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
LDLRAP1	26119	hgsc.bcm.edu	hg19	1	25889193	25889193	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	LDLRAP1	NM_015627	exon5	c.A518G	p.Q173R	TTTGGCAGGTGTC	.	68.0	28.0	77.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
GTF2B	2959	hgsc.bcm.edu	hg19	1	89325567	89325567	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	GTF2B	NM_001514	exon5	c.A533G	p.K178R	TTACCTTTAAATG	.	101.0	46.0	121.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
GOLPH3L	55204	hgsc.bcm.edu	hg19	1	150634375	150634375	+	Silent	SNP	A	A	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	GOLPH3L	NM_018178	exon4	c.T345A	p.G115G	AACATCACCTGTT	.	110.0	39.0	92.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
DENND4B	9909	hgsc.bcm.edu	hg19	1	153915526	153915526	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	DENND4B	NM_014856	exon3	c.T398A	p.L133Q	GGGGCCAGGTTTG	.	74.0	26.0	103.0	0.0	.	210	.	.	.	none	.	.	PASS	Atlas-SNP
FAM5C	339479	hgsc.bcm.edu	hg19	1	190068039	190068039	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	FAM5C	NM_199051	exon8	c.C1410G	p.S470R	CCCCTGGCTGAGC	.	170.0	40.0	244.0	0.0	.	343	.	.	.	none	.	.	PASS	Atlas-SNP
PCNXL2	80003	hgsc.bcm.edu	hg19	1	233190130	233190130	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	PCNXL2	NM_014801	exon25	c.A4235G	p.N1412S	CTGTAGTTGCCCC	.	43.0	19.0	34.0	0.0	.	204	.	.	.	none	.	.	PASS	Atlas-SNP
NCKAP5	344148	hgsc.bcm.edu	hg19	2	133721438	133721438	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	NCKAP5	NM_207481	exon8	c.A434C	p.K145T	GACAGCTTTTCCT	.	105.0	38.0	94.0	0.0	.	322	.	.	.	none	.	.	PASS	Atlas-SNP
ACVR2A	92	hgsc.bcm.edu	hg19	2	148677893	148677893	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	ACVR2A,NS,carcinoma,0,1	ACVR2A	NM_001616	exon8	c.G1057A	p.A353T	AAGTCTGCAGGCG	.	94.0	34.0	67.0	0.0	.	125	.	.	.	none	.	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	hg19	2	152482148	152482148	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	NEB	NM_001271208	exon71	c.T10352C	p.L3451S	GTGTATAAGCGCT	.	28.0	10.0	11.0	0.0	.	1697	.	.	.	none	.	.	PASS	Atlas-SNP
ICOS	29851	hgsc.bcm.edu	hg19	2	204822592	204822592	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	ICOS	NM_012092	exon4	c.A572C	p.K191T	CCAAAAAATCTAG	.	86.0	36.0	45.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
DNPEP	23549	hgsc.bcm.edu	hg19	2	220239739	220239739	+	Silent	SNP	G	G	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	DNPEP	NM_012100	exon14	c.C1245T	p.L415L	GACCATGAGATCC	.	60.0	23.0	56.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
GOLGB1	2804	hgsc.bcm.edu	hg19	3	121433805	121433805	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	GOLGB1	NM_001256486	exon10	c.C1307T	p.S436F	TCTTTGGATTTTT	.	64.0	32.0	55.0	0.0	.	319	.	.	.	none	.	.	PASS	Atlas-SNP
TNIP2	79155	hgsc.bcm.edu	hg19	4	2746482	2746482	+	Missense_Mutation	SNP	G	G	A	rs150823075		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	TNIP2	NM_024309	exon4	c.C848T	p.A283V	GAGGCCGCCAGCT	.	107.0	46.0	124.0	0.0	.	28	.	.	.	weak	G|1.000;A|0.000	0.000	PASS	Atlas-SNP
DCUN1D4	23142	hgsc.bcm.edu	hg19	4	52765463	52765463	+	Silent	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	DCUN1D4	NM_015115	exon8	c.T534C	p.N178N	CAGAAATACTTTG	.	25.0	10.0	17.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
HMGB2	3148	hgsc.bcm.edu	hg19	4	174254247	174254247	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	HMGB2,NS,carcinoma,0,1	HMGB2	NM_001130689	exon2	c.A269G	p.K90R	GGGTCCTTTTTCT	.	276.0	104.0	226.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
SNX25	83891	hgsc.bcm.edu	hg19	4	186188140	186188140	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	SNX25,NS,carcinoma,0,1	SNX25	NM_031953	exon5	c.G430A	p.E144K	GTAGTGGAGTTAC	.	95.0	39.0	74.0	0.0	.	100	.	.	.	none	.	.	PASS	Atlas-SNP
CLPTM1L	81037	hgsc.bcm.edu	hg19	5	1323010	1323010	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	CLPTM1L	NM_030782	exon13	c.A1297G	p.I433V	TGTTGATTAACCA	.	143.0	42.0	111.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
ADAMTS16	170690	hgsc.bcm.edu	hg19	5	5240027	5240027	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	ADAMTS16	NM_139056	exon16	c.C2512G	p.L838V	GAGACACTGATTG	.	135.0	15.0	127.0	0.0	.	543	.	.	.	none	.	.	PASS	Atlas-SNP
PDZD2	23037	hgsc.bcm.edu	hg19	5	32059458	32059458	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	PDZD2	NM_178140	exon12	c.C2314A	p.L772M	AGCAACCTGAGGT	.	53.0	20.0	50.0	0.0	.	306	.	.	.	none	.	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	hg19	5	37181023	37181023	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	C5orf42	NM_023073	exon27	c.G5506A	p.V1836I	TTGCTACTGCAAC	.	65.0	24.0	55.0	0.0	.	422	.	.	.	none	.	.	PASS	Atlas-SNP
DAB2	1601	hgsc.bcm.edu	hg19	5	39390645	39390645	+	Silent	SNP	A	A	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	DAB2	NM_001343	exon5	c.T363C	p.I121I	GAAAGAAATCTTA	.	78.0	34.0	62.0	0.0	.	124	.	.	.	none	.	.	PASS	Atlas-SNP
DAB2	1601	hgsc.bcm.edu	hg19	5	39394411	39394411	+	Silent	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	DAB2	NM_001343	exon2	c.A12G	p.E4E	TTCTACTTCGTTA	.	81.0	32.0	66.0	0.0	.	124	.	.	.	none	.	.	PASS	Atlas-SNP
PLK2	10769	hgsc.bcm.edu	hg19	5	57753133	57753133	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	PLK2	NM_006622	exon7	c.G883A	p.A295T	ACCTTGCTTCCCT	.	48.0	14.0	40.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
FBN2	2201	hgsc.bcm.edu	hg19	5	127641530	127641530	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	FBN2	NM_001999	exon43	c.C5533G	p.L1845V	CCAACAGCAGGTC	.	122.0	11.0	88.0	0.0	.	858	.	.	.	none	.	.	PASS	Atlas-SNP
RUFY1	80230	hgsc.bcm.edu	hg19	5	178987050	178987050	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	RUFY1	NM_025158	exon2	c.A335G	p.E112G	TGGAGGAGCGTGC	.	32.0	17.0	38.0	0.0	.	101	.	.	.	none	.	.	PASS	Atlas-SNP
DDAH2	23564	hgsc.bcm.edu	hg19	6	31696435	31696435	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	DDAH2	NM_013974	exon3	c.G385A	p.V129I	AGAGAACGTCAGT	.	44.0	18.0	53.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
DAXX	1616	hgsc.bcm.edu	hg19	6	33287891	33287891	+	Silent	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	DAXX,NS,malignant_melanoma,0,1	DAXX	NM_001141970	exon5	c.A1398G	p.E466E	CTCCTCTTCTTCT	.	41.0	2.0	41.0	0.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
GSTA1	2938	hgsc.bcm.edu	hg19	6	52658943	52658943	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	GSTA1	NM_145740	exon5	c.T394C	p.Y132H	GGAAGTAGCGATT	.	342.0	114.0	263.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
IBTK	25998	hgsc.bcm.edu	hg19	6	82904254	82904254	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	IBTK	NM_015525	exon23	c.A3280C	p.I1094L	TGGGAATAGGCTG	.	49.0	21.0	42.0	0.0	.	128	.	.	.	none	.	.	PASS	Atlas-SNP
KLHL32	114792	hgsc.bcm.edu	hg19	6	97562031	97562031	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	KLHL32	NM_052904	exon7	c.G1000T	p.V334L	ATGCCTGTGGGAA	.	101.0	7.0	109.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
RGS17	26575	hgsc.bcm.edu	hg19	6	153332802	153332802	+	Silent	SNP	A	A	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	RGS17	NM_012419	exon5	c.T540A	p.T180T	CATTAAAGTATAT	.	44.0	10.0	38.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
PPIA	5478	hgsc.bcm.edu	hg19	7	44839397	44839397	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	PPIA	NM_021130	exon4	c.G286T	p.G96C	GGTCCTGGCATCT	.	126.0	23.0	98.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
SLC7A2	6542	hgsc.bcm.edu	hg19	8	17419589	17419589	+	Silent	SNP	G	G	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	SLC7A2	NM_001164771	exon10	c.G1761A	p.Q587Q	GAGGCAGCCCCAG	.	67.0	32.0	76.0	0.0	.	157	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA0196	9897	hgsc.bcm.edu	hg19	8	126085409	126085409	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	KIAA0196	NM_014846	exon9	c.A1136C	p.H379P	GCTGTATGAAGCA	.	90.0	39.0	82.0	0.0	.	90	.	.	.	none	.	.	PASS	Atlas-SNP
ADCY8	114	hgsc.bcm.edu	hg19	8	132052526	132052526	+	Silent	SNP	G	G	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	ADCY8	NM_001115	exon1	c.C54T	p.I18I	CGGGTGGATGGTG	.	7.0	4.0	10.0	0.0	.	291	.	.	.	none	.	.	PASS	Atlas-SNP
CYP11B1	1584	hgsc.bcm.edu	hg19	8	143957217	143957217	+	Silent	SNP	G	G	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	CYP11B1	NM_000497	exon6	c.C1032T	p.S344S	GGCCAGGCTCTCC	.	169.0	70.0	267.0	0.0	.	128	.	.	.	none	.	.	PASS	Atlas-SNP
NFX1	4799	hgsc.bcm.edu	hg19	9	33307212	33307212	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	NFX1	NM_147134	exon5	c.T1291C	p.W431R	CCTGAGTGGAGCA	.	143.0	6.0	117.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	hg19	9	78953204	78953204	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	PCSK5	NM_001190482	exon34	c.T4726C	p.C1576R	AAGGGGTGCCAGG	.	35.0	13.0	47.0	0.0	.	329	.	.	.	none	.	.	PASS	Atlas-SNP
HNRNPK	3190	hgsc.bcm.edu	hg19	9	86587099	86587099	+	Silent	SNP	G	G	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	HNRNPK	NM_031262	exon11	c.C651A	p.P217P	TTTGATGGGAGAC	.	75.0	35.0	60.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	hg19	10	17157562	17157562	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	CUBN	NM_001081	exon7	c.T628C	p.C210R	ATGCACACTGGGG	.	110.0	37.0	92.0	0.0	.	515	.	.	.	none	.	.	PASS	Atlas-SNP
IDE	3416	hgsc.bcm.edu	hg19	10	94239044	94239044	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	IDE	NM_004969	exon15	c.A1874G	p.Y625C	ATCCCATAGATGG	.	140.0	57.0	117.0	0.0	.	77	.	.	.	none	.	.	PASS	Atlas-SNP
SLC22A8	9376	hgsc.bcm.edu	hg19	11	62782340	62782340	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	SLC22A8	NM_001184732	exon2	c.A91G	p.M31V	TGGCCATGTTGAG	.	256.0	85.0	289.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
PITPNM1	9600	hgsc.bcm.edu	hg19	11	67263727	67263727	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	PITPNM1	NM_004910	exon15	c.A2239G	p.K747E	GGAACTTCGGGGC	.	73.0	36.0	110.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
ALG9	79796	hgsc.bcm.edu	hg19	11	111715419	111715419	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	ALG9	NM_001077690	exon10	c.T923C	p.I308T	CCATTAATTAAAT	.	83.0	38.0	80.0	0.0	.	77	.	.	.	none	.	.	PASS	Atlas-SNP
NCAPD2	9918	hgsc.bcm.edu	hg19	12	6638743	6638743	+	Silent	SNP	C	C	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	NCAPD2	NM_014865	exon28	c.C3637A	p.R1213R	TGTCAGCGGTTCC	.	114.0	20.0	116.0	0.0	.	99	.	.	.	none	.	.	PASS	Atlas-SNP
ESD	2098	hgsc.bcm.edu	hg19	13	47345616	47345616	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	ESD	NM_001984	exon10	c.T784C	p.Y262H	AGTAGTAGCTATG	.	83.0	21.0	52.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
ATP7B	540	hgsc.bcm.edu	hg19	13	52511445	52511445	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	ATP7B	NM_000053	exon19	c.A3988C	p.I1330L	TATAAATCAGTGC	.	76.0	33.0	83.0	0.0	.	123	.	.	.	none	.	.	PASS	Atlas-SNP
SERPINA10	51156	hgsc.bcm.edu	hg19	14	94756790	94756790	+	Silent	SNP	C	C	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	SERPINA10	NM_001100607	exon2	c.G141A	p.E47E	CTCTTCCTCCTTG	.	33.0	13.0	54.0	0.0	.	83	.	.	.	none	.	.	PASS	Atlas-SNP
RORA	6095	hgsc.bcm.edu	hg19	15	60849084	60849084	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	RORA	NM_134260	exon3	c.A263G	p.E88G	TTATCTTCCTTTT	.	169.0	83.0	129.0	0.0	.	114	.	.	.	none	.	.	PASS	Atlas-SNP
GFER	2671	hgsc.bcm.edu	hg19	16	2035934	2035934	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	GFER	NM_005262	exon3	c.A523C	p.N175H	CTGCACAATGAAG	.	201.0	121.0	185.0	0.0	.	8	.	.	.	none	.	.	PASS	Atlas-SNP
GFER	2671	hgsc.bcm.edu	hg19	16	2035967	2035967	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	GFER	NM_005262	exon3	c.T556A	p.F186I	CCTGACTTCGACT	.	171.0	101.0	182.0	1.0	.	8	.	.	.	none	.	.	PASS	Atlas-SNP
TSC2	7249	hgsc.bcm.edu	hg19	16	2134472	2134472	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.,5	TSC2	NM_000548	exon34	c.C4249T	p.R1417W	AAGGCCCGGTCAC	.	41.0	2.0	47.0	0.0	.	364	.	.	.	none	.	.	PASS	Atlas-SNP
BFAR	51283	hgsc.bcm.edu	hg19	16	14755823	14755823	+	Silent	SNP	G	G	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	BFAR	NM_016561	exon6	c.G858T	p.L286L	CTACCTGTACCTG	.	280.0	161.0	211.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
XYLT1	64131	hgsc.bcm.edu	hg19	16	17202725	17202725	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	XYLT1,NS,carcinoma,0,1	XYLT1	NM_022166	exon12	c.G2707T	p.E903X	ATCCCTCCAGCGC	.	125.0	9.0	98.0	0.0	.	147	.	.	.	none	.	.	PASS	Atlas-SNP
SLC12A4	6560	hgsc.bcm.edu	hg19	16	67982000	67982000	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	SLC12A4	NM_001145962	exon13	c.C1817T	p.T606I	TTGGGGGTCCTCA	.	263.0	64.0	244.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
CLUH	23277	hgsc.bcm.edu	hg19	17	2595388	2595388	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	.	NM_015229	exon23	c.C3447A	p.H1149Q	AAGGTGGTGGCTG	.	13.0	9.0	19.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
NDEL1	81565	hgsc.bcm.edu	hg19	17	8350137	8350137	+	Silent	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	NDEL1	NM_001025579	exon4	c.T306C	p.S102S	TTTAAGTCAGACT	.	115.0	60.0	64.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
ACLY	47	hgsc.bcm.edu	hg19	17	40025023	40025023	+	Silent	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	ACLY	NM_001096	exon28	c.A3150G	p.E1050E	AATATATTCATCA	.	180.0	46.0	110.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
CDC27	996	hgsc.bcm.edu	hg19	17	45216135	45216135	+	Silent	SNP	G	G	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	CDC27	NM_001114091	exon13	c.C1692T	p.D564D	TGTTAAGTCTTTT	.	63.0	5.0	44.0	0.0	.	337	.	.	.	none	.	.	PASS	Atlas-SNP
CSNK1D	1453	hgsc.bcm.edu	hg19	17	80202675	80202675	+	Silent	SNP	C	C	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	CSNK1D	NM_001893	exon9	c.G1230A	p.Q410Q	GACAGACTGAAGA	.	98.0	47.0	92.0	0.0	.	118	.	.	.	none	.	.	PASS	Atlas-SNP
SMARCA4	6597	hgsc.bcm.edu	hg19	19	11132430	11132430	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	SMARCA4	NM_003072	exon19	c.A2646T	p.E882D	GGACGAAGGTCAC	.	34.0	11.0	55.0	0.0	.	502	.	.	.	none	.	.	PASS	Atlas-SNP
HRC	3270	hgsc.bcm.edu	hg19	19	49657889	49657889	+	Silent	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.,1	HRC	NM_002152	exon1	c.A606G	p.E202E	CTCCTCTTCCTCC	.	46.0	2.0	59.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
PPP6R1	22870	hgsc.bcm.edu	hg19	19	55752903	55752903	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	PPP6R1	NM_014931	exon8	c.T950A	p.L317X	GCGTGCAAGGCGC	.	15.0	4.0	20.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
DNMT3B	1789	hgsc.bcm.edu	hg19	20	31375212	31375212	+	Silent	SNP	G	G	A	rs376501500		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	DNMT3B	NM_175850	exon6	c.G645A	p.P215P	GTCCCCGCAGGTG	.	87.0	50.0	79.0	0.0	.	196	.	.	.	weak	.	.	PASS	Atlas-SNP
NCOA6	23054	hgsc.bcm.edu	hg19	20	33330861	33330861	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	NCOA6	NM_014071	exon11	c.A3199G	p.R1067G	GCATTCTCTGGGA	.	349.0	214.0	220.0	0.0	.	219	.	.	.	none	.	.	PASS	Atlas-SNP
ARFGEF2	10564	hgsc.bcm.edu	hg19	20	47628617	47628617	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	ARFGEF2	NM_006420	exon28	c.C3914A	p.P1305H	AGAGGCCTCGGGT	.	215.0	55.0	95.0	0.0	.	160	.	.	.	none	.	.	PASS	Atlas-SNP
APOL6	80830	hgsc.bcm.edu	hg19	22	36055131	36055131	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	APOL6	NM_030641	exon3	c.C520G	p.L174V	TATAATCTTAGAA	.	72.0	8.0	74.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
BCOR	54880	hgsc.bcm.edu	hg19	X	39932880	39932880	+	Silent	SNP	G	G	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	BCOR	NM_001123385	exon4	c.C1719A	p.A573A	ATTGGGGGCGGGT	.	38.0	32.0	70.0	0.0	.	351	.	.	.	none	.	.	PASS	Atlas-SNP
CXorf38	159013	hgsc.bcm.edu	hg19	X	40506303	40506303	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	CXorf38	NM_144970	exon2	c.T307C	p.C103R	GCCGGCAGTTTCC	.	22.0	14.0	38.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
GJB1	2705	hgsc.bcm.edu	hg19	X	70444364	70444364	+	Silent	SNP	C	C	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	GJB1	NM_000166	exon2	c.C807T	p.T269T	TGGCACCGGGGCT	.	10.0	7.0	19.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
PASD1	139135	hgsc.bcm.edu	hg19	X	150828200	150828200	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	PASD1	NM_173493	exon10	c.G733T	p.A245S	GATATTGCAGAGG	.	40.0	4.0	32.0	0.0	.	286	.	.	.	none	.	.	PASS	Atlas-SNP
COX3	5742	hgsc.bcm.edu	hg19	MT	9450	9450	+	Nonsense_Mutation	SNP	G	G	A	rs28358272	bycluster;byfrequency;alternate_allele	TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	.	ENST00000362079	exon1	c.G244A	p.G82X	CGATACGGGATAA	.	14.0	10.0	5.0	0.0	.	.	.	.	.	alt	C|0.942;T|0.058	.	PASS	Atlas-SNP
HECTD2	143279	hgsc.bcm.edu	hg19	10	93252242	93252243	+	Splice_Site	INS	-	-	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	HECTD2	NM_182765	exon13	c.1432+1->T	.	.	.	38.0	14.0	33.0	0.0	.	60	.	0.368421	0	none	.	.	PASS	Atlas-INDEL
ACMSD	130013	hgsc.bcm.edu	hg19	2	135659397	135659398	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	ACMSD	NM_138326	exon10	c.978_979insT	p.A326fs	.	.	42.0	18.0	44.0	0.0	.	43	.	0.428571	0	none	.	.	PASS	Atlas-INDEL
STK24	8428	hgsc.bcm.edu	hg19	13	99114124	99114125	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.,1	STK24	NM_003576	exon8	c.993_994insG	p.G331fs	.	.	113.0	41.0	103.0	0.0	.	40	.	0.362832	0	none	.	.	PASS	Atlas-INDEL
ASAP3	55616	hgsc.bcm.edu	hg19	1	23779230	23779231	+	Frame_Shift_Ins	INS	-	-	GG	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	ASAP3	NM_001143778	exon4	c.383_384insCC	p.L128fs	.	.	214.0	80.0	233.0	0.0	.	65	.	0.373832	0	none	.	.	PASS	Atlas-INDEL
CCDC18	343099	hgsc.bcm.edu	hg19	1	93680444	93680444	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	CCDC18,rectum,carcinoma,0,2	CCDC18	NM_206886	exon12	c.1639delG	p.A547fs	.	.	33.0	11.0	21.0	0.0	.	93	.	0.333333	0	none	.	.	PASS	Atlas-INDEL
FBXO42	54455	hgsc.bcm.edu	hg19	1	16577319	16577320	+	Frame_Shift_Ins	INS	-	-	TATTAAA	novel		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	.	FBXO42	NM_018994	exon10	c.2000_2001insTTTAATA	p.S667_S668delinsIX	.	.	217.0	30.0	261.0	0.0	.	53	.	0.138249	0	none	.	.	PASS	Atlas-INDEL
