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
MYSM1	114803	hgsc.bcm.edu	hg19	1	59125680	59125680	+	Silent	SNP	A	A	G	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	MYSM1	NM_001085487	exon20	c.T2476C	p.L826L	TTAACAATTCCTT	.	88.0	4.0	84.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179611917	179611917	+	Silent	SNP	T	T	C	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	TTN_ENST00000360870,NS,carcinoma,0,1	TTN	NM_133379	exon46	c.A15210G	p.L5070L	TCTCTCTAGAGTC	.	133.0	8.0	123.0	1.0	.	18412	.	.	.	none	.	.	PASS	Atlas-SNP
PGAP1	80055	hgsc.bcm.edu	hg19	2	197767380	197767380	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	PGAP1	NM_024989	exon5	c.G736A	p.D246N	GGTAATCCCGGAA	.	90.0	32.0	98.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
LRRFIP1	9208	hgsc.bcm.edu	hg19	2	238636568	238636568	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	LRRFIP1	NM_001137550	exon8	c.G434C	p.R145T	ATAGAAGATCTGG	.	189.0	66.0	194.0	0.0	.	171	.	.	.	none	.	.	PASS	Atlas-SNP
PRRT3	285368	hgsc.bcm.edu	hg19	3	9990555	9990555	+	Missense_Mutation	SNP	C	C	A	rs187203537	bycluster;by1000genomes;alternate_allele	TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	PRRT3	NM_207351	exon3	c.G1058T	p.R353L	CTCACCCGCTGGG	.	146.0	6.0	131.0	0.0	.	35	.	.	.	alt	C|0.999;T|0.001	.	PASS	Atlas-SNP
VPRBP	9730	hgsc.bcm.edu	hg19	3	51457622	51457622	+	Silent	SNP	C	C	G	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	VPRBP	NM_014703	exon14	c.G2643C	p.R881R	GGGGGGCCGTGGC	.	60.0	27.0	78.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
GMPS	8833	hgsc.bcm.edu	hg19	3	155654202	155654202	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	GMPS	NM_003875	exon15	c.A1883T	p.Q628L	AAAAGCAGCCTTC	.	165.0	49.0	169.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
MAP3K13	9175	hgsc.bcm.edu	hg19	3	185146747	185146747	+	Silent	SNP	C	C	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	MAP3K13	NM_004721	exon2	c.C378T	p.G126G	CAGTGGCAGTGGT	.	94.0	27.0	80.0	0.0	.	209	.	.	.	none	.	.	PASS	Atlas-SNP
WFS1	7466	hgsc.bcm.edu	hg19	4	6303094	6303094	+	Silent	SNP	C	C	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	WFS1	NM_001145853	exon8	c.C1572T	p.F524F	GAATTTCAAGGGC	.	196.0	79.0	223.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
LRBA	987	hgsc.bcm.edu	hg19	4	151935707	151935707	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	LRBA	NM_006726	exon2	c.G88T	p.G30W	CACCCCCTTCAGT	.	60.0	23.0	47.0	0.0	.	253	.	.	.	none	.	.	PASS	Atlas-SNP
EGFLAM	133584	hgsc.bcm.edu	hg19	5	38407020	38407020	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	EGFLAM	NM_001205301	exon8	c.A919G	p.R307G	ATTTCTAGGCTCA	.	99.0	4.0	101.0	0.0	.	302	.	.	.	none	.	.	PASS	Atlas-SNP
XRCC4	7518	hgsc.bcm.edu	hg19	5	82406899	82406899	+	Silent	SNP	G	G	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	XRCC4	NM_003401	exon3	c.G192T	p.G64G	AAAAGGGAAATAT	.	53.0	22.0	65.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
ERAP1	51752	hgsc.bcm.edu	hg19	5	96139212	96139212	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	ERAP1	NM_001198541	exon2	c.C418T	p.L140F	CGACAAGGAGGGG	.	101.0	40.0	107.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
LY6G6F	259215	hgsc.bcm.edu	hg19	6	31677862	31677862	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	LY6G6F	NM_001003693	exon4	c.A706T	p.I236F	CCTTGGATTCTGA	.	54.0	17.0	71.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
GSTA2	2939	hgsc.bcm.edu	hg19	6	52617715	52617715	+	Missense_Mutation	SNP	T	T	A	rs200252041	by1000genomes;alternate_allele	TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	GSTA2	NM_000846	exon5	c.A351T	p.Q117H	GGCATCTTGTTCC	.	366.0	132.0	329.0	0.0	.	33	.	.	.	alt	T|1.000;C|0.000	.	PASS	Atlas-SNP
SOBP	55084	hgsc.bcm.edu	hg19	6	107955224	107955224	+	Silent	SNP	G	G	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	SOBP	NM_018013	exon6	c.G1176T	p.P392P	CGGCCCGGTGCCG	.	141.0	6.0	148.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
CPVL	54504	hgsc.bcm.edu	hg19	7	29135764	29135764	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	CPVL	NM_019029	exon4	c.C358A	p.L120I	CAAAGAGTCCAAA	.	218.0	71.0	216.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
EIF3E	3646	hgsc.bcm.edu	hg19	8	109215296	109215296	+	Silent	SNP	A	A	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	EIF3E	NM_001568	exon12	c.T1215A	p.I405I	CTTTTCAATCACT	.	112.0	41.0	88.0	0.0	.	73	.	.	.	none	.	.	PASS	Atlas-SNP
CNTNAP3	79937	hgsc.bcm.edu	hg19	9	39140600	39140600	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	CNTNAP3	NM_033655	exon12	c.C1792T	p.R598X	TCCCTCGGTGCTT	.	98.0	32.0	107.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
INVS	27130	hgsc.bcm.edu	hg19	9	103059359	103059359	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	INVS	NM_014425	exon15	c.C2947A	p.P983T	AAGGCCCCCAAGA	.	53.0	31.0	50.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
PRKG1	5592	hgsc.bcm.edu	hg19	10	53227571	53227571	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	PRKG1	NM_006258	exon3	c.C567G	p.N189K	TTACAACTGTACC	.	119.0	40.0	94.0	0.0	.	167	.	.	.	none	.	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	hg19	10	73406335	73406335	+	Silent	SNP	C	C	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	CDH23	NM_052836	exon13	c.C1410T	p.Y470Y	CCTGTACGAGAAC	.	219.0	64.0	235.0	0.0	.	365	.	.	.	none	.	.	PASS	Atlas-SNP
HNRNPUL2	221092	hgsc.bcm.edu	hg19	11	62491826	62491826	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	HNRNPUL2	NM_001079559	exon2	c.G611T	p.R204L	TCATCCCGCTGTC	.	177.0	12.0	175.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
PC	5091	hgsc.bcm.edu	hg19	11	66636376	66636376	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	PC	NM_000920	exon9	c.C963A	p.Y321X	GATGAAGTAGTGC	.	123.0	38.0	94.0	0.0	.	116	.	.	.	none	.	.	PASS	Atlas-SNP
MMP27	64066	hgsc.bcm.edu	hg19	11	102573542	102573542	+	Silent	SNP	C	C	A	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	MMP27,NS,carcinoma,0,2	MMP27	NM_022122	exon4	c.G561T	p.P187P	CAGACCCGGACCA	.	160.0	8.0	134.0	1.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
GNPTAB	79158	hgsc.bcm.edu	hg19	12	102147162	102147162	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	GNPTAB	NM_024312	exon19	c.A3590G	p.E1197G	TGCAGCTCATGCA	.	77.0	28.0	68.0	0.0	.	120	.	.	.	none	.	.	PASS	Atlas-SNP
RASAL1	8437	hgsc.bcm.edu	hg19	12	113565934	113565934	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	RASAL1	NM_004658	exon4	c.A172T	p.T58S	GCACCGTGTACTC	.	349.0	118.0	327.0	0.0	.	89	.	.	.	none	.	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	hg19	13	23906994	23906994	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	SACS	NM_014363	exon10	c.A11021G	p.N3674S	GTTCCATTTACCT	.	102.0	43.0	82.0	0.0	.	871	.	.	.	none	.	.	PASS	Atlas-SNP
IQGAP1	8826	hgsc.bcm.edu	hg19	15	91009552	91009552	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	IQGAP1	NM_003870	exon17	c.G1919T	p.G640V	ATGTTGGCAAAAC	.	123.0	33.0	147.0	0.0	.	140	.	.	.	none	.	.	PASS	Atlas-SNP
CNOT1	23019	hgsc.bcm.edu	hg19	16	58620607	58620607	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	CNOT1	NM_206999	exon7	c.A479G	p.Y160C	TCAATGTAAGAAC	.	385.0	106.0	397.0	0.0	.	359	.	.	.	none	.	.	PASS	Atlas-SNP
BCMO1	53630	hgsc.bcm.edu	hg19	16	81298288	81298288	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	BCMO1	NM_017429	exon5	c.A515G	p.H172R	CGTCACATCCCCA	.	102.0	31.0	115.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
MED13	9969	hgsc.bcm.edu	hg19	17	60040331	60040331	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	MED13	NM_005121	exon21	c.A4846C	p.T1616P	CCATCGTGCTAAA	.	131.0	34.0	91.0	0.0	.	181	.	.	.	none	.	.	PASS	Atlas-SNP
ITGB4	3691	hgsc.bcm.edu	hg19	17	73746316	73746316	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	ITGB4	NM_001005731	exon28	c.G3441A	p.W1147X	CAACTGGCTGCCC	.	90.0	46.0	58.0	0.0	.	165	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	hg19	19	1061844	1061844	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	ABCA7	NM_019112	exon41	c.G5527A	p.D1843N	ACGGGGGACACAT	.	60.0	16.0	72.0	0.0	.	174	.	.	.	none	.	.	PASS	Atlas-SNP
SH2D3A	10045	hgsc.bcm.edu	hg19	19	6760836	6760836	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	SH2D3A	NM_005490	exon3	c.T232C	p.F78L	GTTGAAAGAGGGC	.	99.0	32.0	95.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
MAP2K7	5609	hgsc.bcm.edu	hg19	19	7976338	7976338	+	Silent	SNP	A	A	G	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	MAP2K7	NM_145185	exon9	c.A954G	p.G318G	AACAGGACAGTTT	.	40.0	12.0	76.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF613	79898	hgsc.bcm.edu	hg19	19	52448014	52448014	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	ZNF613	NM_001031721	exon6	c.G878T	p.C293F	GTGATTGTGGAAA	.	107.0	30.0	91.0	0.0	.	62	.	.	.	none	.	.	PASS	Atlas-SNP
SGSM3	27352	hgsc.bcm.edu	hg19	22	40803806	40803806	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	SGSM3	NM_015705	exon14	c.A1538C	p.K513T	CTCAGAAGGACGA	.	108.0	31.0	83.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
TEX11	56159	hgsc.bcm.edu	hg19	X	69898664	69898664	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	TEX11	NM_001003811	exon16	c.G1277A	p.S426N	AAACTACTGGCAG	.	48.0	17.0	56.0	0.0	.	132	.	.	.	none	.	.	PASS	Atlas-SNP
TRIM2	23321	hgsc.bcm.edu	hg19	4	154237027	154237027	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	TRIM2	NM_015271	exon8	c.1657delC	p.R553fs	.	.	136.0	52.0	162.0	0.0	.	105	.	0.382353	0	none	.	.	PASS	Atlas-INDEL
CHRFAM7A	89832	hgsc.bcm.edu	hg19	15	30665308	30665308	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	CHRFAM7A	NM_139320	exon6	c.202delC	p.P68fs	.	.	732.0	118.0	779.0	0.0	.	15	.	0.161202	0	none	.	.	PASS	Atlas-INDEL
KCNJ15	3772	hgsc.bcm.edu	hg19	21	39672237	39672239	+	In_Frame_Del	DEL	GAG	GAG	-	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	KCNJ15	NM_170736	exon3	c.1053_1055del	p.351_352del	.	.	66.0	18.0	74.0	0.0	.	43	.	0.272727	0	none	.	.	PASS	Atlas-INDEL
TMEM30A	55754	hgsc.bcm.edu	hg19	6	75975041	75975042	+	Frame_Shift_Del	DEL	AT	AT	-	novel		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	.	TMEM30A	NM_018247	exon3	c.359_360del	p.120_120del	.	.	35.0	14.0	39.0	0.0	.	40	.	0.4	0	none	.	.	PASS	Atlas-INDEL