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
TMEM52	339456	hgsc.bcm.edu	hg19	1	1849559	1849559	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	TMEM52	NM_178545	exon5	c.T392C	p.L131P	AAGGGCAGGGGCA	.	78.0	39.0	90.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
EPHA8	2046	hgsc.bcm.edu	hg19	1	22903066	22903066	+	Silent	SNP	T	T	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	EPHA8	NM_020526	exon3	c.T516C	p.S172S	GCGCAGTGTGGGT	.	69.0	35.0	99.0	0.0	.	221	.	.	.	none	.	.	PASS	Atlas-SNP
PEX11B	8799	hgsc.bcm.edu	hg19	1	145522603	145522603	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	PEX11B	NM_003846	exon4	c.G464A	p.R155Q	GTAGCCGGCGACT	.	85.0	26.0	103.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
LYST	1130	hgsc.bcm.edu	hg19	1	235904811	235904811	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	LYST	NM_000081	exon31	c.G8269A	p.A2757T	GTGCAGCGTGGGC	.	170.0	57.0	220.0	0.0	.	370	.	.	.	none	.	.	PASS	Atlas-SNP
OR2M4	26245	hgsc.bcm.edu	hg19	1	248402822	248402822	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	OR2M4	NM_017504	exon1	c.C592G	p.L198V	GAAAGACTACTTG	.	295.0	18.0	312.0	0.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
PXDN	7837	hgsc.bcm.edu	hg19	2	1687921	1687921	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	PXDN	NM_012293	exon5	c.A419G	p.Y140C	TGCAGGTATCTAG	.	43.0	22.0	43.0	0.0	.	255	.	.	.	none	.	.	PASS	Atlas-SNP
PUM2	23369	hgsc.bcm.edu	hg19	2	20483190	20483190	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	PUM2	NM_015317	exon10	c.G1349A	p.G450D	CCAGGGCCAACCA	.	114.0	10.0	149.0	0.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
CLIP4	79745	hgsc.bcm.edu	hg19	2	29404714	29404714	+	Silent	SNP	C	C	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	CLIP4	NM_024692	exon16	c.C2073A	p.T691T	AGTGACCTATCGG	.	106.0	47.0	124.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
BIRC6	57448	hgsc.bcm.edu	hg19	2	32640306	32640306	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	BIRC6_ENST00000421745,NS,carcinoma,0,2	BIRC6	NM_016252	exon10	c.G1947T	p.M649I	ACAGATGAACAAT	.	101.0	54.0	105.0	0.0	.	838	.	.	.	none	.	.	PASS	Atlas-SNP
GCFC2	6936	hgsc.bcm.edu	hg19	2	75907421	75907421	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	.	NM_003203	exon12	c.G1710T	p.W570C	AGGATCCCAAAGG	.	109.0	52.0	124.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC141	285025	hgsc.bcm.edu	hg19	2	179720165	179720165	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	CCDC141	NM_173648	exon19	c.T2969A	p.L990X	TTTTGCAAATCCT	.	325.0	144.0	384.0	0.0	.	362	.	.	.	none	.	.	PASS	Atlas-SNP
ABI2	10152	hgsc.bcm.edu	hg19	2	204267454	204267454	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	ABI2	NM_005759	exon7	c.C988G	p.P330A	CAGAATCCAGGTT	.	145.0	9.0	148.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
ATP2B2	491	hgsc.bcm.edu	hg19	3	10400378	10400378	+	Silent	SNP	T	T	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	ATP2B2	NM_001001331	exon14	c.A2133G	p.P711P	TACCTCTGGCCGC	.	66.0	30.0	61.0	0.0	.	304	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC58	116064	hgsc.bcm.edu	hg19	3	120050190	120050190	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	LRRC58	NM_001099678	exon4	c.C973T	p.P325S	TCAGTGGGAGGCG	.	237.0	119.0	276.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
GOLGB1	2804	hgsc.bcm.edu	hg19	3	121435943	121435943	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	GOLGB1	NM_001256486	exon9	c.C929A	p.T310N	CTCAAAGTATTAT	.	150.0	62.0	156.0	0.0	.	319	.	.	.	none	.	.	PASS	Atlas-SNP
PDIA5	10954	hgsc.bcm.edu	hg19	3	122880182	122880182	+	Silent	SNP	T	T	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	PDIA5	NM_006810	exon16	c.T1359C	p.A453A	TGCCGCTGTTGAC	.	45.0	32.0	54.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
PLOD2	5352	hgsc.bcm.edu	hg19	3	145824360	145824360	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	PLOD2	NM_182943	exon5	c.C574A	p.Q192K	AGAGCTGATCATC	.	89.0	35.0	134.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
PLOD2	5352	hgsc.bcm.edu	hg19	3	145824369	145824369	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	PLOD2	NM_182943	exon5	c.G565A	p.D189N	CATCATCATTATC	.	92.0	36.0	140.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
GFM1	85476	hgsc.bcm.edu	hg19	3	158362456	158362456	+	Silent	SNP	T	T	G	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	GFM1	NM_024996	exon1	c.T33G	p.A11A	CGCGGCTCTGGGG	.	140.0	68.0	153.0	0.0	.	83	.	.	.	none	.	.	PASS	Atlas-SNP
ATP8A1	10396	hgsc.bcm.edu	hg19	4	42457327	42457327	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	ATP8A1	NM_006095	exon29	c.A2804T	p.D935V	TTGAAGTCCAGGG	.	140.0	67.0	182.0	0.0	.	206	.	.	.	none	.	.	PASS	Atlas-SNP
UGT2A1	10941	hgsc.bcm.edu	hg19	4	70512663	70512663	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	UGT2A1	NM_001252274	exon2	c.T700A	p.Y234N	TACTATAGTATGA	.	76.0	28.0	75.0	0.0	.	131	.	.	.	none	.	.	PASS	Atlas-SNP
PCDH10	57575	hgsc.bcm.edu	hg19	4	134072787	134072787	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	PCDH10	NM_032961	exon1	c.C1492G	p.L498V	GCCCAGCTTGCCT	.	71.0	25.0	125.0	0.0	.	290	.	.	.	none	.	.	PASS	Atlas-SNP
MAML3	55534	hgsc.bcm.edu	hg19	4	140640884	140640884	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	MAML3	NM_018717	exon6	c.C2998G	p.Q1000E	GTCCCTGTGGGAA	.	45.0	19.0	77.0	0.0	.	192	.	.	.	none	.	.	PASS	Atlas-SNP
SRPK1	6732	hgsc.bcm.edu	hg19	6	35803124	35803124	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	SRPK1	NM_003137	exon16	c.C1925T	p.A642V	GCAGTGGCTCTCT	.	25.0	23.0	93.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
SRPK1	6732	hgsc.bcm.edu	hg19	6	35803125	35803125	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	SRPK1	NM_003137	exon16	c.G1924A	p.A642T	CAGTGGCTCTCTT	.	25.0	23.0	94.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	hg19	6	51913390	51913390	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	PKHD1_ENST00000340994,NS,carcinoma,0,2	PKHD1	NM_170724	exon23	c.G2307C	p.E769D	AGATCCCTCTTCT	.	34.0	26.0	70.0	0.0	.	927	.	.	.	none	.	.	PASS	Atlas-SNP
CD164	8763	hgsc.bcm.edu	hg19	6	109699166	109699166	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	CD164	NM_006016	exon3	c.T268A	p.Y90N	AACAATAGCTCTC	.	17.0	12.0	34.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	hg19	7	48431545	48431545	+	Silent	SNP	C	C	T	rs189672968	bycluster;by1000genomes;alternate_allele	TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	ABCA13	NM_152701	exon38	c.C11682T	p.P3894P	CCCTCCCACTTCT	.	88.0	8.0	123.0	0.0	.	1192	.	.	.	alt	C|0.999;G|0.001	.	PASS	Atlas-SNP
MCPH1	79648	hgsc.bcm.edu	hg19	8	6266814	6266814	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	MCPH1	NM_001172575	exon2	c.G37A	p.V13I	GCCTATGTTGAAG	.	199.0	81.0	251.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
WWP1	11059	hgsc.bcm.edu	hg19	8	87410646	87410646	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	WWP1	NM_007013	exon6	c.T410C	p.V137A	TGACAGTTGTGCT	.	204.0	109.0	234.0	0.0	.	97	.	.	.	none	.	.	PASS	Atlas-SNP
PARP10	84875	hgsc.bcm.edu	hg19	8	145057194	145057194	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	PARP10	NM_032789	exon9	c.A2462T	p.E821V	AGACGCTCCAGGT	.	27.0	11.0	36.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
DAPK1	1612	hgsc.bcm.edu	hg19	9	90312114	90312114	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	DAPK1	NM_004938	exon22	c.C2606G	p.P869R	AAGAACCCATAGG	.	180.0	85.0	234.0	0.0	.	329	.	.	.	none	.	.	PASS	Atlas-SNP
LMX1B	4010	hgsc.bcm.edu	hg19	9	129456044	129456044	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	LMX1B	NM_001174146	exon6	c.G839C	p.R280P	CGCGGCGGCACCA	.	21.0	13.0	16.0	0.0	.	86	.	.	.	none	.	.	PASS	Atlas-SNP
SEC16A	9919	hgsc.bcm.edu	hg19	9	139360854	139360854	+	Silent	SNP	A	A	G	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	SEC16A	NM_014866	exon7	c.T3990C	p.D1330D	GGGGTCATCGTCA	.	73.0	28.0	79.0	0.0	.	249	.	.	.	none	.	.	PASS	Atlas-SNP
ZMYND19	116225	hgsc.bcm.edu	hg19	9	140477471	140477471	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	ZMYND19	NM_138462	exon5	c.G504T	p.E168D	GTGGCACTCATAG	.	43.0	19.0	81.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
FRMD4A	55691	hgsc.bcm.edu	hg19	10	13803654	13803654	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	FRMD4A	NM_018027	exon8	c.T457A	p.F153I	TAGAAAAATCTCC	.	144.0	65.0	194.0	0.0	.	108	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1279	26128	hgsc.bcm.edu	hg19	10	70748678	70748678	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	KIAA1279	NM_015634	exon1	c.G90C	p.K30N	GGAGAAGGAACCA	.	158.0	70.0	164.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
TEX36	387718	hgsc.bcm.edu	hg19	10	127371554	127371554	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	.	NM_001128202	exon1	c.C5A	p.T2N	CCTTTGGTCATTC	.	124.0	49.0	150.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ZBED5	58486	hgsc.bcm.edu	hg19	11	10875463	10875463	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	ZBED5	NM_021211	exon3	c.G1030T	p.D344Y	AAGCATCACTACA	.	104.0	38.0	119.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
OR4C13	283092	hgsc.bcm.edu	hg19	11	49974862	49974862	+	Silent	SNP	T	T	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	OR4C13	NM_001001955	exon1	c.T888C	p.I296I	TGCCATTAGGAAA	.	27.0	12.0	43.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
CASP4	837	hgsc.bcm.edu	hg19	11	104819264	104819264	+	Silent	SNP	C	C	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	CASP4,NS,carcinoma,0,2	CASP4	NM_001225	exon6	c.G921A	p.T307T	ACGTGGCGTTGAA	.	62.0	23.0	77.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
C11orf93	120376	hgsc.bcm.edu	hg19	11	111179041	111179041	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	C11orf93	NM_001271458	exon5	c.A635G	p.D212G	ACTTGGATGCTCT	.	51.0	25.0	53.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
NCAPD3	23310	hgsc.bcm.edu	hg19	11	134023240	134023240	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	NCAPD3	NM_015261	exon33	c.C4271T	p.T1424M	CCAAACGTGACAT	.	83.0	35.0	126.0	0.0	.	141	.	.	.	none	.	.	PASS	Atlas-SNP
BCDIN3D	144233	hgsc.bcm.edu	hg19	12	50232203	50232203	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	BCDIN3D	NM_181708	exon2	c.T830A	p.L277Q	TCTATCAGTGATT	.	22.0	7.0	24.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
NABP2	79035	hgsc.bcm.edu	hg19	12	56619250	56619250	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	.	NM_024068	exon3	c.T173C	p.V58A	ACGATGTTGGCAA	.	83.0	40.0	137.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
KIF5A	3798	hgsc.bcm.edu	hg19	12	57963875	57963875	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	KIF5A	NM_004984	exon12	c.G1223A	p.R408H	TGGTGCGCATCGC	.	47.0	21.0	65.0	0.0	.	143	.	.	.	none	.	.	PASS	Atlas-SNP
FICD	11153	hgsc.bcm.edu	hg19	12	108913231	108913231	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	FICD	NM_007076	exon3	c.G1356C	p.E452D	CAAGGAGACGCTT	.	34.0	11.0	42.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
CHAMP1	283489	hgsc.bcm.edu	hg19	13	115091586	115091586	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	.	NM_001164144	exon3	c.G2269A	p.V757I	AATCATGTAGCAG	.	97.0	45.0	139.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
NRDE2	55051	hgsc.bcm.edu	hg19	14	90755068	90755068	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	.	NM_017970	exon11	c.A2651G	p.D884G	AAACAGTCCTGCA	.	78.0	42.0	61.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
MAPK6	5597	hgsc.bcm.edu	hg19	15	52357196	52357196	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	MAPK6	NM_002748	exon6	c.A2165T	p.X722L	TGAACTAAAACAC	.	112.0	44.0	131.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
MPG	4350	hgsc.bcm.edu	hg19	16	135675	135675	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	MPG	NM_002434	exon5	c.C796A	p.H266N	GTCGGCCATGCAG	.	95.0	58.0	91.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
CRAMP1L	57585	hgsc.bcm.edu	hg19	16	1717963	1717963	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	CRAMP1L	NM_020825	exon17	c.G3103A	p.G1035S	CAGCAGGGCTCAT	.	122.0	65.0	103.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
ANKFY1	51479	hgsc.bcm.edu	hg19	17	4087143	4087143	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	ANKFY1	NM_001257999	exon13	c.C1888T	p.R630X	GGTCTCGGGAATC	.	35.0	9.0	68.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
MYO18A	399687	hgsc.bcm.edu	hg19	17	27441098	27441098	+	Silent	SNP	C	C	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	MYO18A	NM_078471	exon15	c.G2529T	p.A843A	GTCAAACGCCAGC	.	24.0	6.0	23.0	0.0	.	217	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM106A	113277	hgsc.bcm.edu	hg19	17	41365867	41365867	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	TMEM106A	NM_145041	exon4	c.G232T	p.A78S	TTGGTGGCTCTCA	.	22.0	9.0	50.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
MED13	9969	hgsc.bcm.edu	hg19	17	60038289	60038289	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	MED13	NM_005121	exon23	c.T5419A	p.C1807S	CTGTGCAAGATGC	.	180.0	106.0	166.0	0.0	.	181	.	.	.	none	.	.	PASS	Atlas-SNP
PSMC5	5705	hgsc.bcm.edu	hg19	17	61909160	61909160	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	PSMC5	NM_002805	exon11	c.C1157T	p.A386V	AGATGGCAGTAGC	.	142.0	46.0	118.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
PPAN	56342	hgsc.bcm.edu	hg19	19	10218531	10218531	+	Splice_Site	SNP	G	G	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	PPAN	NM_020230	exon4	c.342+1G>C	.	AAGAAGGTGAGAG	.	57.0	25.0	43.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
COX7A1	1346	hgsc.bcm.edu	hg19	19	36641914	36641914	+	Silent	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	COX7A1	NM_001864	exon4	c.C210T	p.S70S	GCCAAGGGAGTAC	.	74.0	35.0	109.0	0.0	.	9	.	.	.	none	.	.	PASS	Atlas-SNP
FIZ1	84922	hgsc.bcm.edu	hg19	19	56109104	56109104	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	FIZ1,NS,carcinoma,0,1	FIZ1	NM_032836	exon2	c.C128A	p.A43D	TGCCGGGCAAAGT	.	77.0	33.0	109.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
SNRPB2	6629	hgsc.bcm.edu	hg19	20	16719517	16719517	+	Silent	SNP	T	T	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	SNRPB2	NM_003092	exon5	c.T399C	p.N133N	AGCTAATACCCAA	.	210.0	131.0	166.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
SYS1	90196	hgsc.bcm.edu	hg19	20	43995569	43995569	+	Silent	SNP	T	T	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	SYS1	NM_001197129	exon5	c.T285A	p.T95T	TTTCACTGTCACT	.	145.0	47.0	135.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
CDH22	64405	hgsc.bcm.edu	hg19	20	44806794	44806794	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	CDH22	NM_021248	exon11	c.G1706T	p.R569L	TCCTGCCGGTTGA	.	69.0	37.0	74.0	0.0	.	112	.	.	.	none	.	.	PASS	Atlas-SNP
MYT1	4661	hgsc.bcm.edu	hg19	20	62843457	62843457	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	MYT1	NM_004535	exon9	c.G1483A	p.G495S	GGCCAGGGTCACG	.	29.0	21.0	25.0	0.0	.	152	.	.	.	none	.	.	PASS	Atlas-SNP
TIAM1	7074	hgsc.bcm.edu	hg19	21	32638851	32638851	+	Silent	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	TIAM1	NM_003253	exon5	c.C438T	p.G146G	CCTCCTGCCTCCC	.	62.0	30.0	52.0	0.0	.	522	.	.	.	none	.	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	hg19	21	33687358	33687358	+	Silent	SNP	A	A	G	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	URB1	NM_014825	exon39	c.T6687C	p.A2229A	CCGCTGAGCCCCC	.	88.0	41.0	110.0	0.0	.	176	.	.	.	none	.	.	PASS	Atlas-SNP
RANBP1	5902	hgsc.bcm.edu	hg19	22	20109843	20109843	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	RANBP1	NM_002882	exon3	c.G209A	p.R70Q	AGGAGCGAGGCAC	.	62.0	10.0	101.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
IGLL1	3543	hgsc.bcm.edu	hg19	22	23922377	23922377	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	IGLL1	NM_020070	exon1	c.A1G	p.M1V	GCCTCATCGGCCC	.	40.0	36.0	57.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
SGSM3	27352	hgsc.bcm.edu	hg19	22	40803843	40803843	+	Silent	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	SGSM3	NM_015705	exon14	c.G1575A	p.L525L	CGGCCTGCGAGGT	.	44.0	41.0	81.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
GPR173	54328	hgsc.bcm.edu	hg19	X	53106377	53106377	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	GPR173	NM_018969	exon2	c.A574C	p.M192L	ATGCTTATGTTGG	.	31.0	31.0	46.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
PAK3	5063	hgsc.bcm.edu	hg19	X	110385396	110385396	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	PAK3	NM_001128166	exon4	c.G248A	p.G83E	ATGTGGGGTTTGA	.	51.0	48.0	78.0	0.0	.	179	.	.	.	none	.	.	PASS	Atlas-SNP
CYTB	0	hgsc.bcm.edu	hg19	MT	14804	14804	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	.	ENST00000361789	exon1	c.G58C	p.D20H	TTCATCGACCTCC	.	11.0	10.0	50.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ABHD3	171586	hgsc.bcm.edu	hg19	18	19283591	19283591	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	ABHD3	NM_138340	exon2	c.281delT	p.L94fs	.	.	59.0	20.0	73.0	0.0	.	32	.	0.338983	0	none	.	.	PASS	Atlas-Indel,Pindel
WDR35	57539	hgsc.bcm.edu	hg19	2	20113904	20113904	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	WDR35	NM_001006657	exon27	c.3290delT	p.L1097fs	.	.	230.0	95.0	256.0	0.0	.	92	.	0.413043	0	none	.	.	PASS	Atlas-Indel,Pindel
NF2	4771	hgsc.bcm.edu	hg19	22	30050649	30050649	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	NF2	NM_181832	exon5	c.450delT	p.Y150X	.	.	105.0	98.0	156.0	0.0	.	1312	.	0.933333	0	none	.	.	PASS	Atlas-Indel,Pindel
MIOS	54468	hgsc.bcm.edu	hg19	7	7612994	7612994	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	MIOS	NM_019005	exon4	c.887delA	p.Y296fs	.	.	103.0	41.0	104.0	0.0	.	68	.	0.398058	0	none	.	.	PASS	Atlas-Indel,Pindel
TRIM65	201292	hgsc.bcm.edu	hg19	17	73887900	73887901	+	Frame_Shift_Del	DEL	AG	AG	-	rs372788583		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	TRIM65	NM_173547	exon5	c.979_980del	p.327_327del	.	.	68.0	41.0	72.0	0.0	.	23	.	0.602941	0	weak	.	.	PASS	Atlas-Indel,Pindel
WDR81	124997	hgsc.bcm.edu	hg19	17	1634163	1634164	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	WDR81	NM_001163809	exon3	c.3890_3891insA	p.S1297fs	.	.	34.0	16.0	53.0	0.0	.	180	.	0.470588	0	none	.	.	PASS	Atlas-INDEL
SGSM2	9905	hgsc.bcm.edu	hg19	17	2282478	2282480	+	In_Frame_Del	DEL	CAT	CAT	-	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	SGSM2	NM_014853	exon23	c.3047_3049del	p.1016_1017del	.	.	93.0	32.0	124.0	0.0	.	60	.	0.344086	0	none	.	.	PASS	Atlas-Indel,Pindel
RPGRIP1L	23322	hgsc.bcm.edu	hg19	16	53674983	53674984	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	RPGRIP1L	NM_001127897	exon19	c.2920_2921insT	p.K974_V975delinsX	.	.	152.0	92.0	130.0	0.0	.	118	.	0.605263	0	none	.	.	PASS	Atlas-Indel,Pindel
NXPH4	11247	hgsc.bcm.edu	hg19	12	57619136	57619140	+	Frame_Shift_Del	DEL	CTACG	CTACG	-	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	CTACG	CTACG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	NXPH4	NM_007224	exon2	c.532_536del	p.178_179del	.	.	25.0	14.0	51.0	0.0	.	40	.	0.56	0	none	.	.	PASS	Atlas-INDEL
CLEC1A	51267	hgsc.bcm.edu	hg19	12	10251473	10251480	+	Frame_Shift_Del	DEL	CCCCATCA	CCCCATCA	-	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	CCCCATCA	CCCCATCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	CLEC1A	NM_016511	exon1	c.43_50del	p.15_17del	.	.	100.0	34.0	175.0	0.0	.	48	.	0.34	0	none	.	.	PASS	Atlas-Indel,Pindel
DET1	55070	hgsc.bcm.edu	hg19	15	89074206	89074214	+	In_Frame_Del	DEL	ACCTGGAAG	ACCTGGAAG	-	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	ACCTGGAAG	ACCTGGAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	DET1	NM_017996	exon3	c.757_765del	p.253_255del	.	.	54.0	11.0	105.0	0.0	.	55	.	0.203704	0	none	.	.	PASS	Atlas-Indel,Pindel
CDCP2	200008	hgsc.bcm.edu	hg19	1	54605763	54605763	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	CDCP2	NM_201546	exon4	c.781delT	p.Y261fs	.	.	61.0	34.0	85.0	0.0	.	52	.	0.557377	0	none	.	.	PASS	Atlas-Indel,Pindel
NEFH	4744	hgsc.bcm.edu	hg19	22	29885585	29885586	+	In_Frame_Ins	INS	-	-	AAGTCCCCTGAGAAGGCC	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.,1	NEFH	NM_021076	exon4	c.1956_1957insAAGTCCCCTGAGAAGGCC	p.A652delinsAKSPEKA	.	.	38.0	19.0	43.0	0.0	.	178	.	0.5	0	none	.	.	PASS	Atlas-INDEL
MTMR14	64419	hgsc.bcm.edu	hg19	3	9730673	9730673	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	MTMR14	NM_001077525	exon16	c.1339delT	p.S447fs	.	.	21.0	11.0	39.0	0.0	.	43	.	0.52381	0	none	.	.	PASS	Atlas-INDEL
PPM1G	5496	hgsc.bcm.edu	hg19	2	27604506	27604506	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	PPM1G	NM_177983	exon10	c.1602delT	p.N534fs	.	.	218.0	101.0	231.0	0.0	.	42	.	0.463303	0	none	.	.	PASS	Atlas-Indel,Pindel
SGSM2	9905	hgsc.bcm.edu	hg19	17	2278871	2278878	+	Frame_Shift_Del	DEL	CCGGGACT	CCGGGACT	-	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	CCGGGACT	CCGGGACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	SGSM2	NM_014853	exon18	c.2185_2192del	p.729_731del	.	.	38.0	15.0	49.0	0.0	.	60	.	0.394737	0	none	.	.	PASS	Atlas-Indel,Pindel
HN1L	90861	hgsc.bcm.edu	hg19	16	1735486	1735486	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	.	HN1L	NM_144570	exon2	c.90delT	p.S30fs	.	.	73.0	48.0	79.0	0.0	.	17	.	0.657534	0	none	.	.	PASS	Atlas-Indel,Pindel
