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	TTotCov	TVarCov	NTotCov	NVarCov	TVarRat	NVarRat	dbSNP_AF	dbSNP_PopFreq	dbSNP_Strength	COSMIC_Codon	COSMIC_Gene	COSMIC_Gene_Freq	COSMIC_Site_Freq	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	Confidence	Algorithm
TBP	6908	hgsc.bcm.edu	37	6	170871044	170871046	+	In_Frame_Del	DEL	CAA	CAA	-	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	22.0	14.0	31.0	0.0	0.636364	0	.	.	none	TBP,NS,carcinoma,0,1	TBP	58	1	NM_003194	exon3	c.219_221del	p.73_74del	.	.	PASS	Atlas-Indel
HIST1H1E	3008	hgsc.bcm.edu	37	6	26156977	26156977	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	11.0	11.0	0.0	0.0	1.000	.	.	.	none	.	HIST1H1E	69	.	NM_005321	exon1	c.358delG	p.A120fs	.	.	PASS	Pindel,Atlas-Indel
KRT81	3887	hgsc.bcm.edu	37	12	52684932	52684934	+	In_Frame_Del	DEL	CTC	CTC	-	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	527.0	44.0	461.0	0.0	0.0834915	0	.	.	none	.	KRT81	46	.	NM_002281	exon1	c.317_319del	p.106_107del	.	.	PASS	Atlas-Indel
ACADVL	37	hgsc.bcm.edu	37	17	7124102	7124103	+	Frame_Shift_Del	DEL	AC	AC	-	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	13.0	13.0	0.0	0.0	1.000	.	.	.	none	ACADVL,NS,carcinoma,0,1	ACADVL	43	1	NM_001270447	exon6	c.363_364del	p.121_122del	.	.	PASS	Pindel,Atlas-Indel
KRT86	3892	hgsc.bcm.edu	37	12	52696011	52696013	+	In_Frame_Del	DEL	AGG	AGG	-	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	526.0	55.0	483.0	0.0	0.104563	0	.	.	none	.	KRT86	33	.	NM_002284	exon1	c.310_312del	p.104_104del	.	.	PASS	Atlas-Indel
USP3	9960	hgsc.bcm.edu	37	15	63829314	63829314	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	278.0	97.0	311.0	0.0	0.348921	0	.	.	none	.	USP3	37	.	NM_006537	exon3	c.G243T	p.Q81H	AGTTCAGCACACA	.	PASS	Atlas-SNP
TMEM229A	730130	hgsc.bcm.edu	37	7	123672769	123672769	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	86.0	63.0	115.0	0.0	0.732558	0	.	.	none	.	TMEM229A	31	.	NM_001136002	exon1	c.C289T	p.H97Y	GCGAGTGCAGCAG	.	PASS	Atlas-SNP
HIST1H2AE	3012	hgsc.bcm.edu	37	6	26217410	26217410	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	106.0	13.0	138.0	0.0	0.122642	0	.	.	none	.	HIST1H2AE	25	.	NM_021052	exon1	c.G208A	p.A70T	GGCAACGCGGCTC	.	PASS	Atlas-SNP
PRDM15	63977	hgsc.bcm.edu	37	21	43256244	43256244	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	133.0	28.0	159.0	0.0	0.210526	0	.	.	none	.	PRDM15	110	.	NM_022115	exon17	c.C2354T	p.S785F	TTGTAGGAAACGT	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152420390	152420390	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	129.0	23.0	163.0	0.0	0.178295	0	.	.	none	.	NEB	1697	.	NM_001271208	exon118	c.G18526A	p.E6176K	AGCGCTCATCCAG	.	PASS	Atlas-SNP
CAST	831	hgsc.bcm.edu	37	5	96073629	96073629	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	61.0	17.0	50.0	0.0	0.278689	0	.	.	none	CAST,NS,carcinoma,0,2	CAST	58	2	NM_001042440	exon9	c.C653T	p.T218M	ATACAACGTATAC	.	PASS	Atlas-SNP
H1FOO	132243	hgsc.bcm.edu	37	3	129266464	129266464	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	47.0	24.0	44.0	0.0	0.510638	0	.	.	none	.	H1FOO	20	.	NM_153833	exon2	c.C319T	p.R107C	ATGCGCCGTGGCC	.	PASS	Atlas-SNP
XRN1	54464	hgsc.bcm.edu	37	3	142123761	142123761	+	Missense_Mutation	SNP	C	C	T	rs150688965		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	157.0	32.0	146.0	0.0	0.203822	0	C|1.000;T|0.000	0.000	weak	.	XRN1	138	.	NM_001042604	exon16	c.G1871A	p.R624Q	CAACATCGTTCTA	.	PASS	Atlas-SNP
TNFRSF6B	8771	hgsc.bcm.edu	37	20	62328311	62328311	+	Missense_Mutation	SNP	G	G	T	rs61760056	alternate_allele	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	62.0	20.0	75.0	0.0	0.322581	0	.	.	alt	.	TNFRSF6B	22	.	NM_003823	exon1	c.G191T	p.R64L	GCCGCCGAGACAG	.	PASS	Atlas-SNP
SLC7A13	157724	hgsc.bcm.edu	37	8	87235201	87235201	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	86.0	16.0	122.0	0.0	0.186047	0	.	.	none	.	SLC7A13	97	.	NM_138817	exon2	c.G817T	p.D273Y	ACAAACCTGAAGA	.	PASS	Atlas-SNP
C8orf48	157773	hgsc.bcm.edu	37	8	13425042	13425042	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	65.0	16.0	75.0	0.0	0.246154	0	.	.	none	C8orf48,NS,carcinoma,-1,1	C8orf48	18	1	NM_001007090	exon1	c.T542C	p.M181T	AAAACATGAGGAC	.	PASS	Atlas-SNP
EXT1	2131	hgsc.bcm.edu	37	8	118830723	118830723	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	56.0	15.0	105.0	0.0	0.267857	0	.	.	none	.	EXT1	98	.	NM_000127	exon7	c.G1583C	p.R528P	GGCCAGCGGTGTT	.	PASS	Atlas-SNP
OLFM1	10439	hgsc.bcm.edu	37	9	138011665	138011665	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	85.0	59.0	88.0	0.0	0.694118	0	.	.	none	.	OLFM1	57	.	NM_014279	exon6	c.G1045A	p.V349M	TGGGCCGTGTACG	.	PASS	Atlas-SNP
SLC5A12	159963	hgsc.bcm.edu	37	11	26743090	26743090	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	218.0	107.0	207.0	1.0	0.490826	0.00483092	.	.	none	.	SLC5A12	134	.	NM_178498	exon1	c.A172G	p.T58A	TGGCTGTCAGAGA	.	PASS	Atlas-SNP
LRRC61	65999	hgsc.bcm.edu	37	7	150034703	150034703	+	Silent	SNP	G	G	A	rs149223172	bycluster;byfrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	33.0	16.0	39.0	0.0	0.484848	0	G|0.998;A|0.002	0.002	strong	.	LRRC61	17	.	NM_023942	exon2	c.G753A	p.A251A	CTCTGCGGGCCCC	.	PASS	Atlas-SNP
HIST1H2BM	8342	hgsc.bcm.edu	37	6	27782969	27782969	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	65.0	17.0	108.0	0.0	0.261538	0	.	.	none	HIST1H2BM,NS,malignant_melanoma,0,1	HIST1H2BM	36	1	NM_003521	exon1	c.C148T	p.H50Y	CAGGTCCACCCCG	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144994192	144994192	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	58.0	12.0	65.0	0.0	0.206897	0	.	.	none	.	PLEC	1144	.	NM_201380	exon32	c.A10208G	p.Q3403R	TGCCGCTGCTCCG	.	PASS	Atlas-SNP
FAM104B	90736	hgsc.bcm.edu	37	X	55187411	55187411	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	32.0	25.0	24.0	0.0	0.78125	0	.	.	none	.	FAM104B	28	.	NM_001166702	exon1	c.G8A	p.C3Y	CACCTGCAGGTCA	.	PASS	Atlas-SNP
LANCL3	347404	hgsc.bcm.edu	37	X	37431669	37431669	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	75.0	61.0	45.0	0.0	0.813333	0	.	.	none	.	LANCL3	42	.	NM_001170331	exon1	c.G546A	p.L182L	CGCGCTGGTGCTC	.	PASS	Atlas-SNP
ZNF626	199777	hgsc.bcm.edu	37	19	20807610	20807610	+	Missense_Mutation	SNP	G	G	C	rs201684374		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	26.0	3.0	30.0	0.0	0.115385	0	.	.	weak	ZNF626_ENST00000392298,NS,carcinoma,-1,1	ZNF626	121	1	NM_001076675	exon4	c.C1073G	p.T358R	TTATGTGTAGTAA	.	scavenged	Atlas-SNP
BPIFC	254240	hgsc.bcm.edu	37	22	32841910	32841910	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	113.0	15.0	108.0	0.0	0.132743	0	.	.	none	BPIL2,NS,carcinoma,0,1	.	.	1	NM_174932	exon4	c.G448T	p.D150Y	CAAAGTCATTTCG	.	PASS	Atlas-SNP
P2RY1	5028	hgsc.bcm.edu	37	3	152553954	152553954	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	83.0	37.0	72.0	0.0	0.445783	0	.	.	none	.	P2RY1	49	.	NM_002563	exon1	c.G383A	p.R128K	TGCAGAGGTTCAT	.	PASS	Atlas-SNP
AMZ1	155185	hgsc.bcm.edu	37	7	2748854	2748854	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	37.0	9.0	62.0	0.0	0.243243	0	.	.	none	.	AMZ1	41	.	NM_133463	exon5	c.C747T	p.A249A	CAGTGCCCTGGGG	.	PASS	Atlas-SNP
TIE1	7075	hgsc.bcm.edu	37	1	43779453	43779453	+	Silent	SNP	G	G	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	49.0	31.0	53.0	0.0	0.632653	0	.	.	none	.	TIE1	132	.	NM_005424	exon14	c.G2223T	p.L741L	AGGGCTGCAGGCT	.	PASS	Atlas-SNP
MAP2K4	6416	hgsc.bcm.edu	37	17	12044515	12044515	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	78.0	4.0	94.0	0.0	0.0512821	0	.	.	none	.	MAP2K4	176	.	NM_003010	exon11	c.T1138C	p.Y380H	GCATGCTATGTTT	.	PASS	Atlas-SNP
GABRA1	2554	hgsc.bcm.edu	37	5	161300240	161300240	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	139.0	25.0	163.0	0.0	0.179856	0	.	.	none	.	GABRA1	132	.	NM_001127643	exon6	c.G373A	p.D125N	ACTCCGGACACAT	.	PASS	Atlas-SNP
GC	2638	hgsc.bcm.edu	37	4	72620785	72620785	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	279.0	93.0	314.0	0.0	0.333333	0	.	.	none	.	GC	132	.	NM_001204307	exon10	c.A1131C	p.E377D	GAATACTTCCGGA	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126384754	126384754	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	189.0	57.0	243.0	0.0	0.301587	0	.	.	none	.	FAT4	1752	.	NM_024582	exon10	c.G11831A	p.C3944Y	GTGAATGCAACCC	.	PASS	Atlas-SNP
IRF4	3662	hgsc.bcm.edu	37	6	393159	393159	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	74.0	17.0	62.0	0.0	0.22973	0	.	.	none	.	IRF4	65	.	NM_001195286	exon2	c.C7G	p.L3V	ATGAACCTGGAGG	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109625822	109625822	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	135.0	17.0	136.0	0.0	0.125926	0	.	.	none	.	ACACB	330	.	NM_001093	exon12	c.G1999A	p.G667R	AGCTCCGGGACTG	.	PASS	Atlas-SNP
MARCH11	441061	hgsc.bcm.edu	37	5	16091041	16091041	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	95.0	10.0	106.0	0.0	0.105263	0	.	.	none	.	MARCH11	50	.	NM_001102562	exon3	c.G843A	p.Q281Q	GCAGATCTGAAAA	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230328	23230328	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	134.0	30.0	176.0	0.0	0.223881	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.C95T	p.A32V	GTCTGGCCATGGT	.	PASS	Atlas-SNP
PCNX	22990	hgsc.bcm.edu	37	14	71500228	71500228	+	Missense_Mutation	SNP	G	G	A	rs201430424	by1000genomes	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	154.0	38.0	141.0	0.0	0.246753	0	G|1.000;A|0.000	0.000	strong	.	PCNX	198	.	NM_014982	exon17	c.G3641A	p.R1214Q	TCAGCCGACAAAG	.	PASS	Atlas-SNP
KLRC4	8302	hgsc.bcm.edu	37	12	10560927	10560927	+	Splice_Site	SNP	C	C	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	189.0	53.0	239.0	0.0	0.280423	0	.	.	none	.	KLRC4	23	.	NM_013431	exon4	c.340+1G>C	.	AATGTACCTTTCT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9070331	9070331	+	Silent	SNP	C	C	T	rs186109841	bycluster;by1000genomes	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	136.0	82.0	168.0	0.0	0.602941	0	C|1.000;T|0.000	0.000	strong	.	MUC16	4315	.	NM_024690	exon3	c.G17115A	p.A5705A	TGTGTGCGCAGTG	.	PASS	Atlas-SNP
PCDH9	5101	hgsc.bcm.edu	37	13	67205459	67205459	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	70.0	25.0	88.0	0.0	0.357143	0	.	.	none	PCDH9,NS,carcinoma,+1,1	PCDH9	252	1	NM_203487	exon4	c.G3223T	p.G1075C	CACTACCCACCGG	.	PASS	Atlas-SNP
WISP1	8840	hgsc.bcm.edu	37	8	134225357	134225357	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	104.0	18.0	137.0	0.0	0.173077	0	.	.	none	.	WISP1	64	.	NM_003882	exon2	c.G320A	p.R107H	GGGACCGCCCGAG	.	PASS	Atlas-SNP
CCDC40	55036	hgsc.bcm.edu	37	17	78064015	78064015	+	Missense_Mutation	SNP	G	G	C	rs4889953	bycluster;by2hit2allele;by1000genomes	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	3.0	3.0	0.0	0.0	1	.	G|0.396;C|0.604	0.604	strong	CCDC40_ENST00000374877,NS,other,0,1	CCDC40	198	1	NM_001243342	exon18	c.G2910C	p.K970N	CACGAAGAACACG	.	scavenged	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230409	23230409	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	98.0	36.0	153.0	0.0	0.367347	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.G176A	p.S59N	GAAGCAGCCGATC	.	PASS	Atlas-SNP
KIAA1244	57221	hgsc.bcm.edu	37	6	138645253	138645253	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	43.0	7.0	80.0	0.0	0.162791	0	.	.	none	.	KIAA1244	236	.	NM_020340	exon31	c.G4963A	p.E1655K	AGTGCCGAGGCCG	.	PASS	Atlas-SNP
WHAMM	123720	hgsc.bcm.edu	37	15	83499809	83499809	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	17.0	7.0	8.0	0.0	0.411765	0	.	.	none	.	WHAMM	63	.	NM_001080435	exon9	c.C2100T	p.S700S	TGACTCCTTGGAA	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238253001	238253001	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	47.0	7.0	90.0	0.0	0.148936	0	.	.	none	COL6A3,NS,carcinoma,0,1	COL6A3	608	1	NM_004369	exon36	c.G7660A	p.A2554T	GCAAAGCGTTGAT	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138549	37138549	+	Missense_Mutation	SNP	G	G	A	rs377274719		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	56.0	6.0	53.0	1.0	0.107143	0.0188679	.	.	weak	PIM1,NS,lymphoid_neoplasm,0,3	PIM1	71	3	NM_001243186	exon2	c.G356A	p.G119D	TCCTAGGCAAGGA	.	scavenged	Atlas-SNP
TMX4	56255	hgsc.bcm.edu	37	20	7967957	7967957	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	445.0	120.0	540.0	0.0	0.269663	0	.	.	none	.	TMX4	39	.	NM_021156	exon6	c.T593C	p.V198A	CCAAAAACCAAGG	.	PASS	Atlas-SNP
ZNF208	7757	hgsc.bcm.edu	37	19	22156967	22156967	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	38.0	21.0	45.0	0.0	0.552632	0	.	.	none	.	ZNF208	817	.	NM_007153	exon4	c.G869A	p.C290Y	TTGCCACATTCTT	.	PASS	Atlas-SNP
ZBTB49	166793	hgsc.bcm.edu	37	4	4322555	4322555	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	74.0	14.0	83.0	0.0	0.189189	0	.	.	none	.	ZBTB49	63	.	NM_145291	exon8	c.G1810A	p.E604K	GCCATCGAGACCT	.	PASS	Atlas-SNP
KIAA0355	9710	hgsc.bcm.edu	37	19	34791796	34791796	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	29.0	5.0	34.0	0.0	0.172414	0	.	.	none	KIAA0355,NS,carcinoma,0,1	KIAA0355	105	1	NM_014686	exon2	c.G418A	p.A140T	GAGATCGCCAAGA	.	scavenged	Atlas-SNP
HUNK	30811	hgsc.bcm.edu	37	21	33318469	33318469	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	62.0	11.0	77.0	0.0	0.177419	0	.	.	none	.	HUNK	74	.	NM_014586	exon4	c.C732T	p.I244I	CAAAATCGATGTC	.	PASS	Atlas-SNP
ZNF785	146540	hgsc.bcm.edu	37	16	30594344	30594344	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	87.0	12.0	87.0	0.0	0.137931	0	.	.	none	ZNF785,NS,carcinoma,+1,1	ZNF785	30	1	NM_152458	exon3	c.G755A	p.G252E	TTCTCCCCGGTGT	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157931091	157931091	+	Missense_Mutation	SNP	C	C	G	rs3752368	bycluster;byfrequency;byhapmap;by1000genomes;alternate_allele	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	41.0	28.0	61.0	0.0	0.682927	0	C|0.987;T|0.013	.	alt	.	PTPRN2	243	.	NM_130843	exon7	c.G1027C	p.V343L	GGTCCACGCCTTG	.	PASS	Atlas-SNP
SLC45A1	50651	hgsc.bcm.edu	37	1	8390800	8390800	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	59.0	34.0	77.0	0.0	0.576271	0	.	.	none	.	SLC45A1	85	.	NM_001080397	exon4	c.G1247A	p.R416H	AGGACCGTGGACT	.	PASS	Atlas-SNP
ZDHHC7	55625	hgsc.bcm.edu	37	16	85024162	85024162	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	62.0	27.0	74.0	0.0	0.435484	0	.	.	none	.	ZDHHC7	55	.	NM_001145548	exon3	c.C63T	p.D21D	ATAGTTGTCATTT	.	PASS	Atlas-SNP
TECTA	7007	hgsc.bcm.edu	37	11	121008699	121008699	+	Missense_Mutation	SNP	G	G	A	rs186780639	bycluster;by1000genomes	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	123.0	28.0	102.0	0.0	0.227642	0	G|0.998;A|0.002	0.002	strong	.	TECTA	329	.	NM_005422	exon10	c.G3511A	p.V1171M	AGCATCGTGATCC	.	PASS	Atlas-SNP
IGSF8	93185	hgsc.bcm.edu	37	1	160063649	160063649	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	58.0	33.0	71.0	0.0	0.568965	0	.	.	none	.	IGSF8	59	.	NM_052868	exon3	c.G755A	p.R252Q	CGGTACCGATCGG	.	PASS	Atlas-SNP
KRT85	3891	hgsc.bcm.edu	37	12	52761179	52761179	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	99.0	26.0	91.0	0.0	0.262626	0	.	.	none	.	KRT85	78	.	NM_002283	exon1	c.G11A	p.R4H	TAGGAGCGGCACG	.	PASS	Atlas-SNP
SERINC1	57515	hgsc.bcm.edu	37	6	122766211	122766211	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	43.0	24.0	89.0	0.0	0.55814	0	.	.	none	.	SERINC1	39	.	NM_020755	exon10	c.T1340G	p.L447R	TTTGTAAGAACAA	.	PASS	Atlas-SNP
OR8I2	120586	hgsc.bcm.edu	37	11	55860964	55860964	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	104.0	29.0	101.0	0.0	0.278846	0	.	.	none	.	OR8I2	119	.	NM_001003750	exon1	c.T181C	p.F61L	ATGTACTTTTTCC	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230302	23230302	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	155.0	51.0	190.0	0.0	0.329032	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.C69T	p.R23R	GCAGCGCTGGCCC	.	PASS	Atlas-SNP
PLB1	151056	hgsc.bcm.edu	37	2	28772953	28772953	+	Splice_Site	SNP	T	T	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	87.0	26.0	121.0	0.0	0.298851	0	.	.	none	.	PLB1	255	.	NM_153021	exon16	c.1083+2T>G	.	TTGAGGTAAGGAA	.	PASS	Atlas-SNP
DGKI	9162	hgsc.bcm.edu	37	7	137092719	137092719	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	113.0	62.0	149.0	0.0	0.548673	0	.	.	none	.	DGKI	335	.	NM_004717	exon31	c.G2846C	p.G949A	CTGCCTCCATTTT	.	PASS	Atlas-SNP
NEURL4	84461	hgsc.bcm.edu	37	17	7221436	7221436	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	46.0	5.0	54.0	0.0	0.108696	0	.	.	none	.	NEURL4	192	.	NM_032442	exon25	c.C4008G	p.S1336R	CTCGCAGCTCTTT	.	PASS	Atlas-SNP
KIAA1199	57214	hgsc.bcm.edu	37	15	81188310	81188310	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	118.0	30.0	110.0	0.0	0.254237	0	.	.	none	.	KIAA1199	118	.	NM_018689	exon11	c.C1320T	p.V440V	CCTGGTCATTGCC	.	PASS	Atlas-SNP
HIST1H1E	3008	hgsc.bcm.edu	37	6	26156757	26156757	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	60.0	8.0	66.0	0.0	0.133333	0	.	.	none	HIST1H1E,NS,lymphoid_neoplasm,-1,1	HIST1H1E	69	1	NM_005321	exon1	c.G139C	p.A47P	ACTAAAGCTGTTG	.	PASS	Atlas-SNP
SSR1	6745	hgsc.bcm.edu	37	6	7295651	7295651	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	103.0	11.0	106.0	0.0	0.106796	0	.	.	none	.	SSR1	21	.	NM_003144	exon7	c.T767C	p.I256T	TGAGGAATCCAAC	.	PASS	Atlas-SNP
EPB41L1	2036	hgsc.bcm.edu	37	20	34775618	34775618	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	78.0	18.0	81.0	0.0	0.230769	0	.	.	none	.	EPB41L1	111	.	NM_001258329	exon9	c.C806T	p.A269V	GAGAAGCAGAAAT	.	PASS	Atlas-SNP
FHDC1	85462	hgsc.bcm.edu	37	4	153875426	153875426	+	Silent	SNP	A	A	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	93.0	18.0	105.0	0.0	0.193548	0	.	.	none	.	FHDC1	102	.	NM_033393	exon3	c.A618G	p.S206S	TGGATCAGAGACC	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44152070	44152070	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	63.0	9.0	83.0	0.0	0.142857	0	.	.	none	.	LOXHD1	367	.	NM_144612	exon15	c.G2026A	p.D676N	TGCTGTCACTGGG	.	PASS	Atlas-SNP
GPR88	54112	hgsc.bcm.edu	37	1	101004706	101004706	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	94.0	40.0	127.0	0.0	0.425532	0	.	.	none	.	GPR88	17	.	NM_022049	exon2	c.C184T	p.L62L	CGAAAGCTGCAGA	.	PASS	Atlas-SNP
REEP1	65055	hgsc.bcm.edu	37	2	86459825	86459825	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	33.0	9.0	34.0	0.0	0.272727	0	.	.	none	.	REEP1	22	.	NM_001164730	exon6	c.C539T	p.P180L	GACCCCGGTGGTG	.	PASS	Atlas-SNP
UBQLN1	29979	hgsc.bcm.edu	37	9	86322427	86322427	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	79.0	12.0	103.0	0.0	0.151899	0	.	.	none	.	UBQLN1	49	.	NM_053067	exon1	c.C168G	p.S56R	GACGGAGCTATTC	.	PASS	Atlas-SNP
SOHLH1	402381	hgsc.bcm.edu	37	9	138590933	138590933	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	52.0	38.0	69.0	0.0	0.730769	0	.	.	none	.	SOHLH1	70	.	NM_001012415	exon2	c.G105A	p.S35S	CCGGGCCGAGTCC	.	PASS	Atlas-SNP
C7	730	hgsc.bcm.edu	37	5	40936442	40936442	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	124.0	34.0	130.0	0.0	0.274194	0	.	.	none	.	C7	136	.	NM_000587	exon5	c.C283T	p.Q95X	TCAGGTCAGTGCA	.	PASS	Atlas-SNP
NRXN3	9369	hgsc.bcm.edu	37	14	79432416	79432416	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	87.0	17.0	87.0	0.0	0.195402	0	.	.	none	.	NRXN3	342	.	NM_004796	exon9	c.C1325T	p.T442M	TTGAAACGGGAAT	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115412746	115412746	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	77.0	28.0	76.0	0.0	0.363636	0	.	.	none	.	NRAP	208	.	NM_001261463	exon6	c.T518C	p.M173T	GTGATCATGGCTG	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138791	37138791	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	143.0	28.0	160.0	0.0	0.195804	0	.	.	none	PIM1,NS,carcinoma,0,1	PIM1	71	1	NM_001243186	exon3	c.C497T	p.S166F	GGATTTCCGACTG	.	PASS	Atlas-SNP
CDC16	8881	hgsc.bcm.edu	37	13	115004951	115004951	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	106.0	19.0	95.0	0.0	0.179245	0	.	.	none	.	CDC16	50	.	NM_003903	exon5	c.A367T	p.M123L	TGGGAAATGTCAC	.	PASS	Atlas-SNP
MAGEB5	347541	hgsc.bcm.edu	37	X	26236119	26236119	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	174.0	40.0	152.0	0.0	0.229885	0	.	.	none	.	MAGEB5	5	.	NM_001271752	exon2	c.C701A	p.S234X	TCTCATCACAATA	.	PASS	Atlas-SNP
ADPRM	56985	hgsc.bcm.edu	37	17	10608524	10608524	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	100.0	6.0	157.0	0.0	0.06	0	.	.	none	.	.	.	.	NM_020233	exon2	c.T281C	p.M94T	TTGTTATGGACAT	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126329648	126329648	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	118.0	14.0	143.0	0.0	0.118644	0	.	.	none	.	FAT4	1752	.	NM_024582	exon4	c.T5619A	p.N1873K	TGTGAATGGAGAA	.	PASS	Atlas-SNP
MYO3A	53904	hgsc.bcm.edu	37	10	26446318	26446318	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	153.0	71.0	169.0	0.0	0.464052	0	.	.	none	MYO3A,caecum,carcinoma,0,3	MYO3A	371	3	NM_017433	exon26	c.G2873A	p.R958H	GTGAGCGTCAGGC	.	PASS	Atlas-SNP
DSC3	1825	hgsc.bcm.edu	37	18	28576767	28576767	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	65.0	16.0	94.0	0.0	0.246154	0	.	.	none	DSC3_ENST00000434452,colon,carcinoma,-1,2	DSC3	225	2	NM_024423	exon15	c.G2483A	p.R828H	CCGAGACGGGGTT	.	PASS	Atlas-SNP
CNOT3	4849	hgsc.bcm.edu	37	19	54648016	54648016	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	166.0	35.0	165.0	0.0	0.210843	0	.	.	none	.	CNOT3	133	.	NM_014516	exon7	c.G431A	p.S144N	TTGAGAGTGAAGT	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138953	37138953	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	87.0	23.0	97.0	0.0	0.264368	0	.	.	none	.	PIM1	71	.	NM_001243186	exon4	c.C566A	p.S189X	TGAGCTCGGGTTT	.	PASS	Atlas-SNP
CNTNAP5	129684	hgsc.bcm.edu	37	2	125627339	125627339	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	150.0	15.0	201.0	0.0	0.1	0	.	.	none	.	CNTNAP5	405	.	NM_130773	exon21	c.G3433T	p.E1145X	GTCACAGGTATGT	.	PASS	Atlas-SNP
HIST1H2AM	8336	hgsc.bcm.edu	37	6	27860580	27860580	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	182.0	25.0	172.0	0.0	0.137363	0	.	.	none	.	HIST1H2AM	27	.	NM_003514	exon1	c.G348A	p.L116L	GGGGAGCAGTACG	.	PASS	Atlas-SNP
RASSF10	644943	hgsc.bcm.edu	37	11	13031324	13031324	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	29.0	9.0	28.0	0.0	0.310345	0	.	.	none	.	.	.	.	NM_001080521	exon1	c.C201T	p.P67P	CGAACCCCCGAAC	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73646370	73646370	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	92.0	28.0	98.0	0.0	0.304348	0	.	.	none	.	ALMS1	384	.	NM_015120	exon3	c.G570A	p.L190L	CTCTCTGGAGGAG	.	PASS	Atlas-SNP
FUT8	2530	hgsc.bcm.edu	37	14	66209049	66209049	+	Missense_Mutation	SNP	C	C	A	rs149328619	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	147.0	6.0	134.0	0.0	0.0408163	0	C|0.999;T|0.001	.	alt	.	FUT8	101	.	NM_178155	exon11	c.C1649A	p.T550K	GAAGGACGGGCCT	.	PASS	Atlas-SNP
OR4C3	256144	hgsc.bcm.edu	37	11	48346815	48346815	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	109.0	9.0	103.0	0.0	0.0825688	0	.	.	none	OR4C3,mouth,carcinoma,0,1	OR4C3	75	1	NM_001004702	exon1	c.C323A	p.A108D	TCATTGCTGACTC	.	PASS	Atlas-SNP
PRKCG	5582	hgsc.bcm.edu	37	19	54392899	54392899	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	84.0	60.0	88.0	0.0	0.714286	0	.	.	none	.	PRKCG	246	.	NM_002739	exon4	c.G293A	p.R98Q	ACCCCCGGAACAA	.	PASS	Atlas-SNP
NUDT22	84304	hgsc.bcm.edu	37	11	63994599	63994599	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	42.0	14.0	31.0	0.0	0.333333	0	.	.	none	.	NUDT22	24	.	NM_001128613	exon2	c.C475A	p.P159T	CCTGAGCCTCAGG	.	PASS	Atlas-SNP
MSH3	4437	hgsc.bcm.edu	37	5	79950750	79950750	+	Silent	SNP	T	T	G	rs1047489	bycluster	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	18.0	15.0	2.0	0.0	0.833333	0	.	.	weak	.	MSH3	129	.	NM_002439	exon1	c.T204G	p.A68A	CCCAGCTCCCGCC	.	PASS	Atlas-SNP
DPP7	29952	hgsc.bcm.edu	37	9	140009157	140009157	+	Silent	SNP	G	G	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	6.0	6.0	3.0	0.0	1	0	.	.	none	.	DPP7	22	.	NM_013379	exon1	c.C9A	p.S3S	GGGAGCGGAGCCC	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23523413	23523413	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	140.0	45.0	127.0	0.0	0.321429	0	.	.	none	.	PRDM9	344	.	NM_020227	exon9	c.G896T	p.R299I	AGGGGAGAAACTG	.	PASS	Atlas-SNP
CPNE8	144402	hgsc.bcm.edu	37	12	39299291	39299291	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	32.0	11.0	49.0	0.0	0.34375	0	.	.	none	.	CPNE8	66	.	NM_153634	exon1	c.C46A	p.Q16K	TCAGCTGGTTCAA	.	PASS	Atlas-SNP
TRPM3	80036	hgsc.bcm.edu	37	9	73461506	73461506	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	79.0	58.0	101.0	0.0	0.734177	0	.	.	none	.	TRPM3	700	.	NM_001007471	exon4	c.A464G	p.Y155C	CGCACATACTGGA	.	PASS	Atlas-SNP
MTRR	4552	hgsc.bcm.edu	37	5	7875473	7875473	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	105.0	35.0	142.0	0.0	0.333333	0	.	.	none	.	MTRR	74	.	NM_024010	exon4	c.C467T	p.A156V	GACATGCAGATGA	.	PASS	Atlas-SNP
STAT3	6774	hgsc.bcm.edu	37	17	40485746	40485746	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	71.0	24.0	66.0	0.0	0.338028	0	.	.	none	.	STAT3	268	.	NM_003150	exon10	c.C994T	p.H332Y	CAGGATGCATGGG	.	PASS	Atlas-SNP
NEFL	4747	hgsc.bcm.edu	37	8	24813640	24813640	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	37.0	15.0	34.0	0.0	0.405405	0	.	.	none	.	NEFL	47	.	NM_006158	exon1	c.C390T	p.S130S	TGGCTCGGAGTGC	.	PASS	Atlas-SNP
CPXCR1	53336	hgsc.bcm.edu	37	X	88009293	88009293	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	170.0	51.0	166.0	0.0	0.3	0	.	.	none	.	CPXCR1	83	.	NM_001184771	exon3	c.A878T	p.Q293L	TAAGACAACATTC	.	PASS	Atlas-SNP
NOP9	161424	hgsc.bcm.edu	37	14	24771450	24771450	+	Silent	SNP	A	A	G	rs182491838	bycluster;by1000genomes	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	47.0	18.0	50.0	0.0	0.382979	0	A|1.000;G|0.000	0.000	strong	.	.	.	.	NM_174913	exon5	c.A963G	p.L321L	ACTGCTATTTCTC	.	PASS	Atlas-SNP
ANKS6	203286	hgsc.bcm.edu	37	9	101498863	101498863	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	102.0	28.0	85.0	0.0	0.27451	0	.	.	none	.	ANKS6	59	.	NM_173551	exon15	c.C2554T	p.H852Y	AAGAGTGAAAGTT	.	PASS	Atlas-SNP
CNGB3	54714	hgsc.bcm.edu	37	8	87638258	87638258	+	Missense_Mutation	SNP	C	C	A	rs150642676	bycluster;by1000genomes;alternate_allele	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	98.0	17.0	144.0	0.0	0.173469	0	C|0.999;T|0.001	.	alt	.	CNGB3	176	.	NM_019098	exon13	c.G1531T	p.A511S	CAATGGCGAGGGC	.	PASS	Atlas-SNP
TYMP	1890	hgsc.bcm.edu	37	22	50966942	50966942	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	44.0	14.0	45.0	0.0	0.318182	0	.	.	none	TYMP,NS,carcinoma,-1,1	TYMP	25	1	NM_001257989	exon4	c.A515T	p.Q172L	CGTACCTGCTCTG	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187530476	187530476	+	Splice_Site	SNP	T	T	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	106.0	37.0	93.0	0.0	0.349057	0	.	.	none	.	FAT1	500	.	NM_005245	exon17	c.10069-2A>G	.	ATAACCTAGAACA	.	PASS	Atlas-SNP
PLA2G4C	8605	hgsc.bcm.edu	37	19	48609797	48609797	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	65.0	41.0	82.0	0.0	0.630769	0	.	.	none	.	PLA2G4C	76	.	NM_001159322	exon2	c.C51T	p.T17T	CACTGCGGTCAGA	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230326	23230326	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	139.0	31.0	180.0	0.0	0.223022	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.G93A	p.L31L	GGGTCTGGCCATG	.	PASS	Atlas-SNP
SLC45A1	50651	hgsc.bcm.edu	37	1	8399646	8399646	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	95.0	4.0	99.0	0.0	0.0421053	0	.	.	none	.	SLC45A1	85	.	NM_001080397	exon7	c.T1868C	p.L623P	CCACCCTCTCCAG	.	PASS	Atlas-SNP
OR12D2	26529	hgsc.bcm.edu	37	6	29365028	29365028	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	101.0	17.0	99.0	0.0	0.168317	0	.	.	none	.	OR12D2	42	.	NM_013936	exon1	c.G552A	p.K184K	GCTAAAGCTGGCC	.	PASS	Atlas-SNP
GPR116	221395	hgsc.bcm.edu	37	6	46845956	46845956	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	171.0	29.0	171.0	0.0	0.169591	0	.	.	none	GPR116,NS,malignant_melanoma,-1,1	GPR116	133	1	NM_015234	exon10	c.G1223T	p.G408V	ATTTTTCCTTCCT	.	PASS	Atlas-SNP
BCL11B	64919	hgsc.bcm.edu	37	14	99640652	99640652	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	25.0	6.0	24.0	0.0	0.24	0	.	.	none	BCL11B,NS,carcinoma,+1,2	BCL11B	108	2	NM_138576	exon4	c.C2521T	p.R841C	TGTGGCGCGTGAG	.	PASS	Atlas-SNP
FLT1	2321	hgsc.bcm.edu	37	13	28971155	28971155	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	90.0	16.0	87.0	0.0	0.177778	0	.	.	none	.	FLT1	393	.	NM_002019	exon12	c.T1602G	p.I534M	TATGCAAATGTAG	.	PASS	Atlas-SNP
FCRL3	115352	hgsc.bcm.edu	37	1	157665375	157665375	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	100.0	56.0	139.0	0.0	0.56	0	.	.	none	.	FCRL3	163	.	NM_052939	exon8	c.C1155T	p.L385L	GAAGGTGAGGACA	.	PASS	Atlas-SNP
ZC3H13	23091	hgsc.bcm.edu	37	13	46543189	46543189	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	94.0	11.0	120.0	0.0	0.117021	0	.	.	none	ZC3H13,colon,carcinoma,0,1	ZC3H13	197	1	NM_015070	exon14	c.C3490T	p.R1164X	CTACTCGTGTTCT	.	PASS	Atlas-SNP
FZD10	11211	hgsc.bcm.edu	37	12	130648918	130648918	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	77.0	10.0	100.0	0.0	0.12987	0	.	.	none	.	FZD10	95	.	NM_007197	exon1	c.G1431A	p.A477A	GGCGGCGCAGCAC	.	PASS	Atlas-SNP
TCERG1L	256536	hgsc.bcm.edu	37	10	132896590	132896590	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	45.0	14.0	46.0	0.0	0.311111	0	.	.	none	.	TCERG1L	91	.	NM_174937	exon11	c.A1583C	p.E528A	GATTCCTCTAGAA	.	PASS	Atlas-SNP
ACOT1	641371	hgsc.bcm.edu	37	14	74008216	74008216	+	Silent	SNP	C	C	G	rs201966235	bycluster;by1000genomes	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	5.0	5.0	3.0	1.0	1	0.333333	C|0.785;G|0.215	0.215	strong	ACOT1,NS,carcinoma,0,1	ACOT1	12	1	NM_001037161	exon2	c.C477G	p.G159G	TCCTGGCATTGTG	.	scavenged	Atlas-SNP
VPS13B	157680	hgsc.bcm.edu	37	8	100829995	100829995	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	90.0	21.0	115.0	0.0	0.233333	0	.	.	none	.	VPS13B	811	.	NM_017890	exon45	c.G8400A	p.L2800L	GTGCCTGGAATCC	.	PASS	Atlas-SNP
BNC1	646	hgsc.bcm.edu	37	15	83932823	83932823	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	124.0	33.0	159.0	0.0	0.266129	0	.	.	none	.	BNC1	149	.	NM_001717	exon4	c.A1180T	p.M394L	ACACCATGTTACA	.	PASS	Atlas-SNP
ROBO2	6092	hgsc.bcm.edu	37	3	77693936	77693936	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	58.0	23.0	84.0	1.0	0.396552	0.0119048	.	.	none	ROBO2_ENST00000487694,colon,carcinoma,-1,3	ROBO2	527	3	NM_002942	exon25	c.G4016T	p.G1339V	CTAAGGGATCCAC	.	scavenged	Atlas-SNP
ASIC2	40	hgsc.bcm.edu	37	17	31618815	31618815	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	36.0	4.0	48.0	0.0	0.111111	0	.	.	none	.	.	.	.	NM_183377	exon1	c.C319T	p.R107C	GCAAGCGGTTCGA	.	PASS	Atlas-SNP
IRF2	3660	hgsc.bcm.edu	37	4	185309962	185309962	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	70.0	19.0	64.0	0.0	0.271429	0	.	.	none	IRF2,caecum,carcinoma,0,1	IRF2	53	1	NM_002199	exon9	c.G1000A	p.V334I	TGATGACGCTGGC	.	PASS	Atlas-SNP
TBL1XR1	79718	hgsc.bcm.edu	37	3	176750838	176750838	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	316.0	124.0	278.0	0.0	0.392405	0	.	.	none	.	TBL1XR1	87	.	NM_024665	exon14	c.A1337G	p.Y446C	ACACTGTACACAG	.	PASS	Atlas-SNP
BTG1	694	hgsc.bcm.edu	37	12	92539171	92539171	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	110.0	48.0	91.0	0.0	0.436364	0	.	.	none	.	BTG1	30	.	NM_001731	exon1	c.G141A	p.L47L	TGCCAGCAGCTCC	.	PASS	Atlas-SNP
ZNF319	57567	hgsc.bcm.edu	37	16	58030541	58030541	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	60.0	7.0	42.0	0.0	0.116667	0	.	.	none	.	ZNF319	42	.	NM_020807	exon2	c.G1629A	p.K543K	TACACACTTGAAC	.	PASS	Atlas-SNP
RAPGEF4	11069	hgsc.bcm.edu	37	2	173882186	173882186	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	50.0	10.0	60.0	0.0	0.2	0	.	.	none	RAPGEF4,NS,carcinoma,0,2	RAPGEF4	103	2	NM_007023	exon21	c.C1962T	p.G654G	TACGGGCGATGAG	.	PASS	Atlas-SNP
GABRP	2568	hgsc.bcm.edu	37	5	170235620	170235620	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	87.0	13.0	101.0	0.0	0.149425	0	.	.	none	.	GABRP	65	.	NM_014211	exon8	c.G696A	p.L232L	TAGATTGGTCTTA	.	PASS	Atlas-SNP
DLGAP2	9228	hgsc.bcm.edu	37	8	1624701	1624701	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	91.0	37.0	107.0	0.0	0.406593	0	.	.	none	.	DLGAP2	292	.	NM_004745	exon8	c.G1965A	p.V655V	TTAGGTGGAAACG	.	PASS	Atlas-SNP
FCHO1	23149	hgsc.bcm.edu	37	19	17897428	17897428	+	Silent	SNP	C	C	T	rs370950809		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	35.0	27.0	39.0	0.0	0.771429	0	.	.	weak	.	FCHO1	69	.	NM_001161358	exon26	c.C2472T	p.S824S	TGTGTCCGAGGCA	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90423000	90423000	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	54.0	25.0	70.0	0.0	0.462963	0	.	.	none	.	MDN1	478	.	NM_014611	exon47	c.C7085T	p.S2362F	GATACAGAAGATG	.	PASS	Atlas-SNP
TAS2R39	259285	hgsc.bcm.edu	37	7	142881334	142881334	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	82.0	57.0	117.0	0.0	0.695122	0	.	.	none	.	TAS2R39	42	.	NM_176881	exon1	c.G823A	p.A275T	TTCAATGCAGTTG	.	PASS	Atlas-SNP
NARFL	64428	hgsc.bcm.edu	37	16	787323	787323	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	67.0	32.0	77.0	0.0	0.477612	0	.	.	none	NARFL,NS,carcinoma,0,1	NARFL	31	1	NM_022493	exon3	c.G169C	p.G57R	GGGTCCCGCCGTC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73498388	73498388	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	33.0	7.0	41.0	0.0	0.212121	0	.	.	none	.	CDH23	365	.	NM_022124	exon33	c.C4343T	p.A1448V	CTGATGCTGGCAG	.	PASS	Atlas-SNP
PER2	8864	hgsc.bcm.edu	37	2	239162025	239162025	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	53.0	22.0	64.0	0.0	0.415094	0	.	.	none	.	PER2	85	.	NM_022817	exon19	c.C2639T	p.A880V	GGCACAGCAGGCA	.	PASS	Atlas-SNP
RIPK4	54101	hgsc.bcm.edu	37	21	43161063	43161063	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	45.0	18.0	47.0	0.0	0.4	0	.	.	none	.	RIPK4	151	.	NM_020639	exon8	c.C2290A	p.Q764K	GGCTCTGCAGGTT	.	PASS	Atlas-SNP
ARHGAP21	57584	hgsc.bcm.edu	37	10	24880821	24880821	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	72.0	9.0	119.0	0.0	0.125	0	.	.	none	.	ARHGAP21	185	.	NM_020824	exon22	c.C3997T	p.Q1333X	CGTGCTGGATGAG	.	PASS	Atlas-SNP
HIST1H1E	3008	hgsc.bcm.edu	37	6	26156929	26156929	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	127.0	43.0	157.0	0.0	0.338583	0	.	.	none	.	HIST1H1E	69	.	NM_005321	exon1	c.C311G	p.S104C	CGGGTTCCTTCAA	.	PASS	Atlas-SNP
CD79B	974	hgsc.bcm.edu	37	17	62006833	62006833	+	Silent	SNP	A	A	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	69.0	27.0	80.0	0.0	0.391304	0	.	.	none	.	CD79B	38	.	NM_001039933	exon5	c.T555C	p.D185D	GCTGTCATCCTGG	.	PASS	Atlas-SNP
GGA2	23062	hgsc.bcm.edu	37	16	23498055	23498055	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	102.0	25.0	104.0	0.0	0.245098	0	.	.	none	.	GGA2	49	.	NM_015044	exon7	c.G636A	p.R212R	GATTAACCGGTTT	.	PASS	Atlas-SNP
SLITRK1	114798	hgsc.bcm.edu	37	13	84454325	84454325	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	84.0	32.0	107.0	1.0	0.380952	0.00934579	.	.	none	SLITRK1,NS,carcinoma,0,1	SLITRK1	196	1	NM_052910	exon1	c.C1318T	p.R440W	TCTCCCGGGACAG	.	scavenged	Atlas-SNP
SPDEF	25803	hgsc.bcm.edu	37	6	34511927	34511927	+	Silent	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	43.0	9.0	76.0	0.0	0.209302	0	.	.	none	SPDEF,colon,carcinoma,0,1	SPDEF	34	1	NM_001252294	exon2	c.G306A	p.A102A	GCTGCCCGCTGGG	.	PASS	Atlas-SNP
NFKB2	4791	hgsc.bcm.edu	37	10	104160708	104160708	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	90.0	27.0	97.0	2.0	0.3	0.0206186	.	.	none	NFKB2,NS,carcinoma,+1,1	NFKB2	48	1	NM_001077494	exon18	c.G1973A	p.R658Q	AGCTCCGGGCCAA	.	scavenged	Atlas-SNP
HTR2A	3356	hgsc.bcm.edu	37	13	47409325	47409325	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	113.0	17.0	109.0	0.0	0.150442	0	.	.	none	.	HTR2A	98	.	NM_000621	exon4	c.G1063T	p.E355X	CATCCTCATTGCA	.	PASS	Atlas-SNP
ITIH1	3697	hgsc.bcm.edu	37	3	52817273	52817273	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	113.0	50.0	136.0	0.0	0.442478	0	.	.	none	.	ITIH1	108	.	NM_002215	exon10	c.G1143T	p.L381F	GATCTTGAACCAA	.	PASS	Atlas-SNP
NR0B1	190	hgsc.bcm.edu	37	X	30326889	30326889	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	128.0	99.0	86.0	0.0	0.773438	0	.	.	none	.	NR0B1	61	.	NM_000475	exon1	c.C592T	p.R198C	AGCAGCGGTACAG	.	PASS	Atlas-SNP
CASP1	834	hgsc.bcm.edu	37	11	104899975	104899975	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	89.0	15.0	75.0	0.0	0.168539	0	.	.	none	.	CASP1	53	.	NM_001257118	exon7	c.G882A	p.W294X	TTTAAACCACACC	.	PASS	Atlas-SNP
FARP1	10160	hgsc.bcm.edu	37	13	99091388	99091388	+	Missense_Mutation	SNP	C	C	T	rs142251812		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	89.0	32.0	120.0	0.0	0.359551	0	C|1.000;T|0.000	0.000	weak	FARP1,scalp,carcinoma,0,1	FARP1	207	1	NM_005766	exon21	c.C2371T	p.R791W	ACGAGCCGGGGGC	.	PASS	Atlas-SNP
C9orf41	138199	hgsc.bcm.edu	37	9	77614780	77614780	+	Silent	SNP	A	A	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	108.0	32.0	159.0	0.0	0.296296	0	.	.	none	.	C9orf41	57	.	NM_152420	exon4	c.T597C	p.P199P	TTTAGAAGGATCC	.	PASS	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	228322	228322	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	56.0	4.0	57.0	0.0	0.0714286	0	.	.	none	.	SDHA	80	.	NM_004168	exon6	c.A644G	p.Y215C	CCAGCTATTTTGT	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230359	23230359	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	124.0	29.0	167.0	0.0	0.233871	0	.	.	none	.	IGLL5	26	.	NM_001256296	exon1	c.G20A	p.W7X	CCCAATGGTTGCA	.	PASS	Atlas-SNP
LRCH1	23143	hgsc.bcm.edu	37	13	47224430	47224430	+	Silent	SNP	C	C	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	98.0	18.0	92.0	0.0	0.183673	0	.	.	none	.	LRCH1	104	.	NM_015116	exon2	c.C402A	p.V134V	CAGAGTCATTCCT	.	PASS	Atlas-SNP
GLI2	2736	hgsc.bcm.edu	37	2	121708912	121708912	+	Silent	SNP	C	C	T	rs140711756		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	111.0	21.0	159.0	0.0	0.189189	0	C|1.000;T|0.000	0.000	weak	GLI2,NS,adenocarcinoma,0,1	GLI2	187	1	NM_005270	exon3	c.C348T	p.N116N	CTTCAACGCCCCC	.	PASS	Atlas-SNP
NMUR1	10316	hgsc.bcm.edu	37	2	232393132	232393132	+	Silent	SNP	G	G	A	rs370312738		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	48.0	14.0	51.0	0.0	0.291667	0	.	.	weak	.	NMUR1	46	.	NM_006056	exon2	c.C600T	p.H200H	GATGCCGTGCAGG	.	PASS	Atlas-SNP
CTNNA3	29119	hgsc.bcm.edu	37	10	68940122	68940122	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	78.0	11.0	74.0	0.0	0.141026	0	.	.	none	CTNNA3_ENST00000433211,colon,carcinoma,0,2	CTNNA3	401	2	NM_013266	exon7	c.G1000A	p.A334T	GAATGGCGTTGCA	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230389	23230389	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	115.0	22.0	163.0	0.0	0.191304	0	.	.	none	.	IGLL5	26	.	NM_001256296	exon1	c.T50A	p.L17Q	AGACCCTGGAGCC	.	PASS	Atlas-SNP
HIST1H4K	8362	hgsc.bcm.edu	37	6	27799131	27799131	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	292.0	23.0	358.0	0.0	0.0787671	0	.	.	none	HIST1H4K,NS,carcinoma,+2,1	HIST1H4K	15	1	NM_003541	exon1	c.C175T	p.L59L	CCTTCAGCACCCC	.	scavenged	Atlas-SNP
CTTN	2017	hgsc.bcm.edu	37	11	70265880	70265880	+	Silent	SNP	C	C	T	rs35414621	bycluster;byfrequency;by1000genomes	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	150.0	31.0	136.0	0.0	0.206667	0	C|0.993;T|0.007	0.007	strong	.	CTTN	162	.	NM_001184740	exon9	c.C597T	p.Y199Y	CAAATACGGTATC	.	PASS	Atlas-SNP
GPR101	83550	hgsc.bcm.edu	37	X	136113230	136113230	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	46.0	38.0	20.0	0.0	0.826087	0	.	.	none	.	GPR101	96	.	NM_054021	exon1	c.G604A	p.V202I	GAATGACGATGAA	.	PASS	Atlas-SNP
FAM212B	55924	hgsc.bcm.edu	37	1	112269753	112269753	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	56.0	39.0	88.0	0.0	0.696429	0	.	.	none	.	FAM212B	17	.	NM_019099	exon2	c.G731A	p.R244H	TGTGAGCGGCCGG	.	PASS	Atlas-SNP
PLCB1	23236	hgsc.bcm.edu	37	20	8741074	8741074	+	Silent	SNP	A	A	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	461.0	75.0	521.0	0.0	0.16269	0	.	.	none	.	PLCB1	394	.	NM_015192	exon25	c.C2677C	p.Q893Q	CCTGCCAAAACAG	.	PASS	Atlas-SNP
RNF39	80352	hgsc.bcm.edu	37	6	30039324	30039324	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	16.0	6.0	12.0	0.0	0.375	0	.	.	none	.	RNF39	27	.	NM_025236	exon4	c.C827T	p.A276V	CCCTGCGCACCCA	.	PASS	Atlas-SNP
LTBP2	4053	hgsc.bcm.edu	37	14	74970174	74970174	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	43.0	9.0	43.0	0.0	0.209302	0	.	.	none	.	LTBP2	158	.	NM_000428	exon32	c.C4718T	p.T1573M	TCACCCGTGCTGC	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145010055	145010055	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	68.0	13.0	71.0	0.0	0.191176	0	.	.	none	.	PLEC	1144	.	NM_201380	exon6	c.G974A	p.R325K	CCGTCTCTCCAGC	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230360	23230360	+	Nonsense_Mutation	SNP	G	G	A	rs6003368	byhapmap	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	121.0	28.0	170.0	0.0	0.231405	0	G|1.000;|0.000	.	weak	.	IGLL5	26	.	NM_001256296	exon1	c.G21A	p.W7X	CCAATGGTTGCAC	.	PASS	Atlas-SNP
CADM1	23705	hgsc.bcm.edu	37	11	115110994	115110994	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	85.0	30.0	85.0	0.0	0.352941	0	.	.	none	.	CADM1	74	.	NM_014333	exon2	c.C271T	p.P91S	ACTTACGCCTGAA	.	PASS	Atlas-SNP
PLCB4	5332	hgsc.bcm.edu	37	20	9288481	9288481	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	78.0	20.0	135.0	0.0	0.25641	0	.	.	none	.	PLCB4	204	.	NM_182797	exon2	c.T20G	p.F7C	ATGAATTTAACTG	.	PASS	Atlas-SNP
C8A	731	hgsc.bcm.edu	37	1	57378088	57378088	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	79.0	47.0	111.0	0.0	0.594937	0	.	.	none	.	C8A	103	.	NM_000562	exon10	c.C1393T	p.H465Y	CCTATCCACGAGG	.	PASS	Atlas-SNP
USP24	23358	hgsc.bcm.edu	37	1	55622939	55622939	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	159.0	97.0	183.0	0.0	0.610063	0	.	.	none	.	USP24	323	.	NM_015306	exon11	c.T1332G	p.I444M	CAGTGCAATCGAC	.	PASS	Atlas-SNP
WDR88	126248	hgsc.bcm.edu	37	19	33642122	33642122	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	61.0	39.0	37.0	0.0	0.639344	0	.	.	none	.	WDR88	50	.	NM_173479	exon6	c.G715T	p.D239Y	TGCTTTGACCCCG	.	PASS	Atlas-SNP
TGM3	7053	hgsc.bcm.edu	37	20	2312744	2312744	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	169.0	64.0	183.0	0.0	0.378698	0	.	.	none	.	TGM3	105	.	NM_003245	exon10	c.A1430G	p.E477G	AAACAGAGGAACA	.	PASS	Atlas-SNP
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346765	140346765	+	Silent	SNP	A	A	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	155.0	47.0	162.0	0.0	0.303226	0	.	.	none	.	PCDHAC2	142	.	NM_031883	exon1	c.A414T	p.I138I	GGAAATATTGGAC	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138355	37138355	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	44.0	7.0	48.0	0.0	0.159091	0	.	.	none	PIM1,NS,lymphoid_neoplasm,0,3	PIM1	71	3	NM_001243186	exon1	c.C277G	p.L93V	GGGATGCTCTTGT	.	scavenged	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230311	23230311	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	146.0	49.0	182.0	0.0	0.335616	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.G78A	p.L26L	GCCCCTGCTGCTG	.	PASS	Atlas-SNP
RGS22	26166	hgsc.bcm.edu	37	8	101016183	101016183	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	91.0	12.0	117.0	0.0	0.131868	0	.	.	none	.	RGS22	319	.	NM_015668	exon17	c.C2598A	p.F866L	CTGACGGAAATGT	.	PASS	Atlas-SNP
ARCN1	372	hgsc.bcm.edu	37	11	118463477	118463477	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	140.0	42.0	106.0	0.0	0.3	0	.	.	none	.	ARCN1	33	.	NM_001655	exon7	c.G1038A	p.L346L	TGGCCTGAAGAAT	.	PASS	Atlas-SNP
TRPM3	80036	hgsc.bcm.edu	37	9	73477848	73477848	+	Silent	SNP	T	T	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	181.0	123.0	254.0	0.0	0.679558	0	.	.	none	TRPM3_ENST00000423814,NS,carcinoma,-2,2	TRPM3	700	2	NM_001007471	exon3	c.A438T	p.G146G	GCCACCTCCTTGG	.	PASS	Atlas-SNP
UBAP2L	9898	hgsc.bcm.edu	37	1	154209612	154209612	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	183.0	98.0	273.0	1.0	0.535519	0.003663	.	.	none	.	UBAP2L	197	.	NM_001127320	exon8	c.A703G	p.S235G	GGGACGAGTGAGT	.	PASS	Atlas-SNP
NINL	22981	hgsc.bcm.edu	37	20	25457204	25457204	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	27.0	8.0	18.0	0.0	0.296296	0	.	.	none	.	NINL	148	.	NM_025176	exon17	c.G2723A	p.R908H	TGCATGCGTGACC	.	PASS	Atlas-SNP
OR52W1	120787	hgsc.bcm.edu	37	11	6221264	6221264	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	50.0	8.0	51.0	0.0	0.16	0	.	.	none	.	OR52W1	33	.	NM_001005178	exon1	c.C811T	p.H271Y	TTTGGTCATCACA	.	PASS	Atlas-SNP
PEX1	5189	hgsc.bcm.edu	37	7	92146905	92146905	+	Silent	SNP	T	T	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	119.0	76.0	129.0	0.0	0.638655	0	.	.	none	.	PEX1	102	.	NM_000466	exon5	c.A924G	p.K308K	ACAGTGTTTATGA	.	PASS	Atlas-SNP
ANK1	286	hgsc.bcm.edu	37	8	41577226	41577226	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	68.0	38.0	86.0	0.0	0.558824	0	.	.	none	.	ANK1	497	.	NM_001142446	exon10	c.G1159A	p.A387T	CCTTAGCCACCCT	.	PASS	Atlas-SNP
BTG2	7832	hgsc.bcm.edu	37	1	203274836	203274836	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	78.0	27.0	123.0	0.0	0.346154	0	.	.	none	.	BTG2	16	.	NM_006763	exon1	c.G102A	p.R34R	GCAGAGGCTTAAG	.	PASS	Atlas-SNP
CRB1	23418	hgsc.bcm.edu	37	1	197390429	197390429	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	69.0	40.0	87.0	0.0	0.57971	0	.	.	none	CRB1,bladder,carcinoma,0,1	CRB1	284	1	NM_001257966	exon6	c.G1471A	p.D491N	GAGGGCGATGGCT	.	PASS	Atlas-SNP
L3MBTL4	91133	hgsc.bcm.edu	37	18	6138191	6138191	+	Splice_Site	SNP	A	A	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	43.0	14.0	39.0	0.0	0.325581	0	.	.	none	.	L3MBTL4	87	.	NM_173464	exon15	c.1199+2T>C	.	AATGTTACCTGTG	.	PASS	Atlas-SNP
COL4A5	1287	hgsc.bcm.edu	37	X	107816878	107816878	+	Silent	SNP	A	A	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	142.0	12.0	129.0	0.0	0.084507	0	.	.	none	.	COL4A5	262	.	NM_000495	exon9	c.A540G	p.G180G	TCCTGGAATACAA	.	PASS	Atlas-SNP
CD79B	974	hgsc.bcm.edu	37	17	62006799	62006799	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	72.0	29.0	85.0	0.0	0.402778	0	.	.	none	CD79B,NS,lymphoid_neoplasm,0,13	CD79B	38	13	NM_001039933	exon5	c.T589A	p.Y197N	CCTCGTAGGTGTG	.	PASS	Atlas-SNP
GPHN	10243	hgsc.bcm.edu	37	14	67147830	67147830	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	114.0	18.0	101.0	0.0	0.157895	0	.	.	none	.	GPHN	79	.	NM_001024218	exon2	c.G70T	p.D24Y	GTGAGTGATAGTT	.	PASS	Atlas-SNP
KCNH6	81033	hgsc.bcm.edu	37	17	61622590	61622590	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	45.0	22.0	67.0	0.0	0.488889	0	.	.	none	.	KCNH6	122	.	NM_030779	exon13	c.C2656G	p.P886A	CCAGGGCCCAGGC	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108380629	108380629	+	Missense_Mutation	SNP	C	C	T	rs181581015	bycluster;by1000genomes	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	180.0	47.0	152.0	0.0	0.261111	0	C|1.000;T|0.000	0.000	strong	.	EXPH5	193	.	NM_015065	exon6	c.G5605A	p.G1869R	TTGTCCCGCTGCG	.	PASS	Atlas-SNP
ATG2A	23130	hgsc.bcm.edu	37	11	64662599	64662599	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	51.0	14.0	48.0	0.0	0.27451	0	.	.	none	.	ATG2A	133	.	NM_015104	exon41	c.G5663C	p.G1888A	ATCACGCCCCCCA	.	PASS	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52321593	52321593	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	54.0	24.0	74.0	0.0	0.444444	0	.	.	none	PXDNL_ENST00000356297,colon,carcinoma,-1,3	PXDNL	414	3	NM_144651	exon17	c.G2591A	p.R864H	CTGGAGCGCGCGA	.	PASS	Atlas-SNP
C3	718	hgsc.bcm.edu	37	19	6696418	6696418	+	Silent	SNP	G	G	A	rs139152390		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	77.0	6.0	97.0	0.0	0.0779221	0	G|1.000;A|0.000	0.000	weak	.	C3	192	.	NM_000064	exon23	c.C2922T	p.T974T	AGACTCGGTGTCC	.	PASS	Atlas-SNP
C15orf39	56905	hgsc.bcm.edu	37	15	75500343	75500343	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	60.0	19.0	59.0	0.0	0.316667	0	.	.	none	.	C15orf39	64	.	NM_015492	exon2	c.C1954T	p.R652X	ATGTTCCGAAAGT	.	PASS	Atlas-SNP
CNTLN	54875	hgsc.bcm.edu	37	9	17135258	17135258	+	Silent	SNP	C	C	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	83.0	25.0	102.0	0.0	0.301205	0	.	.	none	.	CNTLN	128	.	NM_017738	exon1	c.C195A	p.G65G	AGGGGGCCGGCGA	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56350230	56350230	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	103.0	21.0	105.0	0.0	0.203883	0	.	.	none	.	DST	1427	.	NM_015548	exon69	c.A13218C	p.Q4406H	TGTGAATTGTCCA	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187539926	187539926	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	101.0	26.0	117.0	0.0	0.257426	0	.	.	none	.	FAT1	500	.	NM_005245	exon10	c.T7814A	p.I2605N	GACCCGATATTCA	.	PASS	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	71264561	71264561	+	Silent	SNP	A	A	G	rs3743953	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	4.0	4.0	0.0	0.0	1	.	A|0.773;G|0.227	0.227	strong	.	HYDIN	788	.	NM_001198542	exon1	c.T30C	p.G10G	CTCCATACCCAGC	.	PASS	Atlas-SNP
SLC5A12	159963	hgsc.bcm.edu	37	11	26700336	26700336	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	107.0	7.0	117.0	0.0	0.0654206	0	.	.	none	.	SLC5A12	134	.	NM_178498	exon13	c.C1502T	p.S501L	GAGATCGAGTACC	.	PASS	Atlas-SNP
KDR	3791	hgsc.bcm.edu	37	4	55961059	55961059	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	105.0	23.0	137.0	0.0	0.219048	0	.	.	none	KDR,NS,carcinoma,0,1	KDR	307	1	NM_002253	exon21	c.C2881T	p.R961W	AGCGCCGTTTCAG	.	PASS	Atlas-SNP
FAM13C	220965	hgsc.bcm.edu	37	10	61028362	61028362	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	50.0	11.0	71.0	0.0	0.22	0	.	.	none	FAM13C,mouth,carcinoma,0,1	FAM13C	124	1	NM_198215	exon8	c.G893A	p.R298Q	ATTTTCCGCTTGA	.	PASS	Atlas-SNP
CCDC57	284001	hgsc.bcm.edu	37	17	80121138	80121138	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	84.0	30.0	95.0	0.0	0.357143	0	.	.	none	.	CCDC57	102	.	NM_198082	exon13	c.C1978T	p.L660F	TCCTGAGTGCCAG	.	PASS	Atlas-SNP
ACACA	31	hgsc.bcm.edu	37	17	35609904	35609904	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	91.0	17.0	95.0	0.0	0.186813	0	.	.	none	.	ACACA	395	.	NM_198834	exon15	c.G1885A	p.E629K	GGTATTCAACTGT	.	PASS	Atlas-SNP
NELFB	25920	hgsc.bcm.edu	37	9	140158730	140158730	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	33.0	10.0	38.0	0.0	0.30303	0	.	.	none	.	.	.	.	NM_015456	exon6	c.C817T	p.R273W	CGAGAGCGGTTCG	.	PASS	Atlas-SNP
PRDM1	639	hgsc.bcm.edu	37	6	106553289	106553289	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	33.0	21.0	46.0	0.0	0.636364	0	.	.	none	.	PRDM1	195	.	NM_001198	exon5	c.C1254G	p.Y418X	CCCCTACGGCATG	.	PASS	Atlas-SNP
AGAP2	116986	hgsc.bcm.edu	37	12	58131511	58131511	+	Silent	SNP	G	G	A	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	50.0	7.0	33.0	0.0	0.14	0	.	.	none	.	AGAP2	167	.	NM_001122772	exon1	c.C519T	p.T173T	GCTGCCGGTGCCA	.	PASS	Atlas-SNP
POMT2	29954	hgsc.bcm.edu	37	14	77762563	77762563	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	51.0	7.0	34.0	0.0	0.137255	0	.	.	none	.	POMT2	47	.	NM_013382	exon9	c.T1060C	p.Y354H	GCAGATAGCCGAT	.	PASS	Atlas-SNP
MYD88	4615	hgsc.bcm.edu	37	3	38182641	38182641	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	80.0	30.0	83.0	0.0	0.375	0	.	.	none	MYD88,NS,lymphoid_neoplasm,0,828	MYD88	900	828	NM_001172569	exon4	c.T613C	p.X205R	AGCGACTGATCCC	.	PASS	Atlas-SNP
SUSD2	56241	hgsc.bcm.edu	37	22	24583607	24583607	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	92.0	30.0	125.0	0.0	0.326087	0	.	.	none	.	SUSD2	68	.	NM_019601	exon12	c.C1960T	p.Q654X	CTGTACCAACCCA	.	PASS	Atlas-SNP
CCER1	196477	hgsc.bcm.edu	37	12	91348068	91348068	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	19.0	6.0	18.0	0.0	0.315789	0	.	.	none	.	.	.	.	NM_152638	exon1	c.G452A	p.R151H	TGGTGGCGCAGGC	.	PASS	Atlas-SNP