg19	9	136216489	136216489	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	RPL7A	NM_000972	exon3	c.C208A	p.L70I	GCCATCCTCTATA	.	88.0	31.0	80.0	0.0	.	9	.	.	.	none	.	.	PASS	Atlas-SNP
LHX3	8022	hgsc.bcm.edu	hg19	9	139089398	139089398	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	LHX3	NM_014564	exon6	c.G982A	p.A328T	GCGGGGCGGCGGG	.	12.0	6.0	7.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
OPTN	10133	hgsc.bcm.edu	hg19	10	13160994	13160994	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	OPTN	NM_001008212	exon7	c.C733T	p.Q245X	GGGAATCAGAAGG	.	175.0	100.0	199.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1462	57608	hgsc.bcm.edu	hg19	10	30336674	30336674	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	KIAA1462	NM_020848	exon2	c.G68A	p.R23H	TCCTCGCGTGATG	.	128.0	6.0	116.0	0.0	.	162	.	.	.	none	.	.	PASS	Atlas-SNP
KNDC1	85442	hgsc.bcm.edu	hg19	10	135013012	135013012	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	KNDC1,rectum,carcinoma,0,2	KNDC1	NM_152643	exon15	c.G2809A	p.A937T	TGTGGCGCCATTT	.	192.0	14.0	151.0	0.0	.	155	.	.	.	none	.	.	PASS	Atlas-SNP
OR51D1	390038	hgsc.bcm.edu	hg19	11	4661643	4661643	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	OR51D1	NM_001004751	exon1	c.A623T	p.N208I	GGGTCAATGTGGT	.	172.0	74.0	141.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
EIF4G2	1982	hgsc.bcm.edu	hg19	11	10820842	10820842	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	EIF4G2	NM_001172705	exon20	c.A2454C	p.K818N	AAGAAATTTCTGC	.	120.0	61.0	101.0	0.0	.	89	.	.	.	none	.	.	PASS	Atlas-SNP
CKAP5	9793	hgsc.bcm.edu	hg19	11	46799004	46799004	+	Silent	SNP	G	G	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	CKAP5	NM_001008938	exon23	c.C2847G	p.V949V	TCCAAGGACTGTG	.	104.0	43.0	81.0	0.0	.	134	.	.	.	none	.	.	PASS	Atlas-SNP
NUP160	23279	hgsc.bcm.edu	hg19	11	47837537	47837537	+	Silent	SNP	A	A	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	NUP160	NM_015231	exon12	c.T1476C	p.S492S	CAGTTCACTCCAG	.	361.0	175.0	264.0	0.0	.	116	.	.	.	none	.	.	PASS	Atlas-SNP
PTPRJ	5795	hgsc.bcm.edu	hg19	11	48142728	48142728	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	PTPRJ	NM_001098503	exon4	c.T526G	p.L176V	ACAGGCTTACGTC	.	323.0	131.0	282.0	1.0	.	225	.	.	.	none	.	.	PASS	Atlas-SNP
ANKK1	255239	hgsc.bcm.edu	hg19	11	113265705	113265705	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	ANKK1	NM_178510	exon3	c.A535C	p.I179L	CAGTACATCGAGA	.	192.0	87.0	113.0	0.0	.	83	.	.	.	none	.	.	PASS	Atlas-SNP
B4GALNT3	283358	hgsc.bcm.edu	hg19	12	660177	660177	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	B4GALNT3	NM_173593	exon11	c.C1087T	p.R363C	CTGCAGCGCTACC	.	163.0	37.0	105.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
LRTM2	654429	hgsc.bcm.edu	hg19	12	1940301	1940301	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	LRTM2	NM_001039029	exon4	c.A268T	p.N90Y	TTCGCCAACCTCT	.	59.0	30.0	47.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
WBP11	51729	hgsc.bcm.edu	hg19	12	14943406	14943406	+	Silent	SNP	A	A	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	WBP11	NM_016312	exon10	c.T1293C	p.P431P	ACCAGGAGGAAGG	.	134.0	24.0	97.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
KCNH3	23416	hgsc.bcm.edu	hg19	12	49944077	49944077	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	KCNH3	NM_012284	exon10	c.A1883C	p.E628A	CCATGGAGGTGCT	.	93.0	48.0	17.0	0.0	.	88	.	.	.	none	.	.	PASS	Atlas-SNP
CSAD	51380	hgsc.bcm.edu	hg19	12	53554015	53554015	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	CSAD	NM_015989	exon14	c.A1136G	p.K379R	ACCACCTTGTCTC	.	120.0	60.0	63.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
GPR84	53831	hgsc.bcm.edu	hg19	12	54756649	54756649	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	GPR84	NM_020370	exon2	c.C987T	p.A329A	GCTCAGGGCAAAG	.	202.0	15.0	153.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
SMARCC2	6601	hgsc.bcm.edu	hg19	12	56578005	56578005	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	SMARCC2	NM_139067	exon6	c.C516A	p.N172K	GGCATTGTTCTTA	.	135.0	55.0	136.0	0.0	.	212	.	.	.	none	.	.	PASS	Atlas-SNP
APAF1	317	hgsc.bcm.edu	hg19	12	99093184	99093184	+	Splice_Site	SNP	A	A	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	APAF1	NM_001160	exon17	c.2272-2A>C	.	ATTCAAAGCTTTG	.	58.0	22.0	54.0	0.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
DCLK1	9201	hgsc.bcm.edu	hg19	13	36383187	36383187	+	Silent	SNP	A	A	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	DCLK1	NM_004734	exon13	c.T1734C	p.Y578Y	CAGGATATAAGTG	.	150.0	51.0	93.0	0.0	.	350	.	.	.	none	.	.	PASS	Atlas-SNP
UGGT2	55757	hgsc.bcm.edu	hg19	13	96684163	96684163	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	UGGT2	NM_020121	exon2	c.T221C	p.L74S	ATTGCTAATTCTT	.	102.0	38.0	103.0	0.0	.	127	.	.	.	none	.	.	PASS	Atlas-SNP
RPGRIP1	57096	hgsc.bcm.edu	hg19	14	21769308	21769308	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	RPGRIP1	NM_020366	exon3	c.C402T	p.A134A	CCCTGCCAGCCCC	.	229.0	57.0	114.0	0.0	.	213	.	.	.	none	.	.	PASS	Atlas-SNP
EFS	10278	hgsc.bcm.edu	hg19	14	23828918	23828918	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	EFS	NM_005864	exon4	c.C769T	p.L257L	CCAGCAGAGGCAC	.	62.0	19.0	50.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
LRR1	122769	hgsc.bcm.edu	hg19	14	50081041	50081041	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	LRR1	NM_152329	exon4	c.G1072T	p.V358F	ATTTGTGTTTGTG	.	53.0	11.0	61.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
ZC2HC1C	79696	hgsc.bcm.edu	hg19	14	75537677	75537677	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	.	NM_024643	exon2	c.G401T	p.G134V	GAGTTGGAGTGGA	.	95.0	31.0	96.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	hg19	14	102478240	102478240	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	DYNC1H1	NM_001376	exon33	c.T6647C	p.I2216T	CCCAGATCAATCA	.	87.0	27.0	80.0	0.0	.	395	.	.	.	none	.	.	PASS	Atlas-SNP
TRIM69	140691	hgsc.bcm.edu	hg19	15	45048565	45048565	+	Splice_Site	SNP	G	G	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	TRIM69	NM_080745	exon2	c.7-1G>C	.	TTCCCAGGAGGAG	.	130.0	61.0	93.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
FBN1	2200	hgsc.bcm.edu	hg19	15	48748937	48748937	+	Silent	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	FBN1	NM_000138	exon44	c.C5319A	p.I1773I	CCCTGGGATCTCC	.	112.0	44.0	70.0	0.0	.	310	.	.	.	none	.	.	PASS	Atlas-SNP
SV2B	9899	hgsc.bcm.edu	hg19	15	91811781	91811781	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	SV2B	NM_014848	exon10	c.T1319A	p.I440N	CCACAATCAACTT	.	271.0	21.0	176.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
RPL3L	6123	hgsc.bcm.edu	hg19	16	1995884	1995884	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	RPL3L	NM_005061	exon8	c.G999A	p.L333L	ACCCTTCAGCATG	.	74.0	5.0	35.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
PKMYT1	9088	hgsc.bcm.edu	hg19	16	3025761	3025761	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	PKMYT1	NM_182687	exon4	c.C431T	p.P144L	CGGAATGGTGACA	.	86.0	33.0	5.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
NLRC3	197358	hgsc.bcm.edu	hg19	16	3614323	3614323	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	NLRC3	NM_178844	exon5	c.C615G	p.S205R	CGCCAGGCTGGGC	.	95.0	32.0	57.0	0.0	.	103	.	.	.	none	.	.	PASS	Atlas-SNP
CREBBP	1387	hgsc.bcm.edu	hg19	16	3779018	3779018	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	CREBBP	NM_004380	exon31	c.G6030A	p.G2010G	GACGGGCCCGCTC	.	58.0	18.0	14.0	0.0	.	546	.	.	.	none	.	.	PASS	Atlas-SNP
METTL22	79091	hgsc.bcm.edu	hg19	16	8736394	8736394	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	METTL22	NM_024109	exon9	c.T982C	p.C328R	AATGCCTGCACAG	.	157.0	65.0	103.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
DHRS7C	201140	hgsc.bcm.edu	hg19	17	9683157	9683157	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	DHRS7C	NM_001220493	exon3	c.A466T	p.I156F	ATGTGATGGGGCC	.	108.0	8.0	95.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
COX10	1352	hgsc.bcm.edu	hg19	17	13980322	13980322	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	COX10	NM_001303	exon3	c.G448C	p.V150L	CTGCAAGTGTATG	.	161.0	69.0	146.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
SLFN12L	100506736	hgsc.bcm.edu	hg19	17	33807110	33807110	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	SLFN12L	NM_001195790	exon2	c.C119T	p.T40I	CCAAGAGTGACTC	.	103.0	8.0	74.0	0.0	.	140	.	.	.	none	.	.	PASS	Atlas-SNP
KRT38	8687	hgsc.bcm.edu	hg19	17	39596920	39596920	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	KRT38	NM_006771	exon1	c.T254G	p.I85S	CCAGGAATGTGGC	.	212.0	88.0	109.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
JUP	3728	hgsc.bcm.edu	hg19	17	39925817	39925817	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	JUP	NM_021991	exon3	c.G321C	p.E107D	CTGCCCCTCCACC	.	123.0	27.0	67.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
HELZ	9931	hgsc.bcm.edu	hg19	17	65105385	65105385	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	HELZ	NM_014877	exon29	c.G4336A	p.E1446K	CAGCTTCTGCAGG	.	111.0	43.0	105.0	0.0	.	160	.	.	.	none	.	.	PASS	Atlas-SNP
EXOC7	23265	hgsc.bcm.edu	hg19	17	74081440	74081440	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	EXOC7,NS,malignant_melanoma,0,1	EXOC7	NM_001145297	exon16	c.C1820T	p.S607F	CGGTAGGAGCGCT	.	45.0	4.0	30.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
SETBP1	26040	hgsc.bcm.edu	hg19	18	42533244	42533244	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	SETBP1	NM_015559	exon4	c.C3939T	p.D1313D	AAAGGACATCCAA	.	144.0	38.0	158.0	0.0	.	577	.	.	.	none	.	.	PASS	Atlas-SNP
PTPRS	5802	hgsc.bcm.edu	hg19	19	5286082	5286082	+	Missense_Mutation	SNP	C	C	A	rs200430287	by1000genomes;alternate_allele	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	PTPRS	NM_130854	exon2	c.G70T	p.V24F	CTCCAACGAGCAG	.	160.0	81.0	150.0	0.0	.	169	.	.	.	alt	C|0.999;T|0.001	.	PASS	Atlas-SNP
KEAP1	9817	hgsc.bcm.edu	hg19	19	10610178	10610178	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	KEAP1	NM_012289	exon2	c.C532T	p.Q178X	CCAGCTGCTGCAC	.	104.0	91.0	141.0	1.0	.	182	.	.	.	none	.	.	PASS	Atlas-SNP
SLC7A9	11136	hgsc.bcm.edu	hg19	19	33350841	33350841	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	SLC7A9	NM_001243036	exon8	c.T779C	p.I260T	AGGGGGATCCCGA	.	210.0	108.0	185.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
CEBPA	1050	hgsc.bcm.edu	hg19	19	33793108	33793108	+	Silent	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.,1	CEBPA	NM_004364	exon1	c.C213A	p.A71A	GAAGGCGGCCGGG	.	83.0	30.0	26.0	0.0	.	986	.	.	.	none	.	.	PASS	Atlas-SNP
CEBPA	1050	hgsc.bcm.edu	hg19	19	33793120	33793120	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.,2	CEBPA	NM_004364	exon1	c.C201A	p.Y67X	GTCGATGTAGGCG	.	84.0	29.0	26.0	0.0	.	986	.	.	.	none	.	.	PASS	Atlas-SNP
WTIP	126374	hgsc.bcm.edu	hg19	19	34991065	34991065	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	WTIP	NM_001080436	exon8	c.G1184A	p.G395E	AGGAGGGACGCCG	.	41.0	20.0	21.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
LSR	51599	hgsc.bcm.edu	hg19	19	35758028	35758028	+	Silent	SNP	C	C	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	LSR	NM_205834	exon9	c.C1305A	p.T435T	AGTCACCTCCCTC	.	161.0	93.0	110.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	hg19	19	40357745	40357745	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	FCGBP	NM_003890	exon34	c.C15568A	p.L5190M	AGGTCAGCAGGGA	.	199.0	23.0	166.0	0.0	.	416	.	.	.	none	.	.	PASS	Atlas-SNP
HRC	3270	hgsc.bcm.edu	hg19	19	49657889	49657889	+	Silent	SNP	T	T	C	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.,1	HRC	NM_002152	exon1	c.A606G	p.E202E	CTCCTCTTCCTCC	.	58.0	6.0	55.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
NUP62	23636	hgsc.bcm.edu	hg19	19	50412996	50412996	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	NUP62	NM_153719	exon3	c.G69A	p.T23T	TGTTGCCGTCTTT	.	88.0	50.0	82.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
MBOAT7	79143	hgsc.bcm.edu	hg19	19	54687463	54687463	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	MBOAT7	NM_001146082	exon5	c.A434T	p.D145V	GGCACGTCGGGCA	.	97.0	52.0	101.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
KCNK15	60598	hgsc.bcm.edu	hg19	20	43378853	43378853	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	KCNK15	NM_022358	exon2	c.G367A	p.V123I	ACGCTGGTCACTT	.	136.0	40.0	61.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
LIPI	149998	hgsc.bcm.edu	hg19	21	15554119	15554119	+	Silent	SNP	C	C	T	rs368826576	bycluster	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	LIPI,NS,carcinoma,-1,1	LIPI	NM_198996	exon4	c.G666A	p.T222T	TGCATCCGTGTAA	.	66.0	18.0	52.0	0.0	.	95	.	.	.	weak	.	.	PASS	Atlas-SNP
NCAM2	4685	hgsc.bcm.edu	hg19	21	22906941	22906941	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	NCAM2	NM_004540	exon17	c.A2366T	p.N789I	CAGTAAATGAGCC	.	122.0	35.0	132.0	0.0	.	220	.	.	.	none	.	.	PASS	Atlas-SNP
PLAC4	191585	hgsc.bcm.edu	hg19	21	42551431	42551431	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	.	NM_182832	exon1	c.G125A	p.R42K	CGGTGTCTGGGGT	.	179.0	49.0	137.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
SHANK3	85358	hgsc.bcm.edu	hg19	22	51160316	51160316	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	SHANK3	NM_033517	exon21	c.C4013T	p.A1338V	AGTCTGCAGCCGA	.	87.0	53.0	30.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
DMD	1756	hgsc.bcm.edu	hg19	X	32305751	32305751	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	DMD	NM_004006	exon43	c.C6185A	p.A2062E	TGCAATGCTGCTG	.	29.0	28.0	31.0	0.0	.	2127	.	.	.	none	.	.	PASS	Atlas-SNP
BMP15	9210	hgsc.bcm.edu	hg19	X	50658768	50658768	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	BMP15	NM_005448	exon2	c.A340T	p.I114L	TGGCATATACAGA	.	113.0	108.0	81.0	0.0	.	62	.	.	.	none	.	.	PASS	Atlas-SNP
ZBTB38	253461	hgsc.bcm.edu	hg19	3	141162052	141162058	+	Frame_Shift_Del	DEL	TTCGGAT	TTCGGAT	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TTCGGAT	TTCGGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	ZBTB38	NM_001080412	exon8	c.821_827del	p.274_276del	.	.	65.0	14.0	74.0	0.0	.	92	.	0.215385	0	none	.	.	PASS	Atlas-Indel,Pindel
TJP2	9414	hgsc.bcm.edu	hg19	9	71869284	71869285	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	TJP2	NM_001170416	exon23	c.3660_3661insT	p.E1220fs	.	.	78.0	21.0	79.0	0.0	.	120	.	0.269231	0	none	.	.	PASS	Atlas-Indel,Pindel
FAM186A	121006	hgsc.bcm.edu	hg19	12	50748961	50748961	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	FAM186A	NM_001145475	exon4	c.1655delG	p.R552fs	.	.	141.0	53.0	129.0	0.0	.	181	.	0.375887	0	none	.	.	PASS	Atlas-Indel,Pindel
RBAK	57786	hgsc.bcm.edu	hg19	7	5104550	5104550	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	RBAK	NM_021163	exon5	c.1462delA	p.S488fs	.	.	105.0	58.0	114.0	0.0	.	82	.	0.552381	0	none	.	.	PASS	Atlas-Indel,Pindel
DNAH8	1769	hgsc.bcm.edu	hg19	6	38818063	38818080	+	In_Frame_Del	DEL	ATAAAAATAATGCAGCGA	ATAAAAATAATGCAGCGA	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	ATAAAAATAATGCAGCGA	ATAAAAATAATGCAGCGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	DNAH8	NM_001206927	exon38	c.5235_5252del	p.1745_1751del	.	.	65.0	25.0	89.0	0.0	.	1239	.	0.384615	0	none	.	.	PASS	Atlas-Indel,Pindel
ZNF814	730051	hgsc.bcm.edu	hg19	19	58385280	58385281	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	ZNF814	NM_001144989	exon3	c.1478_1479del	p.493_493del	.	.	124.0	12.0	130.0	0.0	.	93	.	0.0967742	0	none	.	.	PASS	Atlas-INDEL
PCSK9	255738	hgsc.bcm.edu	hg19	1	55529096	55529096	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	PCSK9	NM_174936	exon12	c.1917delT	p.P639fs	.	.	232.0	129.0	177.0	0.0	.	76	.	0.556035	0	none	.	.	PASS	Atlas-Indel,Pindel
MIR641	693226	hgsc.bcm.edu	hg19	19	40788466	40788466	+	RNA	DEL	A	A	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	.	.	.	.	.	.	.	56.0	17.0	47.0	0.0	.	.	.	0.303571	0	none	.	.	PASS	Atlas-INDEL
UBQLN2	29978	hgsc.bcm.edu	hg19	X	56592091	56592092	+	Frame_Shift_Del	DEL	AA	AA	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	UBQLN2	NM_013444	exon1	c.1784_1785del	p.595_595del	.	.	167.0	146.0	106.0	0.0	.	55	.	0.874251	0	none	.	.	PASS	Atlas-Indel,Pindel
PPP2R5E	5529	hgsc.bcm.edu	hg19	14	63881922	63881922	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	PPP2R5E	NM_006246	exon5	c.486delG	p.L162fs	.	.	95.0	51.0	113.0	0.0	.	43	.	0.536842	0	none	.	.	PASS	Atlas-Indel,Pindel
HECA	51696	hgsc.bcm.edu	hg19	6	139487930	139487930	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	HECA	NM_016217	exon2	c.780delC	p.Y260X	.	.	66.0	21.0	75.0	0.0	.	45	.	0.318182	0	none	.	.	PASS	Atlas-Indel,Pindel
RAPH1	65059	hgsc.bcm.edu	hg19	2	204304774	204304775	+	Frame_Shift_Del	DEL	AC	AC	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	RAPH1	NM_213589	exon14	c.3139_3140del	p.1047_1047del	.	.	79.0	37.0	75.0	0.0	.	118	.	0.468354	0	none	.	.	PASS	Atlas-Indel,Pindel
SPEG	10290	hgsc.bcm.edu	hg19	2	220354060	220354064	+	Frame_Shift_Del	DEL	TCTTC	TCTTC	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TCTTC	TCTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	SPEG	NM_005876	exon36	c.8319_8323del	p.2773_2775del	.	.	61.0	25.0	54.0	0.0	.	272	.	0.409836	0	none	.	.	PASS	Atlas-Indel,Pindel
RCHY1	25898	hgsc.bcm.edu	hg19	4	76416940	76416940	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	RCHY1	NM_001008925	exon6	c.504delA	p.L168fs	.	.	221.0	125.0	282.0	0.0	.	17	.	0.565611	0	none	.	.	PASS	Atlas-Indel,Pindel
HPS3	84343	hgsc.bcm.edu	hg19	3	148857880	148857881	+	Frame_Shift_Ins	INS	-	-	GT	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	HPS3,NS,carcinoma,0,1	HPS3	NM_032383	exon2	c.307_308insGT	p.R103fs	.	.	131.0	30.0	145.0	0.0	.	104	.	0.229008	0	none	.	.	PASS	Atlas-Indel,Pindel
VSTM2A	222008	hgsc.bcm.edu	hg19	7	54612346	54612346	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	VSTM2A	NM_182546	exon2	c.110delC	p.T37fs	.	.	167.0	50.0	128.0	0.0	.	53	.	0.299401	0	none	.	.	PASS	Atlas-Indel,Pindel
MLEC	9761	hgsc.bcm.edu	hg19	12	121132908	121132908	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	MLEC	NM_014730	exon4	c.601delG	p.D201fs	.	.	162.0	72.0	123.0	0.0	.	33	.	0.444444	0	none	.	.	PASS	Atlas-Indel,Pindel
RUSC2	9853	hgsc.bcm.edu	hg19	9	35547875	35547875	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	RUSC2	NM_014806	exon2	c.1356delA	p.E452fs	.	.	86.0	53.0	76.0	0.0	.	88	.	0.616279	0	none	.	.	PASS	Atlas-Indel,Pindel
TYSND1	219743	hgsc.bcm.edu	hg19	10	71905802	71905819	+	In_Frame_Del	DEL	CTCTCAGTTGATCCGCCT	CTCTCAGTTGATCCGCCT	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	CTCTCAGTTGATCCGCCT	CTCTCAGTTGATCCGCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	TYSND1	NM_001040273	exon1	c.525_542del	p.175_181del	.	.	112.0	32.0	24.0	0.0	.	20	.	0.286	.	none	.	.	PASS	Pindel
MAST2	23139	hgsc.bcm.edu	hg19	1	46496701	46496702	+	Frame_Shift_Del	DEL	TC	TC	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	MAST2	NM_015112	exon23	c.2730_2731del	p.910_911del	.	.	99.0	34.0	111.0	0.0	.	136	.	0.343	.	none	.	.	PASS	Pindel
UPRT	139596	hgsc.bcm.edu	hg19	X	74494317	74494318	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	UPRT	NM_145052	exon1	c.227_228del	p.76_76del	.	.	146.0	23.0	82.0	0.0	.	46	.	0.158	.	none	.	.	PASS	Pindel
OFD1	8481	hgsc.bcm.edu	hg19	X	13762547	13762547	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	.	OFD1	NM_003611	exon6	c.425delA	p.H142fs	.	.	290.0	96.0	225.0	0.0	.	109	.	0.331	.	none	.	.	PASS	Pindel