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
TESK2	10420	hgsc.bcm.edu	hg19	1	45811638	45811638	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	TESK2	NM_007170	exon10	c.T908G	p.V303G	ATCTCCACAAAAG	.	65.0	15.0	73.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
AMPD2	271	hgsc.bcm.edu	hg19	1	110168296	110168296	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	AMPD2_ENST00000393689,NS,carcinoma,0,1	AMPD2	NM_004037	exon3	c.C397T	p.R133C	TTCACCCGCTCAC	.	118.0	7.0	151.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
ITGA10	8515	hgsc.bcm.edu	hg19	1	145536864	145536864	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ITGA10	NM_003637	exon18	c.T2244G	p.D748E	ATCAGATTACCTC	.	86.0	24.0	78.0	0.0	.	131	.	.	.	none	.	.	PASS	Atlas-SNP
TOR1AIP2	163590	hgsc.bcm.edu	hg19	1	179834169	179834169	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	TOR1AIP2	NM_022347	exon3	c.A143G	p.Y48C	GGACAATAATCAG	.	356.0	108.0	391.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
MR1	3140	hgsc.bcm.edu	hg19	1	181021439	181021439	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	MR1	NM_001531	exon5	c.C673T	p.H225Y	AAAGCTCATGGCT	.	87.0	23.0	114.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
PRKD3	23683	hgsc.bcm.edu	hg19	2	37501808	37501808	+	Silent	SNP	A	A	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	PRKD3	NM_005813	exon10	c.T1407A	p.S469S	TGGTGAAGATATG	.	93.0	26.0	101.0	0.0	.	170	.	.	.	none	.	.	PASS	Atlas-SNP
ADD2	119	hgsc.bcm.edu	hg19	2	70931469	70931469	+	Silent	SNP	G	G	A	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ADD2	NM_001185055	exon3	c.C354T	p.F118F	TGTCGGGAAGACT	.	50.0	12.0	55.0	0.0	.	261	.	.	.	none	.	.	PASS	Atlas-SNP
CNNM4	26504	hgsc.bcm.edu	hg19	2	97428100	97428100	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	CNNM4	NM_020184	exon1	c.A1364G	p.D455G	TCCATGACACCAA	.	161.0	48.0	188.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
MRPS9	64965	hgsc.bcm.edu	hg19	2	105654555	105654555	+	Missense_Mutation	SNP	C	C	T	rs149402894	bycluster	TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	MRPS9	NM_182640	exon1	c.C5T	p.A2V	ACATGGCGGCGCC	.	105.0	30.0	122.0	0.0	.	32	.	.	.	weak	C|1.000;T|0.000	0.000	PASS	Atlas-SNP
SAP130	79595	hgsc.bcm.edu	hg19	2	128774008	128774008	+	Silent	SNP	G	G	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	SAP130	NM_001145928	exon4	c.C540A	p.I180I	TTGAGGGATGCTA	.	132.0	32.0	146.0	0.0	.	169	.	.	.	none	.	.	PASS	Atlas-SNP
MST1	4485	hgsc.bcm.edu	hg19	3	49723551	49723551	+	Missense_Mutation	SNP	A	A	G	rs199957562		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	MST1,cerebellum,glioma,0,4	MST1	NM_020998	exon9	c.T1091C	p.M364T	GCGCGCATGCCGG	.	67.0	4.0	91.0	0.0	.	84	.	.	.	weak	.	.	PASS	Atlas-SNP
SKIL	6498	hgsc.bcm.edu	hg19	3	170079027	170079027	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	SKIL	NM_001248008	exon1	c.T908C	p.F303S	AGACGTTTGTGAT	.	113.0	35.0	105.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
FAM131A	131408	hgsc.bcm.edu	hg19	3	184062561	184062561	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	FAM131A	NM_144635	exon6	c.C904G	p.Q302E	GAGGCCCAGGACT	.	74.0	19.0	71.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
HGFAC	3083	hgsc.bcm.edu	hg19	4	3446365	3446365	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	HGFAC	NM_001528	exon7	c.C746A	p.P249H	GCAGCCCTTGCCT	.	61.0	11.0	85.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC66	339977	hgsc.bcm.edu	hg19	4	52861855	52861855	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	LRRC66	NM_001024611	exon4	c.G1333A	p.V445I	GAAATACTTGGCG	.	55.0	15.0	64.0	0.0	.	128	.	.	.	none	.	.	PASS	Atlas-SNP
WDFY3	23001	hgsc.bcm.edu	hg19	4	85642588	85642588	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	WDFY3,NS,carcinoma,0,1	WDFY3	NM_014991	exon47	c.C7579A	p.L2527M	GGCGCAGTAAGGT	.	32.0	7.0	47.0	0.0	.	314	.	.	.	none	.	.	PASS	Atlas-SNP
SLC38A9	153129	hgsc.bcm.edu	hg19	5	54965109	54965109	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	SLC38A9	NM_173514	exon7	c.G473C	p.G158A	AAAAGGCCCATCA	.	113.0	32.0	131.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
RASA1	5921	hgsc.bcm.edu	hg19	5	86665669	86665669	+	Silent	SNP	A	A	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	RASA1	NM_002890	exon12	c.A1650G	p.E550E	TAGTGAAGAACAT	.	472.0	155.0	462.0	0.0	.	213	.	.	.	none	.	.	PASS	Atlas-SNP
SEMA6A	57556	hgsc.bcm.edu	hg19	5	115782689	115782689	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	SEMA6A	NM_020796	exon19	c.G2713C	p.E905Q	GCATTTCCAGCCG	.	72.0	26.0	72.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
DMXL1	1657	hgsc.bcm.edu	hg19	5	118480323	118480323	+	Silent	SNP	A	A	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	DMXL1	NM_005509	exon15	c.A2559G	p.L853L	CATTTTATCTAAT	.	328.0	108.0	283.0	0.0	.	268	.	.	.	none	.	.	PASS	Atlas-SNP
PDE6A	5145	hgsc.bcm.edu	hg19	5	149279060	149279060	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	PDE6A	NM_000440	exon9	c.A1141C	p.M381L	TAATCATCCATCC	.	116.0	40.0	85.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
RREB1	6239	hgsc.bcm.edu	hg19	6	7189549	7189549	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	RREB1	NM_001003700	exon6	c.T419C	p.M140T	GGAACATGCACAG	.	58.0	17.0	48.0	0.0	.	242	.	.	.	none	.	.	PASS	Atlas-SNP
ZBTB22	9278	hgsc.bcm.edu	hg19	6	33283498	33283498	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ZBTB22	NM_001145338	exon2	c.C1196A	p.S399X	CCCCCTGAGTCAT	.	66.0	22.0	64.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
KIFC1	3833	hgsc.bcm.edu	hg19	6	33371727	33371727	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	KIFC1	NM_002263	exon6	c.G577T	p.A193S	CATTTAGCCAAGG	.	107.0	5.0	147.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
UTRN	7402	hgsc.bcm.edu	hg19	6	144843189	144843189	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	UTRN	NM_007124	exon39	c.A5615G	p.Y1872C	CAGATTATCTGGT	.	77.0	23.0	99.0	0.0	.	327	.	.	.	none	.	.	PASS	Atlas-SNP
BRAT1	221927	hgsc.bcm.edu	hg19	7	2581812	2581812	+	Silent	SNP	G	G	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	BRAT1	NM_152743	exon7	c.C957G	p.V319V	GAGAAGGACCTGG	.	268.0	132.0	223.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
YAE1D1	57002	hgsc.bcm.edu	hg19	7	39610143	39610143	+	Silent	SNP	T	T	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	YAE1D1	NM_020192	exon2	c.T168C	p.V56V	AGCAGTTACTCTT	.	140.0	64.0	146.0	0.0	.	2	.	.	.	none	.	.	PASS	Atlas-SNP
MBLAC1	255374	hgsc.bcm.edu	hg19	7	99725518	99725518	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	MBLAC1	NM_203397	exon2	c.C500G	p.P167R	CCACGCCGGGCCA	.	89.0	44.0	97.0	0.0	.	13	.	.	.	none	.	.	PASS	Atlas-SNP
REPIN1	29803	hgsc.bcm.edu	hg19	7	150068585	150068585	+	Silent	SNP	G	G	A	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	REPIN1	NM_001099695	exon3	c.G426A	p.L142L	GCCCTTGCCCTGC	.	60.0	33.0	54.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
INTS9	55756	hgsc.bcm.edu	hg19	8	28669861	28669861	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	INTS9	NM_018250	exon8	c.C727T	p.L243F	TGGTAAGCAAGGA	.	100.0	32.0	108.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
VCPIP1	80124	hgsc.bcm.edu	hg19	8	67546979	67546979	+	Silent	SNP	T	T	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	VCPIP1	NM_025054	exon3	c.A3426G	p.E1142E	CACAACTTCTGTT	.	111.0	36.0	82.0	0.0	.	110	.	.	.	none	.	.	PASS	Atlas-SNP
ZFAND5	7763	hgsc.bcm.edu	hg19	9	74975669	74975669	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ZFAND5	NM_001102421	exon2	c.C26A	p.P9Q	GGCCCCGGGGTCT	.	65.0	14.0	95.0	0.0	.	14	.	.	.	none	.	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	hg19	9	78936460	78936460	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	PCSK5	NM_001190482	exon30	c.A3926C	p.Q1309P	TGTGCCAGGAAAA	.	79.0	33.0	63.0	0.0	.	329	.	.	.	none	.	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	hg19	10	29760115	29760115	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.,1	SVIL	NM_021738	exon31	c.A5587G	p.M1863V	CCACCATCCCCCC	.	150.0	42.0	198.0	2.0	.	226	.	.	.	none	.	.	PASS	Atlas-SNP
ABCC2	1244	hgsc.bcm.edu	hg19	10	101595920	101595920	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ABCC2	NM_000392	exon25	c.T3487C	p.F1163L	TCTCACTTCAGCG	.	179.0	58.0	198.0	0.0	.	160	.	.	.	none	.	.	PASS	Atlas-SNP
POLL	27343	hgsc.bcm.edu	hg19	10	103343263	103343263	+	Splice_Site	SNP	A	A	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	POLL	NM_001174085	exon7	c.789+2T>G	.	GGTGTGACCTGTT	.	50.0	12.0	54.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
PPP6R3	55291	hgsc.bcm.edu	hg19	11	68305152	68305152	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	PPP6R3	NM_001164162	exon3	c.T20C	p.L7P	TTGATCTTCACTC	.	236.0	60.0	207.0	0.0	.	159	.	.	.	none	.	.	PASS	Atlas-SNP
DDX25	29118	hgsc.bcm.edu	hg19	11	125787115	125787115	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	DDX25	NM_013264	exon9	c.T1007A	p.I336N	GCAGCATCACCAT	.	58.0	14.0	46.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
SLC6A13	6540	hgsc.bcm.edu	hg19	12	369149	369149	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	SLC6A13	NM_016615	exon2	c.A70G	p.K24E	CCTCCTTCTTTTC	.	153.0	79.0	94.0	0.0	.	62	.	.	.	none	.	.	PASS	Atlas-SNP
LTBR	4055	hgsc.bcm.edu	hg19	12	6494235	6494235	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	LTBR	NM_002342	exon3	c.G241A	p.A81T	GTTTGTGCCACAT	.	80.0	18.0	64.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
PEX5	5830	hgsc.bcm.edu	hg19	12	7351609	7351609	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	PEX5	NM_001131023	exon6	c.C496A	p.P166T	GCAGACCCCTTGT	.	83.0	38.0	62.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
SUOX	6821	hgsc.bcm.edu	hg19	12	56397604	56397604	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	SUOX	NM_000456	exon6	c.A431T	p.N144I	TTCACAACCAGTC	.	180.0	74.0	161.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
RAB21	23011	hgsc.bcm.edu	hg19	12	72167772	72167772	+	Silent	SNP	T	T	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	RAB21	NM_014999	exon4	c.T361C	p.L121L	AAAATGTTGGGAA	.	147.0	75.0	132.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
NAP1L1	4673	hgsc.bcm.edu	hg19	12	76462722	76462722	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	NAP1L1	NM_004537	exon3	c.G70T	p.E24X	CCTCTTCTTCTAC	.	93.0	42.0	80.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
MED13L	23389	hgsc.bcm.edu	hg19	12	116453057	116453057	+	Silent	SNP	A	A	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	MED13L	NM_015335	exon8	c.T1032C	p.S344S	GGCAGCACTCTGC	.	153.0	68.0	106.0	0.0	.	193	.	.	.	none	.	.	PASS	Atlas-SNP
PXN	5829	hgsc.bcm.edu	hg19	12	120660781	120660781	+	Silent	SNP	T	T	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	PXN	NM_001080855	exon4	c.A378C	p.S126S	CTCAGCTGATTTC	.	163.0	43.0	125.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
LTK	4058	hgsc.bcm.edu	hg19	15	41804906	41804906	+	Silent	SNP	G	G	A	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	LTK_ENST00000263800,NS,carcinoma,0,2	LTK	NM_001135685	exon3	c.C358T	p.L120L	CTTACAGATACTG	.	44.0	14.0	62.0	0.0	.	117	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF598	90850	hgsc.bcm.edu	hg19	16	2053710	2053710	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ZNF598	NM_178167	exon4	c.T242C	p.L81P	GCAGGAAGCTTCT	.	90.0	28.0	119.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
NAGPA	51172	hgsc.bcm.edu	hg19	16	5075564	5075564	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	NAGPA	NM_016256	exon10	c.A1463T	p.Y488F	GGGTGGTATGCAT	.	122.0	56.0	99.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
ATP2A1	487	hgsc.bcm.edu	hg19	16	28914368	28914368	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ATP2A1	NM_004320	exon20	c.C2762T	p.S921F	ACCAGTCCCTGCT	.	59.0	17.0	35.0	0.0	.	116	.	.	.	none	.	.	PASS	Atlas-SNP
OR1E2	8388	hgsc.bcm.edu	hg19	17	3336754	3336754	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	OR1E2	NM_003554	exon1	c.T382C	p.F128L	TGGGGAAGCAGAT	.	195.0	86.0	149.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
CTNS	1497	hgsc.bcm.edu	hg19	17	3563642	3563642	+	Silent	SNP	G	G	A	rs371189196		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	CTNS,NS,carcinoma,+1,1	CTNS	NM_001031681	exon12	c.G1083A	p.P361P	GAGACCGGGGTAT	.	90.0	51.0	90.0	0.0	.	42	.	.	.	weak	.	.	PASS	Atlas-SNP
KCTD11	147040	hgsc.bcm.edu	hg19	17	7256855	7256855	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	KCTD11	NM_001002914	exon1	c.G594T	p.E198D	CCTGGAGGAGGTG	.	43.0	10.0	38.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
NF1	4763	hgsc.bcm.edu	hg19	17	29687644	29687644	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	NF1	NM_001042492	exon57	c.A8300G	p.Q2767R	CACTGCAGAGCCA	.	133.0	74.0	89.0	0.0	.	1586	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA10	10349	hgsc.bcm.edu	hg19	17	67146187	67146187	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ABCA10	NM_080282	exon38	c.C4415T	p.A1472V	TTATACGCCATTA	.	163.0	34.0	127.0	0.0	.	209	.	.	.	none	.	.	PASS	Atlas-SNP
METTL23	124512	hgsc.bcm.edu	hg19	17	74729620	74729620	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	METTL23	NM_001206984	exon5	c.A425C	p.E142A	CACTTGAAGCTTT	.	192.0	87.0	179.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF750	79755	hgsc.bcm.edu	hg19	17	80789569	80789569	+	Silent	SNP	G	G	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ZNF750	NM_024702	exon2	c.C762G	p.T254T	GTAGATGGTGGCC	.	113.0	33.0	88.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	hg19	18	3067525	3067525	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	MYOM1	NM_003803	exon38	c.G4793C	p.G1598A	GGGTCTCCCCACA	.	88.0	26.0	61.0	0.0	.	192	.	.	.	none	.	.	PASS	Atlas-SNP
ASXL3	80816	hgsc.bcm.edu	hg19	18	31325189	31325189	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ASXL3	NM_030632	exon12	c.G5377C	p.E1793Q	GCACCAGAGAGAA	.	99.0	34.0	85.0	0.0	.	405	.	.	.	none	.	.	PASS	Atlas-SNP
CTDP1	9150	hgsc.bcm.edu	hg19	18	77440069	77440069	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	CTDP1	NM_004715	exon1	c.C122T	p.A41V	CGGGCGCGGCCGT	.	26.0	12.0	35.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	hg19	19	1051189	1051189	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ABCA7	NM_019112	exon20	c.G2720T	p.R907L	ATGGGCGGCTGAA	.	48.0	11.0	59.0	0.0	.	174	.	.	.	none	.	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	hg19	19	8130912	8130912	+	Missense_Mutation	SNP	C	C	T	rs139098536		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	FBN3,NS,carcinoma,0,1	FBN3	NM_032447	exon63	c.G8321A	p.R2774Q	TCCAGCCGGTAGG	.	104.0	38.0	123.0	1.0	.	300	.	.	.	weak	C|1.000;T|0.000	0.000	PASS	Atlas-SNP
CAPNS1	826	hgsc.bcm.edu	hg19	19	36631958	36631958	+	Silent	SNP	C	C	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	CAPNS1	NM_001749	exon2	c.C45G	p.G15G	CGGCGGCGGGGGA	.	65.0	4.0	84.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
LILRB4	11006	hgsc.bcm.edu	hg19	19	55175397	55175397	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	LILRB4	NM_006847	exon3	c.C256T	p.P86S	TCCATCCCATCCA	.	135.0	32.0	120.0	0.0	.	86	.	.	.	none	.	.	PASS	Atlas-SNP
ZSCAN22	342945	hgsc.bcm.edu	hg19	19	58850450	58850450	+	Missense_Mutation	SNP	G	G	A	rs138721519		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ZSCAN22	NM_181846	exon3	c.G1234A	p.A412T	TGTGACGCGTGTG	.	80.0	6.0	79.0	0.0	.	47	.	.	.	weak	G|1.000;A|0.000	0.000	PASS	Atlas-SNP
SON	6651	hgsc.bcm.edu	hg19	21	34926409	34926409	+	Silent	SNP	T	T	C	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	SON	NM_032195	exon3	c.T4872C	p.N1624N	AGTTAATAAATAT	.	90.0	52.0	137.0	0.0	.	343	.	.	.	none	.	.	PASS	Atlas-SNP
RIPK4	54101	hgsc.bcm.edu	hg19	21	43176834	43176834	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	RIPK4	NM_020639	exon2	c.G325T	p.A109S	CCGAAGCCAGCAG	.	66.0	29.0	106.0	0.0	.	151	.	.	.	none	.	.	PASS	Atlas-SNP
KRTAP12-1	353332	hgsc.bcm.edu	hg19	21	46101934	46101934	+	Nonsense_Mutation	SNP	G	G	T	rs56135164	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	KRTAP12-1	NM_181686	exon1	c.C105A	p.C35X	GGGCACGCACACG	.	96.0	4.0	115.0	0.0	.	9	.	.	.	alt	G|0.954;A|0.046	.	PASS	Atlas-SNP
L3MBTL2	83746	hgsc.bcm.edu	hg19	22	41616759	41616759	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	L3MBTL2	NM_031488	exon7	c.A740G	p.Y247C	TTCGGTATGAAGG	.	40.0	12.0	62.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
PPP6R2	9701	hgsc.bcm.edu	hg19	22	50860699	50860699	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	PPP6R2	NM_001242899	exon9	c.G865A	p.D289N	TTGGTGGACTCCT	.	71.0	15.0	76.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
HAO2	51179	hgsc.bcm.edu	hg19	1	119935262	119935263	+	Frame_Shift_Del	DEL	GT	GT	-	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	HAO2	NM_001005783	exon8	c.951_952del	p.317_318del	.	.	111.0	28.0	107.0	0.0	.	62	.	0.252252	0	none	.	.	PASS	Atlas-Indel,Pindel
KIAA0146	23514	hgsc.bcm.edu	hg19	8	48352889	48352889	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	KIAA0146	NM_001080394	exon8	c.881delG	p.R294fs	.	.	77.0	26.0	49.0	0.0	.	64	.	0.337662	0	none	.	.	PASS	Atlas-Indel,Pindel
MICAL3	57553	hgsc.bcm.edu	hg19	22	18383762	18383762	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	MICAL3	NM_001136004	exon6	c.694delT	p.F232fs	.	.	73.0	18.0	72.0	0.0	.	53	.	0.246575	0	none	.	.	PASS	Atlas-Indel,Pindel
ANKHD1	54882	hgsc.bcm.edu	hg19	5	139919000	139919001	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ANKHD1	NM_017747	exon34	c.7626_7627insT	p.N2542fs	.	.	95.0	23.0	99.0	0.0	.	233	.	0.242105	0	none	.	.	PASS	Atlas-Indel,Pindel
EXT2	2132	hgsc.bcm.edu	hg19	11	44129501	44129501	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	EXT2	NM_000401	exon2	c.337delC	p.R113fs	.	.	149.0	43.0	141.0	0.0	.	129	.	0.288591	0	none	.	.	PASS	Atlas-Indel,Pindel
TSPAN3	10099	hgsc.bcm.edu	hg19	15	77346604	77346612	+	In_Frame_Del	DEL	ATCAACCTC	ATCAACCTC	-	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	ATCAACCTC	ATCAACCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	TSPAN3	NM_005724	exon4	c.341_349del	p.114_117del	.	.	52.0	10.0	58.0	0.0	.	21	.	0.192308	0	none	.	.	PASS	Atlas-Indel,Pindel
NALCN	259232	hgsc.bcm.edu	hg19	13	102047671	102047671	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	NALCN	NM_052867	exon3	c.155delC	p.S52fs	.	.	104.0	29.0	84.0	0.0	.	431	.	0.278846	0	none	.	.	PASS	Atlas-Indel,Pindel
KNTC1	9735	hgsc.bcm.edu	hg19	12	123075197	123075201	+	Frame_Shift_Del	DEL	ACTGC	ACTGC	-	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	ACTGC	ACTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	KNTC1	NM_014708	exon41	c.4042_4046del	p.1348_1349del	.	.	126.0	45.0	136.0	0.0	.	182	.	0.357143	0	none	.	.	PASS	Atlas-Indel,Pindel
LRP2	4036	hgsc.bcm.edu	hg19	2	170063527	170063532	+	In_Frame_Del	DEL	TGACAA	TGACAA	-	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	TGACAA	TGACAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	LRP2	NM_004525	exon39	c.6699_6704del	p.2233_2235del	.	.	146.0	34.0	121.0	0.0	.	751	.	0.232877	0	none	.	.	PASS	Atlas-Indel,Pindel
MAGI1	9223	hgsc.bcm.edu	hg19	3	65425621	65425622	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	MAGI1	NM_001033057	exon9	c.1203_1204del	p.401_402del	.	.	24.0	12.0	28.0	0.0	.	481	.	0.5	0	none	.	.	PASS	Atlas-INDEL
ATP6V1C1	528	hgsc.bcm.edu	hg19	8	104068108	104068109	+	Frame_Shift_Del	DEL	CG	CG	-	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	ATP6V1C1	NM_001695	exon8	c.584_585del	p.195_195del	.	.	176.0	55.0	154.0	0.0	.	33	.	0.3125	0	none	.	.	PASS	Atlas-Indel,Pindel
KIF24	347240	hgsc.bcm.edu	hg19	9	34256932	34256932	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	KIF24	NM_194313	exon11	c.2674delT	p.W892fs	.	.	103.0	35.0	82.0	0.0	.	64	.	0.339806	0	none	.	.	PASS	Atlas-Indel,Pindel
PAMR1	25891	hgsc.bcm.edu	hg19	11	35456322	35456326	+	Frame_Shift_Del	DEL	GGAGC	GGAGC	-	novel		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	GGAGC	GGAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	.	PAMR1	NM_015430	exon11	c.1412_1416del	p.471_472del	.	.	54.0	17.0	53.0	0.0	.	85	.	0.314815	0	none	.	.	PASS	Atlas-Indel,Pindel
