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
ZNF343	79175	hgsc.bcm.edu	37	20	2473385	2473385	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	116	15	88	0	0.12931	0	.	.	none	ZNF343,NS,carcinoma,0,1	ZNF343	47	1	NM_024325	exon5	c.265delG	p.E89fs	.	.	PASS	Atlas-Indel
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067225	46067226	+	Frame_Shift_Ins	INS	-	-	G	rs148239295	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	137	23	90	0	0.167883	0	.	.	strong	.	KRTAP10-11	36	.	NM_198692	exon1	c.850_851insG	p.R284fs	.	.	PASS	Atlas-Indel
ZNF223	7766	hgsc.bcm.edu	37	19	44570830	44570831	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	226	39	91	.	0.173	.	.	.	none	.	ZNF223	61	.	NM_013361	exon5	c.848_849del	p.283_283del	.	.	PASS	Pindel,Atlas-Indel
GAST	2520	hgsc.bcm.edu	37	17	39872062	39872064	+	In_Frame_Del	DEL	GAA	GAA	-	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	113	15	94	0	0.132743	0	.	.	none	.	GAST	13	.	NM_000805	exon3	c.243_245del	p.81_82del	.	.	PASS	Atlas-Indel
NEFH	4744	hgsc.bcm.edu	37	22	29885567	29885568	+	In_Frame_Ins	INS	-	-	AAGTCCCCTGAGAAGGCC	rs147489453	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	81	41	55	0	0.506173	0	.	.	strong	NEFH,rectum,carcinoma,0,1	NEFH	178	1	NM_021076	exon4	c.1938_1939insAAGTCCCCTGAGAAGGCC	p.A646delinsAKSPEKA	.	.	PASS	Atlas-Indel
ATAD5	79915	hgsc.bcm.edu	37	17	29221631	29221635	+	Frame_Shift_Del	DEL	TCTCT	TCTCT	-	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	TCTCT	TCTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	55	14	65	.	0.255	.	.	.	none	.	ATAD5	150	.	NM_024857	exon22	c.5346_5350del	p.1782_1784del	.	.	PASS	Pindel,Atlas-Indel
P2RY10	27334	hgsc.bcm.edu	37	X	78216808	78216808	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	36	20	25	.	0.556	.	.	.	none	.	P2RY10	99	.	NM_198333	exon2	c.790delA	p.I264fs	.	.	PASS	Pindel,Atlas-Indel
FAM157B	100132403	hgsc.bcm.edu	37	9	141107537	141107548	+	In_Frame_Del	DEL	GCAGCAGCAGCA	GCAGCAGCAGCA	-	rs370981092	alternate_allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	GCAGCAGCAGCA	GCAGCAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	172	68	203	0	0.395	0.000	.	.	alt	.	.	.	.	NM_001145249	exon2	c.218_229del	p.73_77del	.	.	PASS	Pindel
FAM45B	55855	hgsc.bcm.edu	37	X	129630851	129630854	+	RNA	DEL	AAGT	AAGT	-	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	AAGT	AAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	248	83	215	.	0.335	.	.	.	none	.	FAM45B	26	.	.	.	.	.	.	.	PASS	Pindel
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20739938	20739943	+	In_Frame_Del	DEL	CTCCTG	CTCCTG	-	rs201222558	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	CTCCTG	CTCCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	97	16	115	.	0.165	.	CTCCTG|0.969;-|0.031	0.031	strong	.	GOLGA6L6	37	.	NM_001145004	exon8	c.1808_1813del	p.603_605del	.	.	PASS	Pindel
FAM22G	441457	hgsc.bcm.edu	37	9	99701229	99701231	+	In_Frame_Del	DEL	CTT	CTT	-	rs372223045		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	219	36	198	.	0.164	.	.	.	weak	.	FAM22G	66	.	NM_001170741	exon7	c.2023_2025del	p.675_675del	.	.	PASS	Pindel
PCDHA4	56144	hgsc.bcm.edu	37	5	140186979	140186990	+	In_Frame_Del	DEL	GGGCCGCGGAGG	GGGCCGCGGAGG	-	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	GGGCCGCGGAGG	GGGCCGCGGAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	48	20	25	.	0.417	.	.	.	none	.	PCDHA4	419	.	NM_031500	exon1	c.206_217del	p.69_73del	.	.	PASS	Pindel
C19orf55	148137	hgsc.bcm.edu	37	19	36258938	36258938	+	Frame_Shift_Del	DEL	G	G	-	rs5827939	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	11	10	8	.	0.909	.	G|0.000;-|1.000	1.000	strong	.	C19orf55	39	.	NM_001039887	exon9	c.1190delA	p.Q397fs	.	.	PASS	Pindel
NFKBIE	4794	hgsc.bcm.edu	37	6	44229563	44229564	+	In_Frame_Ins	INS	-	-	GTACAGCCAGATGGA	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	36	10	35	.	0.278	.	.	.	none	.	NFKBIE	31	.	NM_004556	exon3	c.908_909insTCCATCTGGCTGTAC	p.H303delinsLHLAVH	.	.	PASS	Pindel
NR4A3	8013	hgsc.bcm.edu	37	9	102590616	102590624	+	In_Frame_Del	DEL	CACCACCAC	CACCACCAC	-	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	CACCACCAC	CACCACCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	40	10	34	.	0.250	.	.	.	none	.	NR4A3	80	.	NM_173200	exon4	c.324_332del	p.108_111del	.	.	PASS	Pindel
GP2	2813	hgsc.bcm.edu	37	16	20329589	20329589	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	184	37	199	0	0.201087	0	.	.	none	.	GP2	122	.	NM_001007240	exon8	c.T1180G	p.F394V	GGTTAAACCGGGA	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26422889	26422889	+	Missense_Mutation	SNP	G	G	A	rs187337528	by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	38	13	31	0	0.342105	0	G|1.000;A|0.000	0.000	strong	MYO18B,NS,haematopoietic_neoplasm,0,2	MYO18B	322	2	NM_032608	exon43	c.G6949A	p.A2317T	GGGGCCGCTGGTG	.	PASS	Atlas-SNP
KCNJ18	100134444	hgsc.bcm.edu	37	17	21318948	21318948	+	Silent	SNP	C	C	T	rs112314728		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	168	33	185	43	0.196429	0.232432	C|0.500;T|0.500	0.500	weak	KCNJ12,colon,carcinoma,0,1	.	.	1	NM_001194958	exon3	c.C294T	p.F98F	GCTGTTCGGCATC	.	scavenged	Atlas-SNP
HIVEP3	59269	hgsc.bcm.edu	37	1	41976328	41976328	+	Missense_Mutation	SNP	T	T	C	rs9439043	bycluster;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	4	4	0	0	1	.	T|0.032;C|0.968	0.968	strong	.	HIVEP3	235	.	NM_024503	exon9	c.A7015G	p.T2339A	GGTTGGTCGGTGC	.	PASS	Atlas-SNP
GCC2	9648	hgsc.bcm.edu	37	2	109103005	109103005	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	188	3	203	0	0.0159574	0	.	.	none	GCC2,NS,carcinoma,+2,1	GCC2	129	1	NM_181453	exon16	c.C3831T	p.I1277I	CAAAATCCACGAG	.	scavenged	Atlas-SNP
HAVCR1	26762	hgsc.bcm.edu	37	5	156479523	156479523	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	460	5	396	0	0.0108696	0	.	.	none	HAVCR1,NS,carcinoma,-2,1	HAVCR1	84	1	NM_001099414	exon4	c.G522A	p.T174T	CGTTGTCGTTGGA	.	scavenged	Atlas-SNP
NBEA	26960	hgsc.bcm.edu	37	13	35782857	35782857	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	68	26	89	0	0.382353	0	.	.	none	.	NBEA	340	.	NM_015678	exon32	c.A5387G	p.K1796R	CTGTAAAGAAACC	.	PASS	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2676736	2676736	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	38	16	41	0	0.421053	0	.	.	none	.	CACNA1C	1023	.	NM_001129831	exon13	c.C1671T	p.D557D	GCCAGACACGGCA	.	PASS	Atlas-SNP
STAT3	6774	hgsc.bcm.edu	37	17	40474470	40474470	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	283	137	237	0	0.484099	0	.	.	none	.	STAT3	268	.	NM_003150	exon21	c.A1931G	p.Q644R	TTCAGCTGCTGCT	.	PASS	Atlas-SNP
KIF27	55582	hgsc.bcm.edu	37	9	86457175	86457175	+	Missense_Mutation	SNP	C	C	T	rs146464985		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	220	5	222	0	0.0227273	0	C|1.000;T|0.000	0.000	weak	KIF27,rectum,carcinoma,-1,1	KIF27	103	1	NM_017576	exon17	c.G3698A	p.R1233Q	TGCCGCCGAATTG	.	scavenged	Atlas-SNP
C5	727	hgsc.bcm.edu	37	9	123719614	123719614	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	83	5	92	0	0.060241	0	.	.	none	.	C5	124	.	NM_001735	exon39	c.G4711A	p.E1571K	CATTTTCTACAGT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505858	195505858	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	122	4	109	1	0.0327869	0.00917431	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	NM_018406	exon2	c.C12593T	p.T4198I	GAGGAAGTGTCGG	.	scavenged	Atlas-SNP
TCL1A	8115	hgsc.bcm.edu	37	14	96180291	96180291	+	Missense_Mutation	SNP	G	G	A	rs201228671	by1000genomes;alternate_allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	61	32	59	0	0.52459	0	G|0.999;C|0.001	.	alt	.	TCL1A	26	.	NM_001098725	exon1	c.C113T	p.T38I	TCGATGGTTAAGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512665	195512665	+	Missense_Mutation	SNP	G	G	A	rs79300100	bycluster;byfrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	354	6	293	7	0.0169492	0.0238908	G|0.993;A|0.007	0.007	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C5786T	p.A1929V	GTGGATGCTGAGG	.	scavenged	Atlas-SNP
POTEE	445582	hgsc.bcm.edu	37	2	132021766	132021766	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	300	13	245	4	0.0433333	0.0163265	.	.	none	ENSG00000188219,rectum,NS,0,1	.	.	1	NM_001083538	exon15	c.A2738C	p.K913T	ACATCAAAGAGAA	.	scavenged	Atlas-SNP
ARMCX5	64860	hgsc.bcm.edu	37	X	101858323	101858323	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	92	11	97	0	0.119565	0	.	.	none	.	ARMCX5	55	.	NM_022838	exon3	c.G1254A	p.G418G	ACTAGGGCACTTG	.	PASS	Atlas-SNP
OR2M5	127059	hgsc.bcm.edu	37	1	248309020	248309020	+	Missense_Mutation	SNP	G	G	A	rs139290187	bycluster;byfrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	329	5	295	4	0.0151976	0.0135593	G|0.996;A|0.004	0.004	strong	OR2M5,NS,carcinoma,0,2	OR2M5	117	2	NM_001004690	exon1	c.G571A	p.D191N	TGCAATGACACAT	.	scavenged	Atlas-SNP
LDLRAD2	401944	hgsc.bcm.edu	37	1	22141206	22141206	+	Missense_Mutation	SNP	A	A	C	rs10917051	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	11	7	2	1	0.636364	0.5	A|0.362;C|0.638	0.638	strong	LDLRAD2,NS,carcinoma,0,1	LDLRAD2	17	1	NM_001013693	exon2	c.A401C	p.N134T	GCCTGAACATCCC	.	scavenged	Atlas-SNP
UBALD2	283991	hgsc.bcm.edu	37	17	74261677	74261677	+	Silent	SNP	T	T	C	rs2585751	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	20	20	0	0	1	.	T|0.357;C|0.643	0.643	strong	.	.	.	.	NM_182565	exon1	c.T91C	p.L31L	AAGCAGTTGCTGC	.	PASS	Atlas-SNP
SEH1L	81929	hgsc.bcm.edu	37	18	12955467	12955467	+	Silent	SNP	T	T	C	rs2015378		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	147	4	138	1	0.0272109	0.00724638	.	.	weak	SEH1L,NS,carcinoma,0,3	SEH1L	33	3	NM_001013437	exon3	c.T168C	p.H56H	GACACATAGTGGA	.	scavenged	Atlas-SNP
GPR20	2843	hgsc.bcm.edu	37	8	142367400	142367400	+	Silent	SNP	G	G	A	rs11167054	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	2	2	0	0	1	.	G|0.248;A|0.752	0.752	strong	GPR20,NS,carcinoma,0,2	GPR20	43	2	NM_005293	exon2	c.C624T	p.P208P	CAGCAGGGGCAGC	.	scavenged	Atlas-SNP
FNIP2	57600	hgsc.bcm.edu	37	4	159789387	159789387	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	78	4	80	0	0.0512821	0	.	.	none	.	FNIP2	90	.	NM_020840	exon13	c.C1599T	p.N533N	AGAGAACCAGCTG	.	PASS	Atlas-SNP
FN1	2335	hgsc.bcm.edu	37	2	216289966	216289966	+	Missense_Mutation	SNP	G	G	A	rs145123731	bycluster;byfrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	96	33	117	0	0.34375	0	G|1.000;A|0.000	0.000	strong	FN1_ENST00000354785,colon,carcinoma,+1,2	FN1	521	2	NM_212476	exon7	c.C887T	p.P296L	GGCTGCGGTTGGT	.	PASS	Atlas-SNP
PLXNA2	5362	hgsc.bcm.edu	37	1	208216497	208216497	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	117	38	110	0	0.324786	0	.	.	none	PLXNA2,NS,carcinoma,0,1	PLXNA2	178	1	NM_025179	exon21	c.G3926A	p.R1309H	CCTGAGCGGTCCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513285	195513285	+	Silent	SNP	G	G	T	rs200293322	byfrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	388	11	332	6	0.0283505	0.0180723	G|0.988;T|0.013	0.013	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C5166A	p.S1722S	ACCTGTGGATACT	.	scavenged	Atlas-SNP
SLITRK5	26050	hgsc.bcm.edu	37	13	88329368	88329368	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	114	2	160	0	0.0175439	0	.	.	none	SLITRK5,NS,carcinoma,+1,1	SLITRK5	192	1	NM_015567	exon2	c.G1725A	p.K575K	CATGAAGCTGTGG	.	scavenged	Atlas-SNP
SIRT1	23411	hgsc.bcm.edu	37	10	69672431	69672431	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	96	3	139	0	0.03125	0	.	.	none	SIRT1,NS,carcinoma,0,2	SIRT1	38	2	NM_012238	exon8	c.G1558T	p.E520X	CAAAAAGAATTGG	.	scavenged	Atlas-SNP
COL16A1	1307	hgsc.bcm.edu	37	1	32149326	32149326	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	73	31	64	0	0.424658	0	.	.	none	.	COL16A1	137	.	NM_001856	exon34	c.G2361A	p.R787R	GACTCCCCTTCCT	.	PASS	Atlas-SNP
TTK	7272	hgsc.bcm.edu	37	6	80744802	80744802	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	127	49	190	0	0.385827	0	.	.	none	.	TTK	199	.	NM_003318	exon15	c.T1715A	p.I572K	ACGAAATAGCTTA	.	PASS	Atlas-SNP
TRIM51	84767	hgsc.bcm.edu	37	11	55655597	55655597	+	Silent	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	545	32	584	30	0.0587156	0.0513699	.	.	none	SPRYD5_ENST00000327733,NS,carcinoma,+2,2	.	.	2	NM_032681	exon4	c.A597G	p.E199E	CTTGGAAAGGCTG	.	scavenged	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	37	11	57971203	57971203	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	227	10	204	7	0.0440529	0.0343137	.	.	none	OR1S2,NS,carcinoma,0,3	OR1S2	119	3	NM_001004459	exon1	c.G451C	p.A151P	ACCTGGCCCGCAT	.	scavenged	Atlas-SNP
NLRP13	126204	hgsc.bcm.edu	37	19	56423386	56423386	+	Silent	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	114	2	126	1	0.0175439	0.00793651	.	.	none	NLRP13,NS,carcinoma,-2,3	NLRP13	220	3	NM_176810	exon5	c.A1797G	p.E599E	TTCCAGTTCTCTT	.	scavenged	Atlas-SNP
MCCC1	56922	hgsc.bcm.edu	37	3	182775212	182775212	+	Splice_Site	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	88	3	90	0	0.0340909	0	.	.	none	MCCC1,NS,carcinoma,+2,1	MCCC1	87	1	NM_020166	exon9	c.762-2A>G	.	CATGCCTATATAA	.	scavenged	Atlas-SNP
LYN	4067	hgsc.bcm.edu	37	8	56910951	56910951	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	187	65	194	0	0.347594	0	.	.	none	.	LYN	54	.	NM_002350	exon11	c.G1097A	p.R366Q	TTCACCGGGACCT	.	PASS	Atlas-SNP
ESCO1	114799	hgsc.bcm.edu	37	18	19153337	19153337	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	174	3	188	0	0.0172414	0	.	.	none	ESCO1,caecum,carcinoma,+1,2	ESCO1	89	2	NM_052911	exon4	c.A1468G	p.K490E	AAGGTTTTATCTC	.	scavenged	Atlas-SNP
PRH1	5554	hgsc.bcm.edu	37	12	11035670	11035670	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	129	3	158	1	0.0232558	0.00632911	.	.	none	PRH1,colon,carcinoma,0,1	PRH1	17	1	NM_006250	exon2	c.C90T	p.L30L	TATTACGAGGGGA	.	scavenged	Atlas-SNP
ADO	84890	hgsc.bcm.edu	37	10	64565347	64565347	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	22	4	26	0	0.181818	0	.	.	none	.	ADO	10	.	NM_032804	exon1	c.C528G	p.Y176X	CGAGTACACCGAG	.	PASS	Atlas-SNP
CST2	1470	hgsc.bcm.edu	37	20	23805952	23805952	+	Silent	SNP	G	G	C	rs146039211	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	114	5	109	4	0.0438596	0.0366972	G|0.999;A|0.001	.	alt	CST2,NS,adenoma,-1,1	CST2	39	1	NM_001322	exon2	c.C237G	p.G79G	CACCCCGCCCACG	.	scavenged	Atlas-SNP
LLGL2	3993	hgsc.bcm.edu	37	17	73552167	73552167	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	50	24	28	0	0.48	0	.	.	none	.	LLGL2	155	.	NM_001015002	exon3	c.G116A	p.G39D	CCCTCGGCTACAG	.	PASS	Atlas-SNP
TET2	54790	hgsc.bcm.edu	37	4	106193850	106193850	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	130	108	106	0	0.830769	0	.	.	none	.	TET2	1762	.	NM_001127208	exon10	c.A4312T	p.K1438X	GAGGAGAAAAAAC	.	PASS	Atlas-SNP
FAM186A	121006	hgsc.bcm.edu	37	12	50746166	50746166	+	Silent	SNP	G	G	C	rs368983791		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	266	6	248	4	0.0225564	0.016129	.	.	weak	FAM186A_ENST00000327337,NS,carcinoma,0,3	FAM186A	181	3	NM_001145475	exon4	c.C4449G	p.L1483L	AGGGATGAGAGGG	.	scavenged	Atlas-SNP
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643066	1643066	+	Silent	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	129	6	108	1	0.0465116	0.00925926	.	.	none	KRTAP5-4,NS,carcinoma,0,3	KRTAP5-4	78	3	NM_001012709	exon1	c.T258C	p.G86G	CTTGGAACCCCCA	.	scavenged	Atlas-SNP
RBM14	10432	hgsc.bcm.edu	37	11	66391989	66391989	+	Silent	SNP	C	C	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	50	2	42	1	0.04	0.0238095	.	.	none	RBM14,rectum,carcinoma,+1,1	RBM14	59	1	NM_006328	exon2	c.C642A	p.R214R	CGACCGCAGCCCT	.	scavenged	Atlas-SNP
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067194	46067194	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	136	5	79	0	0.0367647	0	.	.	none	KRTAP10-11,NS,carcinoma,0,1	KRTAP10-11	36	1	NM_198692	exon1	c.C819T	p.C273C	CTCCTGCGTGTCC	.	scavenged	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43585253	43585253	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	141	5	189	0	0.035461	0	.	.	none	PSG2,NS,carcinoma,0,2	PSG2	84	2	NM_031246	exon2	c.G210A	p.G70G	GATTTGCCCTTTG	.	scavenged	Atlas-SNP
OR10G8	219869	hgsc.bcm.edu	37	11	123900411	123900411	+	Missense_Mutation	SNP	G	G	A	rs202220125		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	251	6	294	6	0.0239044	0.0204082	G|0.999;A|0.001	0.001	weak	OR10G8,right_upper_lobe,carcinoma,-2,2	OR10G8	132	2	NM_001004464	exon1	c.G82A	p.V28I	TTTGGAGTCTTCC	.	scavenged	Atlas-SNP
OR52J3	119679	hgsc.bcm.edu	37	11	5068207	5068207	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	221	4	220	0	0.0180995	0	.	.	none	OR52J3,caecum,carcinoma,0,1	OR52J3	77	1	NM_001001916	exon1	c.T452C	p.V151A	GCATTGTAATTCG	.	scavenged	Atlas-SNP
C3	718	hgsc.bcm.edu	37	19	6714453	6714453	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	61	26	87	0	0.42623	0	.	.	none	.	C3	192	.	NM_000064	exon5	c.C509T	p.P170L	CCTTCCGGGTTCT	.	PASS	Atlas-SNP
RFX6	222546	hgsc.bcm.edu	37	6	117248414	117248414	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	114	55	130	0	0.482456	0	.	.	none	.	RFX6	141	.	NM_173560	exon17	c.C2110T	p.Q704X	AACTACCAGACTG	.	PASS	Atlas-SNP
PITPNM3	83394	hgsc.bcm.edu	37	17	6358850	6358850	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	42	16	42	0	0.380952	0	.	.	none	.	PITPNM3	91	.	NM_031220	exon20	c.C2733T	p.H911H	CTGCGCGTGCAGC	.	PASS	Atlas-SNP
NUP210	23225	hgsc.bcm.edu	37	3	13379381	13379381	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	42	18	26	0	0.428571	0	.	.	none	.	NUP210	182	.	NM_024923	exon26	c.G3508A	p.V1170M	TCCTCACGGCCCT	.	PASS	Atlas-SNP
PLXNB3	5365	hgsc.bcm.edu	37	X	153035889	153035889	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	132	6	118	0	0.0454545	0	.	.	none	.	PLXNB3	208	.	NM_001163257	exon10	c.A1952G	p.E651G	CCTTGGAGGCGGC	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32551948	32551948	+	Missense_Mutation	SNP	G	G	A	rs17886882	bycluster	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	28	11	95	4	0.392857	0.0421053	.	.	weak	HLA-DRB1,brain,glioma,0,2	HLA-DRB1	41	2	NM_002124	exon2	c.C308T	p.A103V	TCCACCGCGGCCC	.	scavenged	Atlas-SNP
B2M	567	hgsc.bcm.edu	37	15	45003779	45003779	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	99	76	104	0	0.767677	0	.	.	none	B2M,colon,carcinoma,0,2	B2M	99	2	NM_004048	exon1	c.T35C	p.L12P	TCGCGCTACTCTC	.	PASS	Atlas-SNP
LMOD1	25802	hgsc.bcm.edu	37	1	201869208	201869208	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	159	2	151	0	0.0125786	0	.	.	none	LMOD1,caecum,carcinoma,-2,3	LMOD1	59	3	NM_012134	exon2	c.G933A	p.E311E	TGCCTCCTCCTCC	.	scavenged	Atlas-SNP
ZNF337	26152	hgsc.bcm.edu	37	20	25656946	25656946	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	106	8	95	0	0.0754717	0	.	.	none	.	ZNF337	65	.	NM_015655	exon5	c.G978A	p.G326G	GCCTCGCCCACAC	.	PASS	Atlas-SNP
PBX3	5090	hgsc.bcm.edu	37	9	128692039	128692039	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	144	3	143	0	0.0208333	0	.	.	none	PBX3,colon,carcinoma,0,1	PBX3	45	1	NM_006195	exon4	c.C622T	p.R208X	ATCCATCGAAAAT	.	scavenged	Atlas-SNP
RSPH1	89765	hgsc.bcm.edu	37	21	43913086	43913086	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	154	3	155	0	0.0194805	0	.	.	none	RSPH1,rectum,carcinoma,0,1	RSPH1	36	1	NM_080860	exon2	c.G158C	p.R53T	CCATGTCTTTTAC	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506974	195506974	+	Missense_Mutation	SNP	G	G	A	rs142066159	bycluster	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	90	9	60	1	0.1	0.0166667	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C11477T	p.P3826L	GTGACAGGAAGAG	.	scavenged	Atlas-SNP
MS4A14	84689	hgsc.bcm.edu	37	11	60183214	60183214	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	158	2	139	0	0.0126582	0	.	.	none	MS4A14,NS,carcinoma,0,2	MS4A14	120	2	NM_001261828	exon6	c.A872G	p.K291R	AGAAAAAGCCCTC	.	scavenged	Atlas-SNP
ST18	9705	hgsc.bcm.edu	37	8	53079501	53079501	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	120	4	115	0	0.0333333	0	.	.	none	ST18,extremity,malignant_melanoma,0,1	ST18	212	1	NM_014682	exon11	c.G1115A	p.G372E	TCACATCCAGGGA	.	scavenged	Atlas-SNP
CPSF1	29894	hgsc.bcm.edu	37	8	145623970	145623970	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	209	3	216	0	0.0143541	0	.	.	none	CPSF1,NS,carcinoma,+1,1	CPSF1	92	1	NM_013291	exon18	c.A1697G	p.D566G	TCGTCGTCTGCTT	.	scavenged	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	215972275	215972275	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	144	2	174	0	0.0138889	0	.	.	none	USH2A,NS,carcinoma,+1,1	USH2A	1168	1	NM_206933	exon50	c.A9932G	p.E3311G	ACTCCTTCTTCTC	.	scavenged	Atlas-SNP
MTMR2	8898	hgsc.bcm.edu	37	11	95582866	95582866	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	140	3	143	1	0.0214286	0.00699301	.	.	none	MTMR2_ENST00000346299,colon,carcinoma,+1,2	MTMR2	79	2	NM_016156	exon9	c.G965A	p.R322Q	CTTGGCCGGGCAT	.	scavenged	Atlas-SNP
FAM83H	286077	hgsc.bcm.edu	37	8	144809804	144809804	+	Silent	SNP	G	G	A	rs13254035	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	9	9	0	0	1	.	G|0.132;A|0.868	0.868	strong	.	FAM83H	68	.	NM_198488	exon5	c.C1827T	p.Y609Y	GTCTTCGTAAGCC	.	PASS	Atlas-SNP
ALOX15	246	hgsc.bcm.edu	37	17	4544856	4544856	+	Missense_Mutation	SNP	C	C	T	rs145573801	byfrequency;alternate_allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	95	5	60	0	0.0526316	0	C|1.000;G|0.000	.	alt	.	ALOX15	70	.	NM_001140	exon1	c.G91A	p.G31R	CCTCCCCGTGCTG	.	PASS	Atlas-SNP
TLCD1	116238	hgsc.bcm.edu	37	17	27052991	27052991	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	63	4	60	0	0.0634921	0	.	.	none	.	TLCD1	15	.	NM_138463	exon1	c.C125T	p.T42I	CGCCAGGTGCGCA	.	PASS	Atlas-SNP
COL21A1	81578	hgsc.bcm.edu	37	6	55922465	55922465	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	106	15	102	0	0.141509	0	.	.	none	.	COL21A1	201	.	NM_030820	exon30	c.C2864T	p.P955L	TAGTTTGGTCCTT	.	PASS	Atlas-SNP
SLC17A9	63910	hgsc.bcm.edu	37	20	61594979	61594979	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	131	63	110	0	0.480916	0	.	.	none	.	SLC17A9	54	.	NM_022082	exon7	c.A769G	p.I257V	TTCTTCATCCTCC	.	PASS	Atlas-SNP
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53730084	53730084	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	80	37	86	0	0.4625	0	.	.	none	.	RPGRIP1L	118	.	NM_001127897	exon3	c.A209C	p.K70T	TCCTGCTTGCGGG	.	PASS	Atlas-SNP
ZNF775	285971	hgsc.bcm.edu	37	7	150094853	150094853	+	Silent	SNP	G	G	A	rs7780011	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	3	3	1	1	1	1	G|0.551;A|0.449	0.449	strong	ZNF775,NS,carcinoma,0,1	ZNF775	34	1	NM_173680	exon3	c.G1284A	p.T428T	GGACACGCTGTGG	.	scavenged	Atlas-SNP
NBN	4683	hgsc.bcm.edu	37	8	90967770	90967770	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	78	4	71	0	0.0512821	0	.	.	none	.	NBN	86	.	NM_002485	exon10	c.A1138G	p.R380G	TTGGCCTTTCACT	.	PASS	Atlas-SNP
STK11IP	114790	hgsc.bcm.edu	37	2	220474114	220474114	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	77	4	72	0	0.0519481	0	.	.	none	.	STK11IP	152	.	NM_052902	exon17	c.C1989T	p.T663T	AGTCACCAATGTG	.	PASS	Atlas-SNP
RNF219	79596	hgsc.bcm.edu	37	13	79219011	79219011	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	66	19	63	0	0.287879	0	.	.	none	.	RNF219	94	.	NM_024546	exon2	c.G194C	p.C65S	TCTTTGCAAGGAT	.	PASS	Atlas-SNP
CLPSL1	340204	hgsc.bcm.edu	37	6	35754842	35754842	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	41	10	38	0	0.243902	0	.	.	none	.	.	.	.	NM_001010886	exon2	c.A167G	p.N56S	CAGACAATTGCGA	.	PASS	Atlas-SNP
FSD1L	83856	hgsc.bcm.edu	37	9	108297595	108297595	+	Silent	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	58	14	61	0	0.241379	0	.	.	none	.	FSD1L	31	.	NM_001145313	exon12	c.T1374C	p.D458D	TTTTGATGGGGGT	.	PASS	Atlas-SNP
KDELC2	143888	hgsc.bcm.edu	37	11	108357058	108357058	+	Silent	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	241	4	256	0	0.0165975	0	.	.	none	KDELC2,bladder,carcinoma,-2,1	KDELC2	37	1	NM_153705	exon3	c.T510C	p.F170F	GCTGGGAAAGGAA	.	scavenged	Atlas-SNP
TLX3	30012	hgsc.bcm.edu	37	5	170736474	170736474	+	Silent	SNP	G	G	A	rs2303742	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	14	12	4	2	0.857143	0.5	G|0.995;A|0.005	0.005	strong	TLX3_ENST00000296921,NS,carcinoma,+2,1	TLX3	23	1	NM_021025	exon1	c.G105A	p.P35P	CGCCCCGCGGGGC	.	scavenged	Atlas-SNP
LTK	4058	hgsc.bcm.edu	37	15	41801258	41801258	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	161	4	123	1	0.0248447	0.00813008	.	.	none	LTK_ENST00000263800,NS,carcinoma,0,2	LTK	117	2	NM_002344	exon8	c.G1067A	p.S356N	TCGCTGCTGGGGT	.	scavenged	Atlas-SNP
KIF17	57576	hgsc.bcm.edu	37	1	21031010	21031010	+	Silent	SNP	G	G	A	rs76507805	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	168	53	183	0	0.315476	0	G|1.000;A|0.000	0.000	strong	KIF17,colon,carcinoma,0,1	KIF17	130	1	NM_001122819	exon5	c.C1053T	p.R351R	GTACTCGCGAAGC	.	PASS	Atlas-SNP
OR2T35	403244	hgsc.bcm.edu	37	1	248801592	248801592	+	Missense_Mutation	SNP	C	C	T	rs78622116	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	32	2	17	1	0.0625	0.0588235	C|0.245;T|0.755	0.755	strong	OR2T35,caecum,carcinoma,0,1	OR2T35	19	1	NM_001001827	exon1	c.G968A	p.G323D	TGCTAGCCCTTCC	.	scavenged	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107052698	107052698	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	424	4	455	0	0.00943396	0	.	.	none	RGPD3_ENST00000304514,NS,carcinoma,+1,2	RGPD3	316	2	NM_001144013	exon12	c.G1639A	p.G547R	AGTTTCCAGGTCT	.	scavenged	Atlas-SNP
RIMBP2	23504	hgsc.bcm.edu	37	12	130892335	130892335	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	121	42	128	0	0.347107	0	.	.	none	RIMBP2,NS,carcinoma,+1,1	RIMBP2	220	1	NM_015347	exon16	c.C2861T	p.T954M	CTCCGCGTCGATA	.	PASS	Atlas-SNP
DUSP2	1844	hgsc.bcm.edu	37	2	96809900	96809900	+	Silent	SNP	G	G	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	60	25	60	0	0.416667	0	.	.	none	DUSP2,NS,lymphoid_neoplasm,-1,1	DUSP2	20	1	NM_004418	exon3	c.C723G	p.G241G	AATGAAGCCTATG	.	PASS	Atlas-SNP
CDH13	1012	hgsc.bcm.edu	37	16	83813610	83813610	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	80	17	89	0	0.2125	0	.	.	none	.	CDH13	97	.	NM_001220488	exon13	c.A1860G	p.I620M	GCTGATAACCCTG	.	PASS	Atlas-SNP
SNRPD2	6633	hgsc.bcm.edu	37	19	46191649	46191649	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	209	80	169	0	0.382775	0	.	.	none	.	SNRPD2	7	.	NM_004597	exon2	c.G178A	p.D60N	ACCTATCGAAGGC	.	PASS	Atlas-SNP
RFPL1	5988	hgsc.bcm.edu	37	22	29837976	29837976	+	Silent	SNP	C	C	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	239	9	199	4	0.0376569	0.0201005	.	.	none	RFPL1,NS,carcinoma,0,2	RFPL1	43	2	NM_021026	exon2	c.C819A	p.V273V	GAGTGTCTCTGCT	.	scavenged	Atlas-SNP
AUP1	550	hgsc.bcm.edu	37	2	74756500	74756500	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	77	57	117	0	0.74026	0	.	.	none	.	AUP1	29	.	NM_181575	exon2	c.C177T	p.S59S	AAGGACGCTGTCT	.	PASS	Atlas-SNP
RPS6KB2	6199	hgsc.bcm.edu	37	11	67202509	67202509	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	129	2	80	0	0.0155039	0	.	.	none	RPS6KB2_ENST00000312629,colon,carcinoma,-2,4	RPS6KB2	92	4	NM_003952	exon15	c.C1318T	p.P440S	AGCCTGCCGGAGC	.	scavenged	Atlas-SNP
XPOT	11260	hgsc.bcm.edu	37	12	64812733	64812733	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	188	5	173	1	0.0265957	0.00578035	.	.	none	XPOT,bladder,carcinoma,0,5	XPOT	105	5	NM_007235	exon6	c.G348A	p.E116E	TACAGAGTATCTC	.	scavenged	Atlas-SNP
PTPRQ	374462	hgsc.bcm.edu	37	12	80982059	80982059	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	121	3	145	0	0.0247934	0	.	.	none	PTPRQ,colon,carcinoma,0,1	PTPRQ	119	1	NM_001145026	exon23	c.C3921T	p.S1307S	GGAATCCGAAGAA	.	scavenged	Atlas-SNP
DMKN	93099	hgsc.bcm.edu	37	19	36002412	36002412	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	36	4	29	0	0.111111	0	.	.	none	.	DMKN	116	.	NM_001126058	exon5	c.C819T	p.S273S	GCCACTGCTGCTG	.	PASS	Atlas-SNP
MMP19	4327	hgsc.bcm.edu	37	12	56230903	56230903	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	169	3	133	0	0.0177515	0	.	.	none	MMP19,NS,carcinoma,0,1	MMP19	61	1	NM_002429	exon9	c.T1444C	p.S482P	CACCTGATGGGGT	.	scavenged	Atlas-SNP
ADAM17	6868	hgsc.bcm.edu	37	2	9666322	9666322	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	149	4	146	2	0.0268456	0.0136986	.	.	none	ADAM17,NS,carcinoma,+1,1	ADAM17	61	1	NM_003183	exon6	c.C671T	p.T224M	TTACACGTGTTCT	.	scavenged	Atlas-SNP
PSG3	5671	hgsc.bcm.edu	37	19	43243059	43243059	+	Missense_Mutation	SNP	C	C	T	rs202155567	bycluster	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	144	3	168	1	0.0208333	0.00595238	C|0.999;T|0.001	0.001	weak	PSG3,NS,carcinoma,0,1	PSG3	82	1	NM_021016	exon2	c.G247A	p.V83I	CTACTACGTATGA	.	scavenged	Atlas-SNP
KATNAL2	83473	hgsc.bcm.edu	37	18	44580782	44580782	+	Missense_Mutation	SNP	C	C	T	rs181204080	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	192	3	195	0	0.015625	0	C|1.000;T|0.000	0.000	strong	KATNAL2,NS,carcinoma,0,1	KATNAL2	64	1	NM_031303	exon3	c.C89T	p.P30L	ATTTACCGCAAAG	.	scavenged	Atlas-SNP
BRDT	676	hgsc.bcm.edu	37	1	92445221	92445221	+	Silent	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	205	3	212	0	0.0146341	0	.	.	none	BRDT,NS,carcinoma,+1,1	BRDT	133	1	NM_001242806	exon8	c.T1206C	p.G402G	CACTGGTAGAGAG	.	scavenged	Atlas-SNP
NGFR	4804	hgsc.bcm.edu	37	17	47572823	47572823	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	13	5	7	0	0.384615	0	.	.	none	.	NGFR	46	.	NM_002507	exon1	c.T44C	p.L15P	CGCGCCTGCTGCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195518112	195518112	+	Silent	SNP	T	T	A	rs75263205	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	161	18	120	0	0.111801	0	.	.	strong	.	MUC4	1505	.	NM_018406	exon2	c.A339T	p.T113T	AGGAGCTGTCTCC	.	PASS	Atlas-SNP
GOSR2	9570	hgsc.bcm.edu	37	17	45008492	45008492	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	134	3	142	0	0.0223881	0	.	.	none	GOSR2_ENST00000415811,NS,carcinoma,+1,2	GOSR2	38	2	NM_001012511	exon3	c.T122C	p.I41T	CAAGCATAGACCA	.	scavenged	Atlas-SNP
ZNF837	116412	hgsc.bcm.edu	37	19	58879965	58879965	+	Silent	SNP	A	A	G	rs7255489	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	12	12	0	0	1	.	A|0.094;G|0.906	0.906	strong	.	ZNF837	16	.	NM_138466	exon3	c.T735C	p.S245S	TGGGGGACTCTTG	.	PASS	Atlas-SNP
BPI	671	hgsc.bcm.edu	37	20	36936026	36936026	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	192	4	184	0	0.0208333	0	.	.	none	BPI,NS,carcinoma,0,1	BPI	67	1	NM_001725	exon2	c.A200G	p.D67G	TTCCTGACTACTC	.	scavenged	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239613	31239613	+	Missense_Mutation	SNP	C	C	T	rs2308538	bycluster;byfrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	51	5	33	3	0.0980392	0.0909091	T|0.155;C|0.845	0.155	strong	HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	NM_002117	exon2	c.G106A	p.V36M	GGGACACGGCGGT	.	scavenged	Atlas-SNP
MBD5	55777	hgsc.bcm.edu	37	2	149227670	149227670	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	167	5	153	0	0.0299401	0	.	.	none	MBD5,colon,carcinoma,0,1	MBD5	164	1	NM_018328	exon9	c.A2158G	p.T720A	AATAGTACCCCGG	.	scavenged	Atlas-SNP
PRODH2	58510	hgsc.bcm.edu	37	19	36297486	36297486	+	Missense_Mutation	SNP	G	G	A	rs201263714	by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	54	2	69	0	0.037037	0	G|1.000;A|0.000	0.000	strong	PRODH2,NS,carcinoma,+2,1	PRODH2	68	1	NM_021232	exon8	c.C1075T	p.R359W	CCAGCCGCTCGAA	.	scavenged	Atlas-SNP
ZFHX3	463	hgsc.bcm.edu	37	16	72830766	72830766	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	130	49	135	0	0.376923	0	.	.	none	ZFHX3,NS,carcinoma,0,1	ZFHX3	404	1	NM_006885	exon9	c.G5815A	p.D1939N	TGGCATCTGAAGC	.	PASS	Atlas-SNP
AQR	9716	hgsc.bcm.edu	37	15	35174831	35174831	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	104	3	122	0	0.0288462	0	.	.	none	AQR,NS,lymphoid_neoplasm,+1,1	AQR	139	1	NM_014691	exon27	c.G3037A	p.A1013T	CAGAGGCTCTGAA	.	scavenged	Atlas-SNP
TUBGCP2	10844	hgsc.bcm.edu	37	10	135103445	135103445	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	212	3	183	0	0.0141509	0	.	.	none	TUBGCP2,caecum,carcinoma,+1,1	TUBGCP2	79	1	NM_001256617	exon10	c.C1327T	p.R443W	CCTTCCGCAGCTC	.	scavenged	Atlas-SNP
NPAS4	266743	hgsc.bcm.edu	37	11	66191694	66191694	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	74	4	65	0	0.0540541	0	.	.	none	.	NPAS4	133	.	NM_178864	exon7	c.C1333T	p.Q445X	CCCTTCCAGACCC	.	PASS	Atlas-SNP
LRRK2	120892	hgsc.bcm.edu	37	12	40668487	40668487	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	130	3	98	0	0.0230769	0	.	.	none	LRRK2,NS,carcinoma,0,1	LRRK2	763	1	NM_198578	exon15	c.G1759A	p.D587N	GCTATGGATTCAG	.	scavenged	Atlas-SNP
SLC35G3	146861	hgsc.bcm.edu	37	17	33520470	33520470	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	250	3	254	0	0.012	0	.	.	none	AMAC1,NS,carcinoma,+1,1	.	.	1	NM_152462	exon1	c.T857C	p.L286P	GAATGTAGGACAG	.	scavenged	Atlas-SNP
ALG3	10195	hgsc.bcm.edu	37	3	183960348	183960348	+	Missense_Mutation	SNP	G	G	A	rs79144888	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	270	3	222	0	0.0111111	0	G|0.993;A|0.007	0.007	strong	ALG3_ENST00000445626,NS,carcinoma,+1,3	ALG3	48	3	NM_005787	exon9	c.C1271T	p.P424L	GGCTGCGGGCCCA	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152278049	152278049	+	Missense_Mutation	SNP	A	A	C	rs2065958	bycluster;byfrequency;byhapmap	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	18	18	5	5	1	1	A|0.173;C|0.827	0.827	strong	FLG,NS,carcinoma,+2,1	FLG	900	1	NM_002016	exon3	c.T9313G	p.Y3105D	GACCGTATTGGGA	.	scavenged	Atlas-SNP
FSHR	2492	hgsc.bcm.edu	37	2	49190483	49190483	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	111	3	127	0	0.027027	0	.	.	none	FSHR,NS,carcinoma,+2,1	FSHR	164	1	NM_000145	exon10	c.G1477A	p.G493S	TCCAGCCCATCAC	.	scavenged	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17272075	17272075	+	Missense_Mutation	SNP	G	G	A	rs2781608	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	164	9	166	7	0.054878	0.0421687	G|0.934;A|0.066	0.066	strong	CROCC,NS,carcinoma,0,10	CROCC	185	10	NM_014675	exon15	c.G2110A	p.A704T	GAGAAGGCCGAGG	.	scavenged	Atlas-SNP
ADAMTS2	9509	hgsc.bcm.edu	37	5	178552090	178552090	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	121	5	74	1	0.0413223	0.0135135	.	.	none	ADAMTS2,caecum,carcinoma,0,2	ADAMTS2	190	2	NM_014244	exon19	c.G2842A	p.D948N	TGTTGTCGTGTAG	.	scavenged	Atlas-SNP
TP73	7161	hgsc.bcm.edu	37	1	3649562	3649562	+	Silent	SNP	G	G	A	rs9662633	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	15	12	3	0	0.8	0	G|0.903;A|0.097	0.097	strong	.	TP73	54	.	NM_005427	exon14	c.G1830A	p.A610A	GTGGGCGGACTTC	.	PASS	Atlas-SNP
PDS5B	23047	hgsc.bcm.edu	37	13	33316792	33316792	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	123	38	115	0	0.308943	0	.	.	none	.	PDS5B	141	.	NM_015032	exon23	c.G2539A	p.G847R	AAATCAGGAACTT	.	PASS	Atlas-SNP
ADAMTS5	11096	hgsc.bcm.edu	37	21	28327094	28327094	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	58	14	73	0	0.241379	0	.	.	none	.	ADAMTS5	184	.	NM_007038	exon2	c.G1201A	p.G401S	GGAGGCCATCGTC	.	PASS	Atlas-SNP
CNPPD1	27013	hgsc.bcm.edu	37	2	220041491	220041491	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	75	4	46	0	0.0533333	0	.	.	none	.	CNPPD1	22	.	NM_015680	exon1	c.G60A	p.Q20Q	GAAGTCCTGGAAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510910	195510910	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	440	14	398	8	0.0318182	0.0201005	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C7541A	p.P2514H	GTGACAGGTAGAG	.	scavenged	Atlas-SNP
PLCH1	23007	hgsc.bcm.edu	37	3	155205862	155205862	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	84	7	80	0	0.0833333	0	.	.	none	.	PLCH1	406	.	NM_001130960	exon20	c.A2538C	p.E846D	GGATGCTTCTGTC	.	PASS	Atlas-SNP
AKAP9	10142	hgsc.bcm.edu	37	7	91625060	91625060	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	38	15	68	0	0.394737	0	.	.	none	AKAP9_ENST00000356239,NS,carcinoma,+2,2	AKAP9	788	2	NM_005751	exon7	c.A876C	p.E292D	GAAAGAAGACTTC	.	PASS	Atlas-SNP
OR7A5	26659	hgsc.bcm.edu	37	19	14938184	14938184	+	Silent	SNP	A	A	G	rs200531878		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	96	4	62	1	0.0416667	0.016129	A|0.999;G|0.001	0.001	weak	OR7A5,NS,carcinoma,0,1	OR7A5	43	1	NM_017506	exon1	c.T870C	p.Y290Y	CAGACTATAGATA	.	scavenged	Atlas-SNP
RBM20	282996	hgsc.bcm.edu	37	10	112404302	112404302	+	Silent	SNP	G	G	A	rs35141404	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	6	6	0	0	1	.	G|0.808;A|0.192	0.192	strong	.	RBM20	50	.	NM_001134363	exon1	c.G90A	p.R30R	TGCCCGGGCGTCC	.	PASS	Atlas-SNP
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324348	39324348	+	Missense_Mutation	SNP	C	C	T	rs201948308		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	152	30	138	0	0.197368	0	.	.	weak	.	KRTAP4-3	40	.	NM_033187	exon1	c.G77A	p.R26H	CTGGGGCGGCAGC	.	PASS	Atlas-SNP
LMOD3	56203	hgsc.bcm.edu	37	3	69171353	69171353	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	158	3	173	0	0.0189873	0	.	.	none	LMOD3_ENST00000420581,NS,carcinoma,+1,2	LMOD3	92	2	NM_198271	exon1	c.C185T	p.P62L	CCTGTCGGTGGCT	.	scavenged	Atlas-SNP
GRID2	2895	hgsc.bcm.edu	37	4	94376883	94376883	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	180	62	147	0	0.344444	0	.	.	none	GRID2,NS,carcinoma,+1,1	GRID2	233	1	NM_001510	exon11	c.G1616A	p.R539H	CGACACGTTACAT	.	PASS	Atlas-SNP
PRKCB	5579	hgsc.bcm.edu	37	16	24183630	24183630	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	170	59	193	1	0.347059	0.00518135	.	.	none	PRKCB_ENST00000321728,caecum,carcinoma,0,3	PRKCB	383	3	NM_212535	exon11	c.G1279A	p.D427N	GGGGGCGACCTCA	.	scavenged	Atlas-SNP
GGH	8836	hgsc.bcm.edu	37	8	63951312	63951312	+	Missense_Mutation	SNP	A	A	G	rs1800909	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	13	9	5	0	0.692308	0	A|0.769;G|0.231	0.231	strong	.	GGH	32	.	NM_003878	exon1	c.T16C	p.C6R	GCAGGCAGCCCGG	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190873379	190873379	+	Missense_Mutation	SNP	A	A	G	rs1803592		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	106	17	90	10	0.160377	0.111111	.	.	weak	FRG1,arm,malignant_melanoma,0,1	FRG1	76	1	NM_004477	exon3	c.A196G	p.K66E	ATGGATAAGGGAA	.	scavenged	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152470904	152470904	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	237	94	210	0	0.396624	0	.	.	none	.	NEB	1697	.	NM_001271208	exon77	c.G11487A	p.K3829K	CTGACACTTCTTG	.	PASS	Atlas-SNP
SYCE2	256126	hgsc.bcm.edu	37	19	13010850	13010850	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	84	5	87	0	0.0595238	0	.	.	none	.	SYCE2	19	.	NM_001105578	exon5	c.T580C	p.F194L	AAACGAACACGTC	.	PASS	Atlas-SNP
C2orf81	388963	hgsc.bcm.edu	37	2	74642265	74642265	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	5	3	7	0	0.6	0	.	.	none	C2orf81,colon,carcinoma,0,1	C2orf81	23	1	NM_001145054	exon4	c.T958G	p.S320A	GGCAGGACGCGGA	.	scavenged	Atlas-SNP
CST2	1470	hgsc.bcm.edu	37	20	23805955	23805955	+	Silent	SNP	C	C	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	110	4	110	3	0.0363636	0.0272727	.	.	none	CST2,colon,carcinoma,-2,1	CST2	39	1	NM_001322	exon2	c.G234T	p.V78V	CCCGCCCACGATC	.	scavenged	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104448968	104448968	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	159	3	141	1	0.0188679	0.0070922	.	.	none	GRIN3A,NS,malignant_melanoma,+1,1	GRIN3A	186	1	NM_133445	exon2	c.T1214C	p.M405T	TGGATCATGGTGG	.	scavenged	Atlas-SNP
OVGP1	5016	hgsc.bcm.edu	37	1	111957523	111957523	+	Missense_Mutation	SNP	G	G	T	rs3767608	bycluster;by1000genomes;alternate_allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	144	22	130	0	0.152778	0	G|1.000;A|0.000	.	alt	OVGP1_ENST00000369728,NS,carcinoma,0,2	OVGP1	177	2	NM_002557	exon11	c.C1600A	p.P534T	TCACAGGGGTCAC	.	PASS	Atlas-SNP
KANK1	23189	hgsc.bcm.edu	37	9	731215	731215	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	153	69	126	0	0.45098	0	.	.	none	.	KANK1	231	.	NM_001256876	exon9	c.A2954G	p.K985R	GTAACAAAGATTC	.	PASS	Atlas-SNP
STPG2	285555	hgsc.bcm.edu	37	4	98893436	98893436	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	175	66	162	0	0.377143	0	.	.	none	.	.	.	.	NM_174952	exon7	c.T928G	p.Y310D	CCTGATAATCAGC	.	PASS	Atlas-SNP
CALCR	799	hgsc.bcm.edu	37	7	93108736	93108736	+	Silent	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	283	4	282	0	0.0141343	0	.	.	none	CALCR_ENST00000359558,rectum,carcinoma,-1,7	CALCR	200	7	NM_001164737	exon5	c.A189G	p.R63R	CTTCTTTCGTCCT	.	scavenged	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	128769016	128769016	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	170	2	146	0	0.0117647	0	.	.	none	DOCK1,NS,carcinoma,-2,1	DOCK1	188	1	NM_001380	exon2	c.G97T	p.G33X	CAGATCGGAGACA	.	scavenged	Atlas-SNP
SLC39A3	29985	hgsc.bcm.edu	37	19	2732986	2732986	+	Silent	SNP	T	T	C	rs759073	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	5	5	0	0	1	.	T|0.411;C|0.589	0.589	strong	SLC39A3,NS,carcinoma,0,1	SLC39A3	20	1	NM_144564	exon3	c.A708G	p.V236V	GGCGCTTACGGTG	.	scavenged	Atlas-SNP
CDH11	1009	hgsc.bcm.edu	37	16	65022114	65022114	+	Silent	SNP	C	C	T	rs28216	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	260	3	276	2	0.0115385	0.00724638	C|0.715;T|0.285	0.285	strong	CDH11_ENST00000394156,NS,carcinoma,-1,2	CDH11	260	2	NM_001797	exon7	c.G945A	p.S315S	TTCAAACGATTCC	.	scavenged	Atlas-SNP
NPY2R	4887	hgsc.bcm.edu	37	4	156135863	156135863	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	96	41	117	0	0.427083	0	.	.	none	.	NPY2R	87	.	NM_000910	exon2	c.C772T	p.H258Y	AATGACCACTACC	.	PASS	Atlas-SNP
SLC14A2	8170	hgsc.bcm.edu	37	18	43262359	43262359	+	Missense_Mutation	SNP	G	G	A	rs3745009	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	234	4	194	0	0.017094	0	G|0.573;A|0.427	0.427	strong	SLC14A2,NS,carcinoma,0,2	SLC14A2	121	2	NM_001242692	exon21	c.G2638A	p.A880T	AACCCCGCCATCT	.	scavenged	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230315	23230315	+	Silent	SNP	C	C	T	rs148489860	by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	140	60	108	0	0.428571	0	C|1.000;T|0.000	0.000	strong	.	IGLL5	26	.	NM_001178126	exon1	c.C82T	p.L28L	CTGCTGCTGCTGG	.	PASS	Atlas-SNP
CLVS1	157807	hgsc.bcm.edu	37	8	62289218	62289218	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	89	32	85	0	0.359551	0	.	.	none	CLVS1,NS,carcinoma,+2,1	CLVS1	74	1	NM_173519	exon3	c.C510T	p.I170I	CCTAATCGAAGAT	.	PASS	Atlas-SNP
ZNF799	90576	hgsc.bcm.edu	37	19	12501620	12501620	+	Missense_Mutation	SNP	G	G	T	rs370276871	alternate_allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	127	2	95	0	0.015748	0	.	.	alt	ZNF799_ENST00000430385,NS,carcinoma,+1,2	ZNF799	111	2	NM_001080821	exon4	c.C1592A	p.P531Q	TCATACGGCTTCT	.	scavenged	Atlas-SNP
DGKZ	8525	hgsc.bcm.edu	37	11	46388920	46388920	+	Missense_Mutation	SNP	C	C	T	rs375162900		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	241	4	228	1	0.0165975	0.00438596	.	.	weak	DGKZ_ENST00000454345,right_upper_lobe,carcinoma,0,3	DGKZ	199	3	NM_001105540	exon3	c.C808T	p.R270W	TCAGAGCGGCAGA	.	scavenged	Atlas-SNP
SCN9A	6335	hgsc.bcm.edu	37	2	167094711	167094711	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	244	3	293	0	0.0122951	0	.	.	none	SCN9A,NS,carcinoma,+2,1	SCN9A	296	1	NM_002977	exon20	c.A3661G	p.I1221V	TGAAGATCTTGTC	.	scavenged	Atlas-SNP
GTF2E1	2960	hgsc.bcm.edu	37	3	120500292	120500292	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	204	3	194	0	0.0147059	0	.	.	none	GTF2E1,colon,carcinoma,0,3	GTF2E1	52	3	NM_005513	exon5	c.G1295A	p.R432H	GACAACGCATGTT	.	scavenged	Atlas-SNP
POTEE	445582	hgsc.bcm.edu	37	2	132021475	132021475	+	Missense_Mutation	SNP	G	G	A	rs11546936	bycluster	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	152	14	162	7	0.0921053	0.0432099	.	.	weak	ENSG00000188219,NS,carcinoma,+1,2	.	.	2	NM_001083538	exon15	c.G2447A	p.R816H	CCAACCGCGAGAA	.	scavenged	Atlas-SNP
GPX5	2880	hgsc.bcm.edu	37	6	28500106	28500106	+	Missense_Mutation	SNP	G	G	A	rs138279209		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	121	95	125	0	0.785124	0	G|1.000;A|0.000	0.000	weak	.	GPX5	42	.	NM_001509	exon4	c.G368A	p.R123H	ATGTCCGTCCAGG	.	PASS	Atlas-SNP
CACNA1G	8913	hgsc.bcm.edu	37	17	48684317	48684317	+	Silent	SNP	C	C	T	rs372261823		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	168	3	150	1	0.0178571	0.00666667	.	.	weak	CACNA1G_ENST00000359106,NS,carcinoma,0,3	CACNA1G	659	3	NM_001256360	exon24	c.C4479T	p.Y1493Y	CATGTACGATGGG	.	scavenged	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124415065	124415065	+	Silent	SNP	C	C	T	rs199791998	by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	151	3	159	0	0.0198676	0	C|1.000;T|0.000	0.000	strong	TRAD,colon,carcinoma,0,2	KALRN	556	2	NM_001024660	exon54	c.C7662T	p.H2554H	TGACCACGGGACC	.	scavenged	Atlas-SNP
TBP	6908	hgsc.bcm.edu	37	6	170871043	170871043	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	41	2	49	2	0.0487805	0.0408163	.	.	none	TBP,NS,carcinoma,0,1	TBP	58	1	NM_003194	exon3	c.G219A	p.Q73Q	GCAACAGCAACAG	.	scavenged	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	37	2	185463692	185463692	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	45	19	42	0	0.422222	0	.	.	none	.	ZNF804A	322	.	NM_194250	exon1	c.G6A	p.E2E	CATGGAGTGTTAC	.	PASS	Atlas-SNP
BTG1	694	hgsc.bcm.edu	37	12	92539304	92539304	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	83	39	57	0	0.46988	0	.	.	none	.	BTG1	30	.	NM_001731	exon1	c.C8G	p.P3R	TAGAAGGGATGCA	.	PASS	Atlas-SNP
ELN	2006	hgsc.bcm.edu	37	7	73474235	73474235	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	155	3	122	2	0.0193548	0.0163934	.	.	none	ELN,NS,carcinoma,+2,2	ELN	81	2	NM_001081754	exon23	c.C1449T	p.G483G	TGTCGGCGTGGCT	.	scavenged	Atlas-SNP
KIAA1199	57214	hgsc.bcm.edu	37	15	81201536	81201536	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	187	2	165	0	0.0106952	0	.	.	none	KIAA1199,NS,lymphoid_neoplasm,0,1	KIAA1199	118	1	NM_018689	exon13	c.C1686T	p.A562A	CCTGGCCGGTGAT	.	scavenged	Atlas-SNP
LPHN1	22859	hgsc.bcm.edu	37	19	14261777	14261777	+	Missense_Mutation	SNP	G	G	A	rs375528213		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	110	41	39	0	0.372727	0	.	.	weak	.	LPHN1	107	.	NM_001008701	exon24	c.C4333T	p.R1445C	TAGGACGCCGCAC	.	PASS	Atlas-SNP
ZNF223	7766	hgsc.bcm.edu	37	19	44571010	44571010	+	Silent	SNP	A	A	G	rs141349301	bycluster;by1000genomes;alternate_allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	68	15	58	0	0.220588	0	A|1.000;T|0.000	.	alt	.	ZNF223	61	.	NM_013361	exon5	c.A1029G	p.P343P	GAAACCATATAAT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494230	134494230	+	Silent	SNP	C	C	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	212	28	188	0	0.132075	0	.	.	none	.	SGK1	387	.	NM_001143676	exon8	c.G765T	p.V255V	AAGGCCCACCAGG	.	PASS	Atlas-SNP
FCAMR	83953	hgsc.bcm.edu	37	1	207140994	207140994	+	Silent	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	139	6	117	0	0.0431655	0	.	.	none	.	FCAMR	125	.	NM_001170631	exon2	c.A42G	p.E14E	CACCACTTCCTGT	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230333	23230333	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	126	50	108	0	0.396825	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.G100A	p.V34I	GCCATGGTCGCCC	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38840382	38840382	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	52	2	76	2	0.0384615	0.0263158	.	.	none	DNAH8_ENST00000359357,NS,carcinoma,+1,2	DNAH8	1239	2	NM_001206927	exon50	c.T7061C	p.V2354A	CAACCGTTATCAC	.	scavenged	Atlas-SNP
PLCH2	9651	hgsc.bcm.edu	37	1	2429995	2429995	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	121	4	106	0	0.0330578	0	.	.	none	PLCH2_ENST00000378486,right_lower_lobe,carcinoma,-1,2	PLCH2	131	2	NM_014638	exon17	c.C2258T	p.P753L	CCCTGCCCGGGCA	.	scavenged	Atlas-SNP
HIST1H1B	3009	hgsc.bcm.edu	37	6	27834991	27834991	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	99	43	132	0	0.434343	0	.	.	none	.	HIST1H1B	54	.	NM_005322	exon1	c.G317C	p.G106A	AAGGAGCCAGAAG	.	PASS	Atlas-SNP
CYP4A11	1579	hgsc.bcm.edu	37	1	47395874	47395874	+	Missense_Mutation	SNP	A	A	C	rs45475502		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	212	3	206	2	0.0141509	0.00970874	.	.	weak	CYP4A11,NS,carcinoma,0,1	CYP4A11	77	1	NM_000778	exon12	c.T1473G	p.I491M	TCGTGCAATGGGG	.	scavenged	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38120300	38120300	+	Silent	SNP	T	T	C	rs58793439	bycluster	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	373	19	302	6	0.0509383	0.0198676	T|0.500;C|0.500	0.500	weak	TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	1	NM_001039141	exon7	c.T1737C	p.C579C	ATCCTGTGCCCAG	.	scavenged	Atlas-SNP
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067104	46067104	+	Silent	SNP	C	C	T	rs75548048	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	111	10	88	0	0.0900901	0	C|0.980;T|0.020	0.020	strong	.	KRTAP10-11	36	.	NM_198692	exon1	c.C729T	p.P243P	CCACCCCGTGTGC	.	PASS	Atlas-SNP
LRRC32	2615	hgsc.bcm.edu	37	11	76371849	76371849	+	Missense_Mutation	SNP	G	G	A	rs201402758	bycluster	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	174	59	121	0	0.33908	0	.	.	weak	.	LRRC32	74	.	NM_005512	exon3	c.C788T	p.A263V	GGGAGCGCGGCCA	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152679666	152679666	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	127	39	135	1	0.307087	0.00740741	.	.	none	SYNE1_ENST00000423061,NS,carcinoma,0,3	SYNE1	3227	3	NM_033071	exon66	c.G10471A	p.V3491I	TGGTTACGGCTTC	.	scavenged	Atlas-SNP
BNIPL	149428	hgsc.bcm.edu	37	1	151018347	151018347	+	Missense_Mutation	SNP	G	G	T	rs200161296	by1000genomes;alternate_allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	137	3	132	0	0.0218978	0	G|1.000;A|0.000	.	alt	BNIPL_ENST00000368931,NS,carcinoma,0,2	BNIPL	45	2	NM_138278	exon8	c.G926T	p.R309L	TGCTTCGGCCCTT	.	scavenged	Atlas-SNP
PTCH1	5727	hgsc.bcm.edu	37	9	98241360	98241360	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	153	4	149	0	0.0261438	0	.	.	none	PTCH1_ENST00000430669,colon,carcinoma,-1,8	PTCH1	1850	8	NM_000264	exon8	c.C1137T	p.Y379Y	ATACTCGTACCCC	.	scavenged	Atlas-SNP
C21orf2	755	hgsc.bcm.edu	37	21	45753031	45753031	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	100	4	63	0	0.04	0	.	.	none	.	C21orf2	10	.	NM_004928	exon4	c.G258A	p.L86L	ACGCGGCAGCCCC	.	PASS	Atlas-SNP
MYO1D	4642	hgsc.bcm.edu	37	17	30932257	30932257	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	103	43	119	0	0.417476	0	.	.	none	.	MYO1D	93	.	NM_015194	exon21	c.G2712T	p.L904F	ACCAGTCAACTGC	.	PASS	Atlas-SNP
ZNF749	388567	hgsc.bcm.edu	37	19	57955884	57955884	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	172	5	189	0	0.0290698	0	.	.	none	ZNF749,NS,carcinoma,0,2	ZNF749	75	2	NM_001023561	exon3	c.C1368T	p.H456H	TCAGCACCAGAAA	.	scavenged	Atlas-SNP
NPSR1	387129	hgsc.bcm.edu	37	7	34917701	34917701	+	Missense_Mutation	SNP	C	C	T	rs370072027		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	209	3	229	0	0.0143541	0	.	.	weak	NPSR1_ENST00000359791,caecum,carcinoma,0,1	NPSR1	134	1	NM_207173	exon9	c.C1039T	p.R347C	CGTCTCCGTCAGC	.	scavenged	Atlas-SNP
PRKACA	5566	hgsc.bcm.edu	37	19	14204559	14204559	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	162	67	152	0	0.41358	0	.	.	none	.	PRKACA	65	.	NM_002730	exon9	c.C811T	p.R271W	GGTTCCGCAGCAG	.	PASS	Atlas-SNP
RTP2	344892	hgsc.bcm.edu	37	3	187416659	187416659	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	247	2	195	0	0.00809717	0	.	.	none	RTP2,colon,carcinoma,+1,1	RTP2	38	1	NM_001004312	exon2	c.C305T	p.A102V	AGCCGCGCCGTGC	.	scavenged	Atlas-SNP
WSCD2	9671	hgsc.bcm.edu	37	12	108620920	108620920	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	102	17	106	0	0.166667	0	.	.	none	.	WSCD2	125	.	NM_014653	exon6	c.G958A	p.V320M	TTCATTGTGTACC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092890	1092890	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	96	7	79	5	0.0729167	0.0632911	.	.	none	MUC2_ENST00000441003,NS,carcinoma,-1,2	MUC2	614	2	NM_002457	exon30	c.C4709T	p.T1570I	CGGTGACCCCAAC	.	scavenged	Atlas-SNP
ND3	0	hgsc.bcm.edu	37	MT	10310	10310	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	4	4	0	0	1	.	.	.	none	.	.	.	.	ENST00000361227	exon1	c.G252A	p.L84L	TAACCTGCCACTA	.	PASS	Atlas-SNP
MPDZ	8777	hgsc.bcm.edu	37	9	13138056	13138056	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	195	4	206	0	0.0205128	0	.	.	none	MPDZ_ENST00000541718,colon,carcinoma,0,2	MPDZ	324	2	NM_003829	exon29	c.A4100G	p.N1367S	TCTTTGTTCCCAG	.	scavenged	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60887468	60887468	+	Silent	SNP	G	G	A	rs16985970	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	4	4	1	0	1	0	G|0.928;A|0.072	0.072	strong	.	LAMA5	268	.	NM_005560	exon68	c.C9348T	p.T3116T	GTCGGCGGTGCAG	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230364	23230364	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	142	58	109	0	0.408451	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.C131A	p.A44E	TGGTTGCACCGCA	.	PASS	Atlas-SNP
DEK	7913	hgsc.bcm.edu	37	6	18249894	18249894	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	89	33	124	0	0.370787	0	.	.	none	DEK,NS,carcinoma,0,1	DEK	31	1	NM_003472	exon7	c.A750C	p.E250D	TTCACTTTCTTTA	.	PASS	Atlas-SNP
CYP2A6	1548	hgsc.bcm.edu	37	19	41355765	41355765	+	Nonsense_Mutation	SNP	G	G	A	rs199545200	by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	344	5	306	4	0.0145349	0.0130719	G|1.000;A|0.000	0.000	strong	CYP2A6,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	CYP2A6	69	1	NM_000762	exon2	c.C301T	p.R101X	CGCCTCGCCCGCT	.	scavenged	Atlas-SNP
LRP12	29967	hgsc.bcm.edu	37	8	105509255	105509255	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	153	3	177	0	0.0196078	0	.	.	none	LRP12,NS,adenocarcinoma,0,1	LRP12	124	1	NM_013437	exon5	c.G1525A	p.V509I	CTATGACGAGTAA	.	scavenged	Atlas-SNP
RNF133	168433	hgsc.bcm.edu	37	7	122338692	122338692	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	73	26	112	0	0.356164	0	.	.	none	.	RNF133	41	.	NM_139175	exon1	c.G281A	p.R94Q	TTTGATCGGCTGA	.	PASS	Atlas-SNP
GPR32	2854	hgsc.bcm.edu	37	19	51274851	51274851	+	Missense_Mutation	SNP	A	A	C	rs78840344	bycluster	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	106	9	67	0	0.0849057	0	.	.	weak	GPR32,NS,carcinoma,0,5	GPR32	68	5	NM_001506	exon1	c.A994C	p.T332P	TCTTTGACTTCTG	.	scavenged	Atlas-SNP
TECRL	253017	hgsc.bcm.edu	37	4	65188493	65188493	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	98	4	128	0	0.0408163	0	.	.	none	.	TECRL	106	.	NM_001010874	exon4	c.G349A	p.D117N	TGTAGTCCTTCAA	.	PASS	Atlas-SNP
CADM2	253559	hgsc.bcm.edu	37	3	85932591	85932591	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	59	22	79	0	0.372881	0	.	.	none	.	CADM2	195	.	NM_001167675	exon4	c.T389G	p.L130R	CCGTTCTGGGTAA	.	PASS	Atlas-SNP
HTR7	3363	hgsc.bcm.edu	37	10	92509323	92509323	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	87	4	83	0	0.045977	0	.	.	none	.	HTR7	122	.	NM_019860	exon2	c.T568C	p.Y190H	CAGGGTATGTGAG	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26165124	26165124	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	86	2	65	0	0.0232558	0	.	.	none	MYO18B,NS,carcinoma,0,1	MYO18B	322	1	NM_032608	exon4	c.A1241G	p.K414R	CAGAGAAGGGCTG	.	scavenged	Atlas-SNP
ITSN1	6453	hgsc.bcm.edu	37	21	35190669	35190669	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	142	60	155	0	0.422535	0	.	.	none	.	ITSN1	166	.	NM_001001132	exon23	c.C2826T	p.V942V	CACCGTCCTGGAA	.	PASS	Atlas-SNP
MYOF	26509	hgsc.bcm.edu	37	10	95089487	95089487	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	143	63	131	0	0.440559	0	.	.	none	.	MYOF	177	.	NM_013451	exon44	c.T4916C	p.I1639T	AGATCAATAATTG	.	PASS	Atlas-SNP
PARD6G	84552	hgsc.bcm.edu	37	18	77960661	77960661	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	91	42	136	0	0.461538	0	.	.	none	.	PARD6G	20	.	NM_032510	exon2	c.A227G	p.N76S	TCATCATTGTTGA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105411852	105411852	+	Silent	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	222	5	196	1	0.0225225	0.00510204	.	.	none	AHNAK2_ENST00000333244,NS,carcinoma,-1,1	AHNAK2	719	1	NM_138420	exon7	c.A9936G	p.K3312K	CTTGAATTTGGGC	.	scavenged	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487265	32487265	+	Missense_Mutation	SNP	C	C	G	rs139485758	bycluster;byfrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	47	24	104	5	0.510638	0.0480769	A|0.003;C|0.930;G|0.067	0.067	strong	HLA-DRB5,NS,NS,0,1	HLA-DRB5	31	1	NM_002125	exon3	c.G534C	p.Q178H	TCCATTCTGAATC	.	scavenged	Atlas-SNP
DENND4B	9909	hgsc.bcm.edu	37	1	153907303	153907303	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	83	2	71	0	0.0240964	0	.	.	none	DENND4B_ENST00000361217,bladder,carcinoma,0,2	DENND4B	210	2	NM_014856	exon18	c.G2706A	p.Q902Q	CTGCTGCTGTTGC	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506555	195506555	+	Missense_Mutation	SNP	C	C	T	rs368695884		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	33	6	31	1	0.181818	0.0322581	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G11896A	p.A3966T	AGGTGGCGTGACC	.	scavenged	Atlas-SNP
CEP170B	283638	hgsc.bcm.edu	37	14	105354293	105354293	+	Silent	SNP	A	A	G	rs2582548	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	11	6	4	0	0.545455	0	A|0.444;G|0.556	0.556	strong	KIAA0284_ENST00000414716,NS,carcinoma,0,2	.	.	2	NM_001112726	exon12	c.A3717G	p.S1239S	CCGCTCAGGCAGT	.	PASS	Atlas-SNP
LCP2	3937	hgsc.bcm.edu	37	5	169695446	169695446	+	Silent	SNP	C	C	T	rs2292254	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	5	4	6	4	0.8	0.666667	C|0.530;T|0.470	0.470	strong	LCP2_ENST00000046794,NS,carcinoma,0,2	LCP2	133	2	NM_005565	exon8	c.G564A	p.V188V	GGGGGGCACAGGA	.	scavenged	Atlas-SNP
ZNF653	115950	hgsc.bcm.edu	37	19	11598600	11598600	+	Silent	SNP	C	C	T	rs184960221	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	57	5	36	1	0.0877193	0.0277778	C|0.959;T|0.041	0.041	strong	ZNF653,NS,carcinoma,0,1	ZNF653	48	1	NM_138783	exon4	c.G678A	p.T226T	GGTGGGCGTCGCT	.	scavenged	Atlas-SNP
ARHGAP5	394	hgsc.bcm.edu	37	14	32560563	32560563	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	200	3	254	0	0.015	0	.	.	none	ARHGAP5,colon,NS,0,1	ARHGAP5	166	1	NM_001173	exon2	c.C688T	p.R230X	TCAGCACGATTTA	.	scavenged	Atlas-SNP
MGARP	84709	hgsc.bcm.edu	37	4	140187819	140187819	+	Silent	SNP	G	G	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	124	2	98	1	0.016129	0.0102041	.	.	none	C4orf49,NS,carcinoma,0,1	.	.	1	NM_032623	exon4	c.C657A	p.S219S	AGCAGAGGACTCT	.	scavenged	Atlas-SNP
POLR3C	10623	hgsc.bcm.edu	37	1	145601603	145601603	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	191	3	153	0	0.0157068	0	.	.	none	POLR3C,caecum,carcinoma,0,1	POLR3C	41	1	NM_006468	exon7	c.G803A	p.R268Q	ATGGTTCGCACAA	.	scavenged	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017575	1017575	+	Silent	SNP	C	C	T	rs76222533	bycluster;byfrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	985	100	854	72	0.101523	0.0843091	C|0.500;T|0.500	0.500	strong	MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.G5226A	p.T1742T	TTTGGCCGTGCTA	.	scavenged	Atlas-SNP
L3HYPDH	112849	hgsc.bcm.edu	37	14	59950587	59950587	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	16	8	9	0	0.5	0	.	.	none	.	.	.	.	NM_144581	exon1	c.G448A	p.D150N	GGCCGTCCTCGCA	.	PASS	Atlas-SNP
BAI1	575	hgsc.bcm.edu	37	8	143625724	143625724	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	43	20	12	0	0.465116	0	.	.	none	.	BAI1	146	.	NM_001702	exon30	c.C4701T	p.G1567G	GTCGGGCGCCACG	.	PASS	Atlas-SNP
BRIP1	83990	hgsc.bcm.edu	37	17	59853911	59853911	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	77	3	89	0	0.038961	0	.	.	none	BRIP1_ENST00000259008,caecum,carcinoma,+2,3	BRIP1	237	3	NM_032043	exon14	c.A1948G	p.T650A	CAATGGTACCAAC	.	scavenged	Atlas-SNP
CYP2D6	1565	hgsc.bcm.edu	37	22	42523539	42523539	+	Silent	SNP	A	A	G	rs28371726	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	260	8	230	2	0.0307692	0.00869565	A|0.959;G|0.041	0.041	strong	CYP2D6_ENST00000360608,NS,carcinoma,0,4	CYP2D6	104	4	NM_000106	exon7	c.T1083C	p.H361H	CACCTCATGAATC	.	scavenged	Atlas-SNP
ATP2B4	493	hgsc.bcm.edu	37	1	203680025	203680025	+	Missense_Mutation	SNP	G	G	A	rs200815867	bycluster	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	137	3	144	0	0.0218978	0	G|0.999;A|0.001	0.001	weak	ATP2B4_ENST00000367218,bladder,carcinoma,-1,2	ATP2B4	226	2	NM_001001396	exon12	c.G1820A	p.R607Q	TGGACCGGAAAGG	.	scavenged	Atlas-SNP
OR4D9	390199	hgsc.bcm.edu	37	11	59282709	59282709	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	119	2	142	0	0.0168067	0	.	.	none	OR4D9,brain,glioma,+2,1	OR4D9	47	1	NM_001004711	exon1	c.G324A	p.G108G	TCTGGGGGGAGCA	.	scavenged	Atlas-SNP
KIAA1377	57562	hgsc.bcm.edu	37	11	101834043	101834043	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	80	9	69	0	0.1125	0	.	.	none	.	KIAA1377	111	.	NM_020802	exon6	c.A2277C	p.K759N	TAGAAAACCAGGA	.	PASS	Atlas-SNP
COL16A1	1307	hgsc.bcm.edu	37	1	32164126	32164126	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	83	7	58	0	0.0843373	0	.	.	none	.	COL16A1	137	.	NM_001856	exon5	c.G348A	p.T116T	ATACCACGTCTTC	.	PASS	Atlas-SNP
HIST2H2BE	8349	hgsc.bcm.edu	37	1	149857830	149857830	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	117	38	80	0	0.324786	0	.	.	none	.	HIST2H2BE	33	.	NM_003528	exon1	c.A361G	p.K121E	TGTACTTGGTGAC	.	PASS	Atlas-SNP
FAM171A1	221061	hgsc.bcm.edu	37	10	15255321	15255321	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	171	3	148	1	0.0175439	0.00675676	.	.	none	FAM171A1_ENST00000378116,colon,carcinoma,+1,2	FAM171A1	252	2	NM_001010924	exon8	c.A2266G	p.R756G	CTCCCCTTCCCTT	.	scavenged	Atlas-SNP
PCDHA10	56139	hgsc.bcm.edu	37	5	140236835	140236835	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	189	77	130	0	0.407407	0	.	.	none	.	PCDHA10	358	.	NM_031859	exon1	c.A1202G	p.K401R	CCTACAAGAATTA	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44891010	44891010	+	Missense_Mutation	SNP	G	G	C	rs150792548	bycluster;byfrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	119	7	128	1	0.0588235	0.0078125	A|0.002;C|0.002;G|0.995	0.002	strong	ZNF285,NS,carcinoma,+1,2	ZNF285	86	2	NM_152354	exon4	c.C1397G	p.A466G	CTATACGCAAAAT	.	scavenged	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9012826	9012826	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	220	4	174	1	0.0181818	0.00574713	.	.	none	MUC16_ENST00000397910,NS,lymphoid_neoplasm,0,2	MUC16	4315	2	NM_024690	exon34	c.A38618G	p.H12873R	GGGTGATGCATGT	.	scavenged	Atlas-SNP
P2RY8	286530	hgsc.bcm.edu	37	X	1585217	1585217	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	260	105	218	0	0.403846	0	.	.	none	.	P2RY8	53	.	NM_178129	exon2	c.C235A	p.Q79K	AGATTTGGAAAGG	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230312	23230312	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	142	61	108	0	0.429577	0	.	.	none	IGLL5,NS,lymphoid_neoplasm,-2,1	IGLL5	26	1	NM_001178126	exon1	c.C79G	p.L27V	CCCCTGCTGCTGC	.	PASS	Atlas-SNP
OR5B3	441608	hgsc.bcm.edu	37	11	58170412	58170412	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	100	4	89	0	0.04	0	.	.	none	OR5B3,right_upper_lobe,carcinoma,-2,1	OR5B3	65	1	NM_001005469	exon1	c.C471T	p.H157H	CCCAGTGTGGATG	.	PASS	Atlas-SNP
PGM3	5238	hgsc.bcm.edu	37	6	83898451	83898451	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	90	34	108	0	0.377778	0	.	.	none	.	PGM3	39	.	NM_001199917	exon4	c.G355A	p.A119T	AGGTGGCATGTTC	.	PASS	Atlas-SNP
RIMS2	9699	hgsc.bcm.edu	37	8	104513174	104513174	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	93	6	71	0	0.0645161	0	.	.	none	.	RIMS2	1357	.	NM_001100117	exon1	c.G60A	p.P20P	TCAGCCGCCTCTG	.	PASS	Atlas-SNP
PPP2R5B	5526	hgsc.bcm.edu	37	11	64700699	64700699	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	64	4	54	0	0.0625	0	.	.	none	.	PPP2R5B	47	.	NM_006244	exon13	c.T1327C	p.Y443H	GCCTCCTACAAGC	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230402	23230402	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	146	61	101	0	0.417808	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.G169A	p.G57R	TCAGTTGGAAGCA	.	PASS	Atlas-SNP
BTBD10	84280	hgsc.bcm.edu	37	11	13410601	13410601	+	Missense_Mutation	SNP	C	C	T	rs75019394	bycluster	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	186	2	201	0	0.0107527	0	.	.	weak	BTBD10,NS,carcinoma,0,1	BTBD10	43	1	NM_032320	exon9	c.G1205A	p.R402Q	GACATTCGAATAA	.	scavenged	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	37	7	2977605	2977605	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	69	33	52	0	0.478261	0	.	.	none	CARD11,colon,carcinoma,-1,4	CARD11	339	4	NM_032415	exon8	c.T1079C	p.M360T	TTGTACATTTCAC	.	PASS	Atlas-SNP
GDPD4	220032	hgsc.bcm.edu	37	11	76996151	76996151	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	88	26	67	0	0.295455	0	.	.	none	.	GDPD4	49	.	NM_182833	exon2	c.G32A	p.S11N	TATTCACTGGATG	.	PASS	Atlas-SNP
PDGFC	56034	hgsc.bcm.edu	37	4	157689051	157689051	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	94	38	110	0	0.404255	0	.	.	none	.	PDGFC	46	.	NM_016205	exon5	c.A795T	p.R265S	ATCGGTTCTCTTT	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216495278	216495278	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	151	9	172	0	0.0596026	0	.	.	none	.	USH2A	1168	.	NM_007123	exon9	c.A1591C	p.S531R	GCTGGCTTGTTGT	.	PASS	Atlas-SNP
TXK	7294	hgsc.bcm.edu	37	4	48096117	48096117	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	86	2	89	0	0.0232558	0	.	.	none	TXK,rectum,carcinoma,+1,1	TXK	58	1	NM_003328	exon8	c.G686A	p.W229X	TGATACCAGATTA	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195518110	195518110	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	156	11	121	0	0.0705128	0	.	.	none	MUC4_ENST00000463781,caecum,adenoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C341T	p.A114V	GGAGGAGCTGTCT	.	PASS	Atlas-SNP
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197304	39197304	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	120	7	71	3	0.0583333	0.0422535	.	.	none	KRTAP1-1,NS,malignant_melanoma,0,1	KRTAP1-1	23	1	NM_030967	exon1	c.A346G	p.I116V	ACCTGATACGGGT	.	scavenged	Atlas-SNP
OR2W5	441932	hgsc.bcm.edu	37	1	247654916	247654916	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	124	4	120	0	0.0322581	0	.	.	none	OR2W5,NS,adenocarcinoma,-2,1	OR2W5	97	1	NM_001004698	exon1	c.A487G	p.T163A	CCTCAGACGATGC	.	scavenged	Atlas-SNP
FAM86C1	55199	hgsc.bcm.edu	37	11	71498601	71498601	+	Missense_Mutation	SNP	G	G	T	rs71466343		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	11	3	8	1	0.272727	0.125	T|1.000;|0.000	1.000	weak	FAM86C1_ENST00000426628,rectum,carcinoma,0,2	FAM86C1	27	2	NM_152563	exon1	c.G19T	p.A7S	GAGAACGCGGGGA	.	scavenged	Atlas-SNP
GUCY1A3	2982	hgsc.bcm.edu	37	4	156634257	156634257	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	113	39	119	0	0.345133	0	.	.	none	.	GUCY1A3	133	.	NM_001130687	exon7	c.A1094G	p.D365G	TTATGGACCTCAA	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138355	37138355	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	33	10	29	0	0.30303	0	.	.	none	PIM1,NS,lymphoid_neoplasm,0,3	PIM1	71	3	NM_001243186	exon1	c.C277T	p.L93F	GGGATGCTCTTGT	.	PASS	Atlas-SNP
OR5C1	392391	hgsc.bcm.edu	37	9	125551542	125551542	+	Silent	SNP	C	C	T	rs201755571	by1000genomes;alternate_allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	81	4	91	0	0.0493827	0	C|1.000;A|0.000	.	alt	.	OR5C1	45	.	NM_001001923	exon1	c.C331T	p.L111L	GCAGGTCTGGCTG	.	PASS	Atlas-SNP
KIR2DL4	3805	hgsc.bcm.edu	37	19	55324635	55324635	+	Silent	SNP	T	T	C	rs649216	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	14	14	2	2	1	1	T|0.315;C|0.685	0.685	strong	KIR2DL4,NS,carcinoma,0,2	KIR2DL4	62	2	NM_001080772	exon6	c.C762C	p.F254F	CCTCTTTACCATC	.	scavenged	Atlas-SNP
DUSP2	1844	hgsc.bcm.edu	37	2	96810590	96810590	+	Silent	SNP	G	G	C	rs187607778	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	97	48	84	0	0.494845	0	C|0.000;G|1.000	0.000	strong	DUSP2,NS,carcinoma,0,1	DUSP2	20	1	NM_004418	exon2	c.C420G	p.P140P	CAGATCGGGACAG	.	PASS	Atlas-SNP
ARHGAP18	93663	hgsc.bcm.edu	37	6	129939832	129939832	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	106	2	107	0	0.0188679	0	.	.	none	ARHGAP18,NS,carcinoma,0,1	ARHGAP18	52	1	NM_033515	exon6	c.G952A	p.D318N	GATTACCTTTTGT	.	scavenged	Atlas-SNP
CNTNAP4	85445	hgsc.bcm.edu	37	16	76555939	76555939	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	95	2	103	0	0.0210526	0	.	.	none	CNTNAP4_ENST00000478060,NS,carcinoma,0,2	CNTNAP4	600	2	NM_138994	exon16	c.C2321T	p.P774L	CAGCTCCGACAGT	.	scavenged	Atlas-SNP
CBX3	11335	hgsc.bcm.edu	37	7	26245986	26245986	+	Splice_Site	SNP	A	A	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	40	5	20	1	0.125	0.05	.	.	none	CBX3,colon,adenoma,0,1	CBX3	25	1	NM_007276	exon3	c.25-2A>T	.	TATTTTAGCAAAA	.	scavenged	Atlas-SNP
UGT1A3	54659	hgsc.bcm.edu	37	2	234638445	234638445	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	328	6	268	2	0.0182927	0.00746269	.	.	none	UGT1A3,NS,carcinoma,0,4	UGT1A3	91	4	NM_019093	exon1	c.C673T	p.H225Y	ATTTGCCATGCTT	.	scavenged	Atlas-SNP
NPAS4	266743	hgsc.bcm.edu	37	11	66191437	66191437	+	Missense_Mutation	SNP	C	C	A	rs145746289	bycluster;by1000genomes;alternate_allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	49	17	48	0	0.346939	0	C|1.000;T|0.000	.	alt	.	NPAS4	133	.	NM_178864	exon7	c.C1076A	p.T359N	CCAGCACTAACCC	.	PASS	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	84785000	84785000	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	51	18	70	0	0.352941	0	.	.	none	.	DNAH6	194	.	NM_001370	exon11	c.A1744G	p.S582G	GGGCCAAGTTTAG	.	PASS	Atlas-SNP
DTD2	112487	hgsc.bcm.edu	37	14	31926584	31926584	+	Missense_Mutation	SNP	G	G	A	rs3087952		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	116	12	71	3	0.103448	0.0422535	.	.	weak	C14orf126,third_ventricle,glioma,0,2	.	.	2	NM_080664	exon1	c.C16T	p.R6W	GAATCCGGCTACC	.	scavenged	Atlas-SNP
CLIP1	6249	hgsc.bcm.edu	37	12	122839024	122839024	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	125	4	139	0	0.032	0	.	.	none	CLIP1,pharynx,carcinoma,+1,1	CLIP1	126	1	NM_002956	exon7	c.T1283C	p.L428P	TGGTTGAGAAGCT	.	scavenged	Atlas-SNP
BOD1L1	259282	hgsc.bcm.edu	37	4	13602085	13602085	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	65	3	65	0	0.0461538	0	.	.	none	BOD1L,NS,carcinoma,0,1	.	.	1	NM_148894	exon10	c.A6439G	p.S2147G	CTATGCTTGTGGA	.	scavenged	Atlas-SNP
RNF123	63891	hgsc.bcm.edu	37	3	49757994	49757994	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	105	42	78	0	0.4	0	.	.	none	.	RNF123	100	.	NM_022064	exon36	c.G3551A	p.R1184H	AGCTACGCTCAAT	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155225950	155225950	+	Missense_Mutation	SNP	C	C	T	rs140326799		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	232	3	213	0	0.012931	0	C|1.000;T|0.000	0.000	weak	DCHS2,colon,carcinoma,0,1	DCHS2	594	1	NM_017639	exon17	c.G4111A	p.A1371T	CTGGTGCGTGATC	.	scavenged	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51920119	51920119	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	198	8	202	1	0.040404	0.00495049	.	.	none	SIGLEC10,NS,carcinoma,-1,1	SIGLEC10	112	1	NM_001171157	exon3	c.C507T	p.A169A	CTCAAAGGCCCAG	.	scavenged	Atlas-SNP
BAG1	573	hgsc.bcm.edu	37	9	33256814	33256814	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	98	3	121	0	0.0306122	0	.	.	none	BAG1,NS,carcinoma,-2,1	BAG1	24	1	NM_004323	exon5	c.G870A	p.E290E	AATCTCCTCCAAG	.	scavenged	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33517507	33517507	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	37	3	34	1	0.0810811	0.0294118	.	.	none	RHPN2,face,carcinoma,0,2	RHPN2	107	2	NM_033103	exon3	c.G217A	p.V73M	GCCGCACTTGCTC	.	scavenged	Atlas-SNP
NFKBIE	4794	hgsc.bcm.edu	37	6	44229533	44229533	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	56	24	50	0	0.428571	0	.	.	none	.	NFKBIE	31	.	NM_004556	exon3	c.T938A	p.L313Q	AGCACCAGTGCCC	.	PASS	Atlas-SNP
GFM2	84340	hgsc.bcm.edu	37	5	74021852	74021852	+	Missense_Mutation	SNP	A	A	T	rs76339998	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	66	6	44	0	0.0909091	0	A|0.971;T|0.029	0.029	strong	GFM2,NS,carcinoma,0,1	GFM2	38	1	NM_032380	exon18	c.T1826A	p.F609Y	TACTCAAACTCAA	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129636794	129636794	+	Silent	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	95	4	78	0	0.0421053	0	.	.	none	.	LAMA2	481	.	NM_000426	exon25	c.A3729G	p.G1243G	TGAAGGAAAGAAG	.	PASS	Atlas-SNP
NSMAF	8439	hgsc.bcm.edu	37	8	59571856	59571856	+	Missense_Mutation	SNP	A	A	C	rs59606339	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	7	4	9	0	0.571429	0	A|0.754;C|0.246	0.246	strong	NSMAF_ENST00000427130,NS,carcinoma,0,2	NSMAF	156	2	NM_001144772	exon1	c.T50G	p.I17S	TGCCGGATAGCTC	.	PASS	Atlas-SNP
PHF20L1	51105	hgsc.bcm.edu	37	8	133844572	133844572	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	101	3	98	0	0.029703	0	.	.	none	Q86U89_HUMAN,NS,carcinoma,-2,2	PHF20L1	129	2	NM_016018	exon15	c.A1837G	p.S613G	TCACGAAGCATGT	.	scavenged	Atlas-SNP
DHRS12	79758	hgsc.bcm.edu	37	13	52345982	52345982	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	142	34	125	0	0.239437	0	.	.	none	.	DHRS12	28	.	NM_001270424	exon8	c.G681A	p.M227I	AGGATGCATGGAA	.	PASS	Atlas-SNP
TMTC4	84899	hgsc.bcm.edu	37	13	101287349	101287349	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	108	37	117	0	0.342593	0	.	.	none	.	TMTC4	103	.	NM_032813	exon11	c.C1303T	p.L435F	TGGGGAGGTAGAG	.	PASS	Atlas-SNP
DROSHA	29102	hgsc.bcm.edu	37	5	31521306	31521306	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	107	5	144	0	0.046729	0	.	.	none	.	DROSHA	130	.	NM_013235	exon5	c.A871G	p.R291G	TGTGTCTCTCCCG	.	PASS	Atlas-SNP
TUBA3C	7278	hgsc.bcm.edu	37	13	19751463	19751463	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	280	3	278	0	0.0107143	0	.	.	none	TUBA3C,NS,carcinoma,-2,1	TUBA3C	166	1	NM_006001	exon4	c.G660A	p.E220E	GGGACGCTCGATG	.	scavenged	Atlas-SNP
SERPINB10	5273	hgsc.bcm.edu	37	18	61600364	61600364	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	61	12	81	0	0.196721	0	.	.	none	.	SERPINB10	53	.	NM_005024	exon6	c.T716G	p.L239R	TGGGCCTTCAACT	.	PASS	Atlas-SNP
ZNF837	116412	hgsc.bcm.edu	37	19	58879976	58879976	+	Missense_Mutation	SNP	C	C	T	rs7255596	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	8	8	0	0	1	.	C|0.095;T|0.905	0.905	strong	.	ZNF837	16	.	NM_138466	exon3	c.G724A	p.A242T	TGCCCGCCTGCTG	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38120282	38120282	+	Silent	SNP	C	C	T	rs368233775		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	382	4	308	2	0.0104712	0.00649351	.	.	weak	TRIOBP_ENST00000344404,NS,carcinoma,0,3	TRIOBP	262	3	NM_001039141	exon7	c.C1719T	p.D573D	ACGAGACAACCCC	.	scavenged	Atlas-SNP
PFDN2	5202	hgsc.bcm.edu	37	1	161071920	161071920	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	123	9	144	0	0.0731707	0	.	.	none	.	PFDN2	10	.	NM_012394	exon3	c.A206C	p.K69T	TAGCACTTACGAG	.	PASS	Atlas-SNP
FAM135B	51059	hgsc.bcm.edu	37	8	139163898	139163898	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	149	3	131	0	0.0201342	0	.	.	none	LOC51059,NS,carcinoma,-1,6	FAM135B	423	6	NM_015912	exon13	c.G2820A	p.T940T	AGCTGACGTACAG	.	scavenged	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25969147	25969147	+	Missense_Mutation	SNP	C	C	T	rs144743073		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	83	31	124	0	0.373494	0	C|1.000;T|0.000	0.000	weak	.	ATP10A	270	.	NM_024490	exon6	c.G1001A	p.R334Q	TGATACCGCCATA	.	PASS	Atlas-SNP
CFH	3075	hgsc.bcm.edu	37	1	196648799	196648799	+	Silent	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	88	29	118	0	0.329545	0	.	.	none	.	CFH	251	.	NM_001014975	exon6	c.T666C	p.S222S	TATATCTCAGAAG	.	PASS	Atlas-SNP
ZAP70	7535	hgsc.bcm.edu	37	2	98340878	98340878	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	30	16	11	0	0.533333	0	.	.	none	.	ZAP70	77	.	NM_001079	exon3	c.G379A	p.V127M	GACTACGTGCGCC	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144996751	144996751	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	110	3	96	0	0.0272727	0	.	.	none	PLEC_ENST00000436759,colon,carcinoma,-1,3	PLEC	1144	3	NM_201380	exon31	c.G7757A	p.R2586Q	GCCTCCCGCAGGC	.	scavenged	Atlas-SNP
ZSWIM5	57643	hgsc.bcm.edu	37	1	45506070	45506070	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	178	3	179	0	0.0168539	0	.	.	none	ZSWIM5,NS,carcinoma,0,1	ZSWIM5	72	1	NM_020883	exon7	c.A1750G	p.K584E	CTTTCTTCTGATG	.	scavenged	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017566	1017566	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	1017	41	898	34	0.0403147	0.0378619	.	.	none	MUC6_ENST00000421673,NS,carcinoma,-2,2	MUC6	408	2	NM_005961	exon31	c.C5235T	p.T1745T	TGTAGAGGTTTTG	.	scavenged	Atlas-SNP
PRB3	5544	hgsc.bcm.edu	37	12	11420773	11420773	+	Missense_Mutation	SNP	C	C	T	rs200940772	bycluster	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	154	15	156	10	0.0974026	0.0641026	C|0.998;T|0.002	0.002	weak	PRB3,NS,carcinoma,0,2	PRB3	84	2	NM_006249	exon3	c.G410A	p.R137H	CCCGGACGAGGCG	.	scavenged	Atlas-SNP
GPR65	8477	hgsc.bcm.edu	37	14	88477518	88477518	+	Silent	SNP	C	C	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	61	2	51	1	0.0327869	0.0196078	.	.	none	GPR65,brain,atypical_teratoid-rhabdoid_tumour,+1,1	GPR65	48	1	NM_003608	exon2	c.C327A	p.A109A	CATTGCCGTTGAT	.	scavenged	Atlas-SNP
CPLX3	594855	hgsc.bcm.edu	37	15	75119053	75119053	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	55	45	26	0	0.818182	0	.	.	none	.	CPLX3	12	.	NM_001030005	exon1	c.C9A	p.F3L	GGCGTTCATGGTG	.	PASS	Atlas-SNP
TSPYL2	64061	hgsc.bcm.edu	37	X	53112146	53112146	+	Missense_Mutation	SNP	C	C	T	rs144264921	bycluster;byfrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	85	4	66	0	0.0470588	0	C|0.998;T|0.002	0.002	strong	.	TSPYL2	53	.	NM_022117	exon1	c.C466T	p.P156S	TGGGCGCCCCAGA	.	PASS	Atlas-SNP
KRTAP6-3	337968	hgsc.bcm.edu	37	21	31964914	31964914	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	169	4	155	2	0.0236686	0.0129032	.	.	none	KRTAP6-3,NS,carcinoma,0,1	KRTAP6-3	30	1	NM_181605	exon1	c.C150T	p.G50G	CTTTGGCTATGGA	.	scavenged	Atlas-SNP
BTG2	7832	hgsc.bcm.edu	37	1	203276256	203276256	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	106	40	84	0	0.377358	0	.	.	none	.	BTG2	16	.	NM_006763	exon2	c.C167T	p.P56L	GGTTTCCCGAAAA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093368	1093368	+	Silent	SNP	G	G	A	rs111440994		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	67	4	74	0	0.0597015	0	.	.	weak	MUC2_ENST00000441003,NS,carcinoma,0,8	MUC2	614	8	NM_002457	exon30	c.G5187A	p.T1729T	CACTACGGTGACC	.	scavenged	Atlas-SNP
CRMP1	1400	hgsc.bcm.edu	37	4	5868477	5868477	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	83	24	100	1	0.289157	0.01	.	.	none	CRMP1,NS,carcinoma,+1,1	CRMP1	118	1	NM_001014809	exon2	c.C388T	p.R130X	GGAGTCGGTCACT	.	scavenged	Atlas-SNP
CIT	11113	hgsc.bcm.edu	37	12	120295436	120295436	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	110	33	104	0	0.3	0	.	.	none	.	CIT	535	.	NM_001206999	exon4	c.T305C	p.L102P	CCTACAAGACTTC	.	PASS	Atlas-SNP
ZNF749	388567	hgsc.bcm.edu	37	19	57955885	57955885	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	174	5	191	0	0.0287356	0	.	.	none	ZNF749,right_upper_lobe,carcinoma,0,14	ZNF749	75	14	NM_001023561	exon3	c.C1369G	p.Q457E	CAGCACCAGAAAA	.	scavenged	Atlas-SNP
PPA1	5464	hgsc.bcm.edu	37	10	71969338	71969338	+	Silent	SNP	C	C	A	rs79719906	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	155	3	161	1	0.0193548	0.00621118	C|0.987;A|0.013	0.013	strong	PPA1,NS,carcinoma,-1,2	PPA1	24	2	NM_021129	exon7	c.G615T	p.A205A	ATTAAACGCAAAC	.	scavenged	Atlas-SNP
VDAC3	7419	hgsc.bcm.edu	37	8	42259311	42259311	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	176	2	157	0	0.0113636	0	.	.	none	VDAC3,colon,carcinoma,-1,1	VDAC3	17	1	NM_001135694	exon7	c.A332G	p.K111R	GAAAGAAGAGTGG	.	scavenged	Atlas-SNP
ECE2	9718	hgsc.bcm.edu	37	3	184009972	184009972	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	184	3	127	1	0.0163043	0.00787402	.	.	none	ECE2_ENST00000402825,bladder,carcinoma,0,6	ECE2	303	6	NM_014693	exon19	c.C2598T	p.F866F	GCACTTCGGCTGC	.	scavenged	Atlas-SNP
HRCT1	646962	hgsc.bcm.edu	37	9	35906583	35906583	+	Missense_Mutation	SNP	T	T	A	rs112821450	bycluster	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	31	3	25	1	0.0967742	0.04	T|0.500;A|0.500	0.500	weak	HRCT1,NS,malignant_melanoma,0,1	HRCT1	14	1	NM_001039792	exon1	c.T299A	p.L100H	ACCACCTCCACCA	.	scavenged	Atlas-SNP
FAM161A	84140	hgsc.bcm.edu	37	2	62066790	62066790	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	244	3	165	0	0.0122951	0	.	.	none	FAM161A_ENST00000405894,NS,carcinoma,0,3	FAM161A	200	3	NM_032180	exon3	c.T1349C	p.L450P	GTTAAGAGTTTTG	.	scavenged	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15519066	15519066	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	231	18	208	0	0.0779221	0	.	.	none	.	CDRT1	83	.	NM_006382	exon2	c.A563C	p.K188T	GCAGACTTGGAGC	.	PASS	Atlas-SNP
ESF1	51575	hgsc.bcm.edu	37	20	13756715	13756715	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	194	4	213	0	0.0206186	0	.	.	none	ESF1,NS,carcinoma,+1,1	ESF1	77	1	NM_001276380	exon3	c.A839G	p.E280G	TCATCTTCATCCT	.	scavenged	Atlas-SNP
PGM5	5239	hgsc.bcm.edu	37	9	71114185	71114185	+	Missense_Mutation	SNP	C	C	T	rs142494212		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	97	3	83	0	0.0309278	0	C|1.000;T|0.000	0.000	weak	PGM5,NS,carcinoma,-1,1	PGM5	80	1	NM_021965	exon10	c.C1522T	p.R508W	ATCTTCCGGCTCA	.	scavenged	Atlas-SNP
TLN2	83660	hgsc.bcm.edu	37	15	63017221	63017221	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	37	31	36	0	0.837838	0	.	.	none	.	TLN2	253	.	NM_015059	exon24	c.C3173T	p.T1058M	TGAATACGGTGCA	.	PASS	Atlas-SNP
KIAA1009	22832	hgsc.bcm.edu	37	6	84895037	84895037	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	233	6	255	0	0.0257511	0	.	.	none	KIAA1009,NS,carcinoma,+2,1	KIAA1009	119	1	NM_014895	exon13	c.A1531G	p.R511G	AGCTCCTAACTGA	.	scavenged	Atlas-SNP
ZFP112	7771	hgsc.bcm.edu	37	19	44832010	44832010	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	243	3	187	0	0.0123457	0	.	.	none	ZFP112_ENST00000337401,NS,carcinoma,+1,2	ZFP112	219	2	NM_001083335	exon5	c.G2318A	p.G773E	TTCCCTCCTGTGT	.	scavenged	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093245	1093245	+	Silent	SNP	A	A	T	rs200003195		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	45	6	44	3	0.133333	0.0681818	.	.	weak	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon30	c.A5064T	p.P1688P	AACCCCAACACCC	.	scavenged	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230412	23230412	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	148	64	94	0	0.432432	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.G179C	p.R60P	GCAGCCGATCCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511925	195511925	+	Missense_Mutation	SNP	A	A	G	rs78031084	bycluster;byfrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	215	20	223	19	0.0930233	0.0852018	A|0.993;G|0.007	0.007	strong	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.T6526C	p.S2176P	GAAGAGAGGTGGC	.	scavenged	Atlas-SNP
VPS35	55737	hgsc.bcm.edu	37	16	46696260	46696260	+	Silent	SNP	G	G	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	135	2	111	0	0.0148148	0	.	.	none	VPS35,NS,carcinoma,-2,1	VPS35	49	1	NM_018206	exon15	c.C1962A	p.A654A	AGCAAGGGCACAC	.	scavenged	Atlas-SNP
PLEKHM2	23207	hgsc.bcm.edu	37	1	16051840	16051840	+	Silent	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	95	4	85	0	0.0421053	0	.	.	none	.	PLEKHM2	94	.	NM_015164	exon8	c.T741C	p.G247G	CAGTGGTCCCCGC	.	PASS	Atlas-SNP
ZNF761	388561	hgsc.bcm.edu	37	19	53950528	53950528	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	34	12	21	0	0.352941	0	.	.	none	.	ZNF761	104	.	NM_001008401	exon4	c.T7G	p.F3V	ATGGCTTTTTCTC	.	PASS	Atlas-SNP
NOSIP	51070	hgsc.bcm.edu	37	19	50063941	50063941	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	59	18	45	0	0.305085	0	.	.	none	.	NOSIP	28	.	NM_015953	exon3	c.G8A	p.R3Q	CCATGCCGCGTCA	.	PASS	Atlas-SNP
MKNK2	2872	hgsc.bcm.edu	37	19	2041911	2041911	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	38	5	35	0	0.131579	0	.	.	none	.	MKNK2	56	.	NM_017572	exon11	c.C873T	p.G291G	CGGGTAGCCGCTG	.	PASS	Atlas-SNP
UHRF2	115426	hgsc.bcm.edu	37	9	6413558	6413558	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	108	28	82	0	0.259259	0	.	.	none	.	UHRF2	50	.	NM_152896	exon1	c.C68G	p.A23G	GCAAAGCCACGAT	.	PASS	Atlas-SNP
PPP1R36	145376	hgsc.bcm.edu	37	14	65053990	65053990	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	154	72	197	0	0.467532	0	.	.	none	.	.	.	.	NM_172365	exon10	c.G790A	p.G264R	GAAGTAGGGAGAC	.	PASS	Atlas-SNP
RUFY3	22902	hgsc.bcm.edu	37	4	71640926	71640926	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	129	2	120	0	0.0155039	0	.	.	none	RUFY3,NS,carcinoma,-1,1	RUFY3	61	1	NM_001130709	exon7	c.T980C	p.V327A	ACTATGTAGAAGA	.	scavenged	Atlas-SNP
SLITRK3	22865	hgsc.bcm.edu	37	3	164907346	164907346	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	49	3	65	0	0.0612245	0	.	.	none	SLITRK3,NS,carcinoma,+1,1	SLITRK3	263	1	NM_014926	exon2	c.C1273A	p.R425S	CAGAACGGTATAT	.	scavenged	Atlas-SNP
ALDH3B2	222	hgsc.bcm.edu	37	11	67432799	67432799	+	Silent	SNP	G	G	A	rs80147122	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	253	5	223	1	0.0197628	0.00448431	.	.	strong	ALDH3B2,NS,haematopoietic_neoplasm,0,2	ALDH3B2	46	2	NM_001031615	exon7	c.C663T	p.R221R	GGCCACGCGGCTG	.	scavenged	Atlas-SNP
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324347	39324347	+	Silent	SNP	G	G	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	154	30	141	0	0.194805	0	.	.	none	.	KRTAP4-3	40	.	NM_033187	exon1	c.C78A	p.R26R	GCTGGGGCGGCAG	.	PASS	Atlas-SNP
TBX18	9096	hgsc.bcm.edu	37	6	85446456	85446456	+	Missense_Mutation	SNP	T	T	C	rs145795174	alternate_allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	91	3	104	0	0.032967	0	T|1.000;A|0.000	.	alt	TBX18,NS,carcinoma,+2,1	TBX18	131	1	NM_001080508	exon8	c.A1771G	p.T591A	CTAGGGTCCTAGA	.	scavenged	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28483809	28483809	+	Silent	SNP	G	G	A	rs149204675	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	346	5	385	3	0.0144509	0.00779221	G|0.998;A|0.002	0.002	strong	HERC2,NS,carcinoma,0,1	HERC2	501	1	NM_004667	exon24	c.C3687T	p.D1229D	CTTCCCGTCAATC	.	scavenged	Atlas-SNP
ADAMTSL5	339366	hgsc.bcm.edu	37	19	1510692	1510692	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	43	16	27	0	0.372093	0	.	.	none	.	ADAMTSL5	24	.	NM_213604	exon3	c.G137A	p.R46H	GAGCAGCGGGTCC	.	PASS	Atlas-SNP
DENND4B	9909	hgsc.bcm.edu	37	1	153907306	153907306	+	Silent	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	83	4	73	0	0.0481928	0	.	.	none	DENND4B,NS,carcinoma,0,2	DENND4B	210	2	NM_014856	exon18	c.A2703G	p.Q901Q	CTGCTGTTGCTGC	.	scavenged	Atlas-SNP
CLEC18B	497190	hgsc.bcm.edu	37	16	74451961	74451961	+	Missense_Mutation	SNP	G	G	A	rs151079980	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	118	6	98	1	0.0508475	0.0102041	G|0.968;A|0.032	0.032	strong	CLEC18B,NS,carcinoma,0,4	CLEC18B	45	4	NM_001011880	exon3	c.C452T	p.T151M	ACCTGCGTGTAGT	.	scavenged	Atlas-SNP
POTEF	728378	hgsc.bcm.edu	37	2	130877802	130877802	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	238	5	226	3	0.0210084	0.0132743	.	.	none	POTEF,NS,carcinoma,0,6	POTEF	140	6	NM_001099771	exon3	c.A287G	p.N96S	ATCTTGTTCCTGA	.	scavenged	Atlas-SNP
ZNF488	118738	hgsc.bcm.edu	37	10	48371094	48371094	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	75	2	55	0	0.0266667	0	.	.	none	ZNF488,middle_lobe,carcinoma,-2,1	ZNF488	38	1	NM_153034	exon2	c.G562A	p.A188T	GCAGATGCCCTGG	.	scavenged	Atlas-SNP
DOCK7	85440	hgsc.bcm.edu	37	1	63003701	63003701	+	Missense_Mutation	SNP	G	G	T	rs188530601	by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	112	3	135	0	0.0267857	0	G|1.000;T|0.000	0.000	strong	DOCK7,NS,malignant_melanoma,-1,1	DOCK7	184	1	NM_001271999	exon28	c.C3332A	p.P1111H	ACACTGGGATTCG	.	scavenged	Atlas-SNP
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056233	26056233	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	152	9	179	0	0.0592105	0	.	.	none	.	HIST1H1C	80	.	NM_005319	exon1	c.G424A	p.A142T	CGCCAGCCGCCTT	.	PASS	Atlas-SNP
ZNF143	7702	hgsc.bcm.edu	37	11	9492960	9492960	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	110	3	89	0	0.0272727	0	.	.	none	ZNF143,NS,carcinoma,0,1	ZNF143	38	1	NM_003442	exon2	c.C105T	p.T35T	AGTCACCGTGGCA	.	scavenged	Atlas-SNP
C15orf60	283677	hgsc.bcm.edu	37	15	73852122	73852122	+	Silent	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	120	3	116	1	0.025	0.00862069	.	.	none	C15orf60,right_upper_lobe,carcinoma,+2,1	C15orf60	26	1	NM_001042367	exon6	c.T666C	p.H222H	GCCCCATGTCTAT	.	scavenged	Atlas-SNP
MST1	4485	hgsc.bcm.edu	37	3	49723379	49723379	+	Silent	SNP	T	T	C	rs4052580	bycluster;by2hit2allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	45	15	16	3	0.333333	0.1875	T|1.000;|0.000	.	weak	MST1,rectum,carcinoma,0,2	MST1	84	2	NM_020998	exon10	c.A1164G	p.A388A	CTCCCCTGCGCCG	.	scavenged	Atlas-SNP
ZCCHC12	170261	hgsc.bcm.edu	37	X	117959875	117959875	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	77	4	66	0	0.0519481	0	.	.	none	.	ZCCHC12	60	.	NM_173798	exon4	c.A668G	p.D223G	ATTGGGATGATGC	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126412648	126412648	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	139	2	159	0	0.0143885	0	.	.	none	FAT4_ENST00000394329,NS,carcinoma,0,2	FAT4	1752	2	NM_024582	exon17	c.C14671T	p.R4891X	AAGCCTCGAAGGT	.	scavenged	Atlas-SNP
COL3A1	1281	hgsc.bcm.edu	37	2	189849577	189849577	+	Silent	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	122	42	124	0	0.344262	0	.	.	none	.	COL3A1	292	.	NM_000090	exon2	c.A171G	p.S57S	TGACTCAGGATCC	.	PASS	Atlas-SNP
ARHGAP11A	9824	hgsc.bcm.edu	37	15	32926229	32926229	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	237	48	282	0	0.202532	0	.	.	none	.	ARHGAP11A	84	.	NM_199357	exon10	c.A1331T	p.N444I	GGAAAAATGGCAG	.	PASS	Atlas-SNP
DSCAM	1826	hgsc.bcm.edu	37	21	41465696	41465696	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	122	3	127	0	0.0245902	0	.	.	none	DSCAM,NS,carcinoma,+1,1	DSCAM	347	1	NM_001271534	exon21	c.G3802T	p.G1268X	CTCTTCCGGCTGA	.	scavenged	Atlas-SNP
TLL1	7092	hgsc.bcm.edu	37	4	166913969	166913969	+	Silent	SNP	C	C	T	rs377042841	alternate_allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	80	4	91	0	0.05	0	.	.	alt	.	TLL1	194	.	NM_001204760	exon3	c.C294T	p.D98D	TGGAGACCATGCT	.	PASS	Atlas-SNP
ZBED2	79413	hgsc.bcm.edu	37	3	111312927	111312927	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	190	76	154	0	0.4	0	.	.	none	.	ZBED2	22	.	NM_024508	exon2	c.C122T	p.A41V	GGCATAGCACTCA	.	PASS	Atlas-SNP
ETV5	2119	hgsc.bcm.edu	37	3	185797673	185797673	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	166	74	145	0	0.445783	0	.	.	none	.	ETV5	106	.	NM_004454	exon7	c.C583T	p.R195X	GTGGTCGGGGGAC	.	PASS	Atlas-SNP
ALX4	60529	hgsc.bcm.edu	37	11	44331309	44331309	+	Missense_Mutation	SNP	G	G	A	rs12421995	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	9	5	1	0	0.555556	0	G|0.635;A|0.365	0.365	strong	.	ALX4	58	.	NM_021926	exon1	c.C304T	p.P102S	GCGGCGGCGGCTG	.	PASS	Atlas-SNP
FOLH1	2346	hgsc.bcm.edu	37	11	49175427	49175427	+	Silent	SNP	A	A	G	rs199517010	bycluster	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	252	9	262	5	0.0357143	0.019084	A|0.999;G|0.001	0.001	weak	FOLH1,mouth,carcinoma,0,1	FOLH1	141	1	NM_004476	exon17	c.T1941C	p.S647S	TCTCTCACTGAAC	.	scavenged	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239040089	239040089	+	Missense_Mutation	SNP	C	C	T	rs199724430	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	11	6	1	1	0.545455	1	C|0.998;T|0.002	0.002	strong	ESPNL,NS,carcinoma,-1,1	ESPNL	63	1	NM_194312	exon9	c.C2734T	p.R912C	GCCGGCCGCCGGG	.	scavenged	Atlas-SNP
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324333	39324333	+	Missense_Mutation	SNP	T	T	A	rs12953139	bycluster;byfrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	208	62	151	2	0.298077	0.013245	A|0.046;T|0.954	0.046	strong	KRTAP4-3,NS,carcinoma,0,1	KRTAP4-3	40	1	NM_033187	exon1	c.A92T	p.Q31L	GTGGTCTGGCAGC	.	scavenged	Atlas-SNP
MST1	4485	hgsc.bcm.edu	37	3	49723296	49723296	+	Missense_Mutation	SNP	G	G	A	rs80308386	byfrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	121	4	68	1	0.0330578	0.0147059	G|0.375;A|0.625	0.625	strong	MST1,trunk,malignant_melanoma,0,3	MST1	84	3	NM_020998	exon10	c.C1247T	p.P416L	CACTGCGGCTTGT	.	scavenged	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17085791	17085791	+	Missense_Mutation	SNP	G	G	A	rs2297532	bycluster;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	143	7	128	3	0.048951	0.0234375	G|0.943;A|0.057	0.057	strong	Q13209_HUMAN,NS,carcinoma,0,4	.	.	4	NM_001271733	exon8	c.C1030T	p.R344C	TACAACGCCGGAT	.	scavenged	Atlas-SNP
SWAP70	23075	hgsc.bcm.edu	37	11	9685820	9685820	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	222	97	121	0	0.436937	0	.	.	none	.	SWAP70	40	.	NM_015055	exon1	c.C94T	p.L32F	TCCCAGCTCAAGG	.	PASS	Atlas-SNP
SH3YL1	26751	hgsc.bcm.edu	37	2	218939	218939	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	94	43	111	0	0.457447	0	.	.	none	.	SH3YL1	49	.	NM_015677	exon10	c.G901A	p.D301N	TCAAATCCCCAGG	.	PASS	Atlas-SNP
PIANP	196500	hgsc.bcm.edu	37	12	6806573	6806573	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	109	5	101	0	0.0458716	0	.	.	none	.	.	.	.	NM_001244014	exon3	c.C403A	p.P135T	CATGAGGGGCTGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515134	195515134	+	Missense_Mutation	SNP	G	G	T	rs374418206		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	118	13	91	8	0.110169	0.0879121	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,5	MUC4	1505	5	NM_018406	exon2	c.C3317A	p.P1106H	GTGACAGGAAGAG	.	scavenged	Atlas-SNP
POTEE	445582	hgsc.bcm.edu	37	2	132021684	132021684	+	Missense_Mutation	SNP	C	C	A	rs28583670		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	507	5	446	4	0.00986193	0.00896861	.	.	weak	ENSG00000188219,NS,carcinoma,-1,1	.	.	1	NM_001083538	exon15	c.C2656A	p.P886T	GAACTGCCTGACT	.	scavenged	Atlas-SNP
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713608	32713608	+	Silent	SNP	G	G	A	rs199931222	bycluster	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	346	9	316	4	0.0260116	0.0126582	G|0.998;A|0.002	0.002	weak	HLA-DQA2,colon,carcinoma,+1,1	HLA-DQA2	27	1	NM_020056	exon3	c.G372A	p.T124T	TGTGACGCTGGGT	.	scavenged	Atlas-SNP
CD1C	911	hgsc.bcm.edu	37	1	158261083	158261083	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	263	3	224	0	0.0114068	0	.	.	none	CD1C,NS,carcinoma,+1,1	CD1C	100	1	NM_001765	exon2	c.G221A	p.G74D	CCAAGGGCAACTT	.	scavenged	Atlas-SNP
CCAR1	55749	hgsc.bcm.edu	37	10	70549639	70549639	+	Silent	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	167	8	158	0	0.0479042	0	.	.	none	.	CCAR1	118	.	NM_018237	exon24	c.G3360A	p.T1120T	ATCTACGGTAATG	.	PASS	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	37	7	82784833	82784833	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	146	7	148	5	0.0479452	0.0337838	.	.	none	Q9Y6V0-3,NS,carcinoma,+1,2	PCLO	1506	2	NM_014510	exon2	c.A1124C	p.Q375P	CCAGTCTGCTGAG	.	scavenged	Atlas-SNP
KRTAP9-9	81870	hgsc.bcm.edu	37	17	39411694	39411694	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	15	2	24	2	0.133333	0.0833333	.	.	none	KRTAP9-9,NS,carcinoma,+2,1	KRTAP9-9	24	1	NM_030975	exon1	c.G57C	p.W19C	CTGCTGGAAGCCC	.	scavenged	Atlas-SNP
FMO5	2330	hgsc.bcm.edu	37	1	146656089	146656089	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	76	4	120	0	0.0526316	0	.	.	none	.	FMO5	94	.	NM_001144829	exon9	c.G1377A	p.K459K	AGGCCCCTTTATT	.	PASS	Atlas-SNP
GOLGA6B	55889	hgsc.bcm.edu	37	15	72954595	72954595	+	Missense_Mutation	SNP	A	A	G	rs74430870		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	357	4	190	2	0.0112045	0.0105263	A|0.500;G|0.500	0.500	weak	GOLGA6B,NS,carcinoma,0,2	GOLGA6B	30	2	NM_018652	exon11	c.A850G	p.K284E	TCAGCTAAGCCCC	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284344	152284344	+	Silent	SNP	T	T	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	405	12	322	5	0.0296296	0.015528	.	.	none	FLG,NS,carcinoma,-2,1	FLG	900	1	NM_002016	exon3	c.A3018C	p.G1006G	AGGAGTTCCTGAT	.	scavenged	Atlas-SNP
PSG4	5672	hgsc.bcm.edu	37	19	43708388	43708388	+	Silent	SNP	A	A	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	190	74	200	0	0.389474	0	.	.	none	.	PSG4	129	.	NM_002780	exon2	c.G80G	p.X27X	TTCCAGAAGTTTA	.	PASS	Atlas-SNP
CYP2A13	1553	hgsc.bcm.edu	37	19	41594954	41594954	+	Nonsense_Mutation	SNP	C	C	T	rs72552266	bycluster;byfrequency;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	256	9	240	10	0.0351562	0.0416667	C|0.985;T|0.015	0.015	strong	CYP2A13,caecum,carcinoma,-1,1	CYP2A13	90	1	NM_000766	exon2	c.C301T	p.R101X	AGCGGGCGAGGCG	.	scavenged	Atlas-SNP
PRKD2	25865	hgsc.bcm.edu	37	19	47193879	47193879	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	157	3	127	0	0.0191083	0	.	.	none	PRKD2,brain,primitive_neuroectodermal_tumour-medulloblastoma,-1,1	PRKD2	94	1	NM_016457	exon13	c.G1787A	p.R596Q	TCATTCCGGAGCT	.	scavenged	Atlas-SNP
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067180	46067180	+	Missense_Mutation	SNP	C	C	T	rs462007	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	132	33	86	0	0.25	0	C|0.202;T|0.798	0.798	strong	.	KRTAP10-11	36	.	NM_198692	exon1	c.C805T	p.R269C	TGCTGCCGCCCGG	.	PASS	Atlas-SNP
ZDBF2	57683	hgsc.bcm.edu	37	2	207174869	207174869	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	77	26	95	0	0.337662	0	.	.	none	ZDBF2_ENST00000374423,caecum,carcinoma,0,2	ZDBF2	531	2	NM_020923	exon5	c.A5617G	p.K1873E	AAGGGGAAAAAAA	.	PASS	Atlas-SNP
NMUR1	10316	hgsc.bcm.edu	37	2	232389859	232389859	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	157	60	125	0	0.382166	0	.	.	none	.	NMUR1	46	.	NM_006056	exon3	c.G1176A	p.M392I	TGTGGTCATCCTG	.	PASS	Atlas-SNP
PLXNC1	10154	hgsc.bcm.edu	37	12	94694764	94694764	+	Silent	SNP	C	C	T	rs113780946	bycluster;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	204	3	152	0	0.0147059	0	C|0.999;T|0.001	0.001	strong	PLXNC1,right_lower_lobe,carcinoma,0,1	PLXNC1	135	1	NM_005761	exon28	c.C4317T	p.D1439D	TATAGACGGCTGT	.	scavenged	Atlas-SNP
IWS1	55677	hgsc.bcm.edu	37	2	128263223	128263223	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	175	55	129	0	0.314286	0	.	.	none	.	IWS1	61	.	NM_017969	exon3	c.G256A	p.E86K	GAAGCTCCTCACT	.	PASS	Atlas-SNP
NFKBIA	4792	hgsc.bcm.edu	37	14	35871695	35871695	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	180	46	142	0	0.255556	0	.	.	none	.	NFKBIA	28	.	NM_020529	exon5	c.C811T	p.Q271X	TCAGCTGGCCCAG	.	PASS	Atlas-SNP
ZNF791	163049	hgsc.bcm.edu	37	19	12735492	12735492	+	Silent	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	208	3	195	1	0.0144231	0.00512821	.	.	none	ZNF791,NS,carcinoma,+2,1	ZNF791	53	1	NM_153358	exon3	c.A159G	p.E53E	TGTTGAAGATCAA	.	scavenged	Atlas-SNP
NAGA	4668	hgsc.bcm.edu	37	22	42463804	42463804	+	Missense_Mutation	SNP	G	G	T	rs140775168	bycluster;byfrequency;alternate_allele	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	80	32	58	0	0.4	0	G|1.000;C|0.000	.	alt	.	NAGA	26	.	NM_000262	exon3	c.C289A	p.R97S	GGAAGCGCTTGGG	.	PASS	Atlas-SNP
ADNP	23394	hgsc.bcm.edu	37	20	49509225	49509225	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	177	2	171	0	0.0112994	0	.	.	none	ADNP,NS,carcinoma,+2,1	ADNP	106	1	NM_015339	exon5	c.A2026G	p.T676A	AGGCGGTCATGTT	.	scavenged	Atlas-SNP
MGAT5	4249	hgsc.bcm.edu	37	2	135102520	135102520	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	90	32	86	0	0.355556	0	.	.	none	.	MGAT5	84	.	NM_002410	exon8	c.G997A	p.G333R	GTTGTAGGAAACC	.	PASS	Atlas-SNP
SOGA2	23255	hgsc.bcm.edu	37	18	8806921	8806921	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	62	3	58	0	0.0483871	0	.	.	none	CCDC165,NS,carcinoma,-2,1	.	.	1	NM_015210	exon11	c.T2467C	p.F823L	AGCGCCTTCAAGG	.	scavenged	Atlas-SNP
CR1L	1379	hgsc.bcm.edu	37	1	207871000	207871000	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	438	5	471	2	0.0114155	0.00424628	.	.	none	CR1L_ENST00000508064,NS,carcinoma,-2,4	CR1L	97	4	NM_175710	exon6	c.A1015G	p.S339G	GACTGGAGCCCTG	.	scavenged	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016835	1016835	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	1704	43	1543	15	0.0252347	0.00972132	.	.	none	MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.T5966C	p.F1989S	GTCTGGAAGGATG	.	scavenged	Atlas-SNP
STAT3	6774	hgsc.bcm.edu	37	17	40474482	40474482	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	271	137	228	0	0.505535	0	.	.	none	STAT3,NS,lymphoid_neoplasm,0,46	STAT3	268	46	NM_003150	exon21	c.A1919T	p.Y640F	TTTGTGTATGGTT	.	PASS	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	37	7	82545106	82545106	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	78	31	99	0	0.397436	0	.	.	none	.	PCLO	1506	.	NM_014510	exon7	c.T12196C	p.F4066L	GGCTAAATGCGGT	.	PASS	Atlas-SNP
DPYD	1806	hgsc.bcm.edu	37	1	97548004	97548004	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	109	44	116	0	0.40367	0	.	.	none	.	DPYD	219	.	NM_000110	exon22	c.A2789G	p.Q930R	AGGTACTGCAGTG	.	PASS	Atlas-SNP
GSX1	219409	hgsc.bcm.edu	37	13	28367061	28367061	+	Silent	SNP	A	A	G	rs1231058	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	6	6	0	0	1	.	A|0.104;G|0.896	0.896	strong	.	GSX1	20	.	NM_145657	exon1	c.A234G	p.L78L	GCCTCTACTCAAG	.	PASS	Atlas-SNP
MORC3	23515	hgsc.bcm.edu	37	21	37734510	37734510	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	188	4	173	0	0.0212766	0	.	.	none	MORC3,caecum,carcinoma,0,1	MORC3	78	1	NM_015358	exon13	c.C1436T	p.P479L	GACAACCGGAAAT	.	scavenged	Atlas-SNP
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067193	46067193	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	134	6	80	0	0.0447761	0	.	.	none	KRTAP10-11,NS,carcinoma,-1,1	KRTAP10-11	36	1	NM_198692	exon1	c.G818C	p.C273S	CCTCCTGCGTGTC	.	PASS	Atlas-SNP
PEX16	9409	hgsc.bcm.edu	37	11	45937288	45937288	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	193	3	177	0	0.015544	0	.	.	none	PEX16,colon,carcinoma,+1,1	PEX16	24	1	NM_004813	exon4	c.C325T	p.R109C	GCCAGCGGCCCAC	.	scavenged	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138424	37138424	+	Silent	SNP	C	C	T	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	12	3	11	0	0.25	0	.	.	none	PIM1,NS,lymphoid_neoplasm,0,1	PIM1	71	1	NM_001243186	exon1	c.C346T	p.L116L	ACCAAGCTGGCGC	.	scavenged	Atlas-SNP
PCDH17	27253	hgsc.bcm.edu	37	13	58207600	58207600	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	66	15	66	0	0.227273	0	.	.	none	PCDH17,NS,carcinoma,+1,1	PCDH17	304	1	NM_001040429	exon1	c.G920A	p.G307D	TGAAGGGCAATCT	.	PASS	Atlas-SNP
