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
SETD1B	23067	hgsc.bcm.edu	37	12	122242657	122242658	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	57	12	79	0	0.210526	0	.	.	none	.	SETD1B	105	.	NM_015048	exon1	c.14_15insC	p.H5fs	.	.	PASS	Atlas-Indel
E2F1	1869	hgsc.bcm.edu	37	20	32267687	32267690	+	Frame_Shift_Del	DEL	CCGT	CCGT	-	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	CCGT	CCGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	91	12	125	0	0.131868	0	.	.	none	.	E2F1	41	.	NM_005225	exon3	c.444_447del	p.148_149del	.	.	PASS	Atlas-Indel
TNFAIP3	7128	hgsc.bcm.edu	37	6	138198239	138198240	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	165	12	286	0	0.0727273	0	.	.	none	.	TNFAIP3	340	.	NM_001270508	exon6	c.831_832del	p.277_278del	.	.	PASS	Atlas-Indel
SCN9A	6335	hgsc.bcm.edu	37	2	167055184	167055185	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	243	22	372	0	0.090535	0	.	.	none	.	SCN9A	296	.	NM_002977	exon27	c.5932_5933insA	p.X1978delinsI	.	.	PASS	Atlas-Indel
ARID1A	8289	hgsc.bcm.edu	37	1	27101417	27101417	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	119	28	124	0	0.235294	0	.	.	none	.	ARID1A	842	.	NM_006015	exon18	c.4698delG	p.R1566fs	.	.	PASS	Atlas-Indel
MLL2	8085	hgsc.bcm.edu	37	12	49436376	49436377	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	66	11	87	0	0.166667	0	.	.	none	.	MLL2	1173	.	NM_003482	exon27	c.5835_5836insC	p.P1945fs	.	.	PASS	Atlas-Indel
CTSH	1512	hgsc.bcm.edu	37	15	79221796	79221797	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	129	12	226	0	0.0930233	0	.	.	none	.	CTSH	23	.	NM_004390	exon8	c.588_589insA	p.N196fs	.	.	PASS	Atlas-Indel
OR2T34	127068	hgsc.bcm.edu	37	1	248737510	248737511	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	230	39	333	0	0.169565	0	.	.	none	OR2T34,NS,haematopoietic_neoplasm,-1,2	OR2T34	72	2	NM_001001821	exon1	c.549_550insT	p.F183fs	.	.	PASS	Atlas-Indel
RIMS1	22999	hgsc.bcm.edu	37	6	73023228	73023228	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	78	19	93	0	0.24359	0	.	.	none	.	RIMS1	278	.	NM_014989	exon28	c.A3983G	p.Q1328R	AAGATCAGTACAG	.	PASS	Atlas-SNP
SMAD9	4093	hgsc.bcm.edu	37	13	37453460	37453460	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	52	6	81	0	0.115385	0	.	.	none	.	SMAD9	91	.	NM_005905	exon2	c.G367A	p.E123K	ACACTTCTTTCTG	.	PASS	Atlas-SNP
KCNN4	3783	hgsc.bcm.edu	37	19	44278489	44278489	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	98	11	119	0	0.112245	0	.	.	none	.	KCNN4	37	.	NM_002250	exon3	c.C538G	p.R180G	TGCTGCGGTAGGA	.	PASS	Atlas-SNP
IRF4	3662	hgsc.bcm.edu	37	6	394899	394899	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	46	8	55	0	0.173913	0	.	.	none	IRF4_ENST00000380956,NS,carcinoma,-1,1	IRF4	65	1	NM_001195286	exon3	c.T295C	p.C99R	CTGCGGTGCGCTT	.	PASS	Atlas-SNP
KCTD3	51133	hgsc.bcm.edu	37	1	215751396	215751396	+	Silent	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	184	23	297	0	0.125	0	.	.	none	.	KCTD3	101	.	NM_016121	exon6	c.C369T	p.V123V	CAGTGTCCTTTTT	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921137	12921137	+	Missense_Mutation	SNP	T	T	A	rs17039283		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	87	4	118	2	0.045977	0.0169492	T|1.000;|0.000	.	weak	PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	NM_023014	exon4	c.T928A	p.L310M	GAGGACTTGAAGT	.	scavenged	Atlas-SNP
RNF145	153830	hgsc.bcm.edu	37	5	158630642	158630642	+	Missense_Mutation	SNP	T	T	C	rs202186112		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	40	3	63	1	0.075	0.015873	.	.	weak	RNF145,NS,carcinoma,0,2	RNF145	110	2	NM_001199380	exon2	c.A74G	p.K25R	TTTTTCTTTTTTT	.	scavenged	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187539303	187539303	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	103	14	151	0	0.135922	0	.	.	none	.	FAT1	500	.	NM_005245	exon10	c.C8437A	p.P2813T	CATATGGACTAGA	.	PASS	Atlas-SNP
GPC1	2817	hgsc.bcm.edu	37	2	241401695	241401695	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	111	11	147	0	0.0990991	0	.	.	none	.	GPC1	32	.	NM_002081	exon3	c.C413T	p.A138V	AGAACGCGAGGGC	.	PASS	Atlas-SNP
XRCC2	7516	hgsc.bcm.edu	37	7	152346254	152346254	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	35	5	59	0	0.142857	0	.	.	none	.	XRCC2	30	.	NM_005431	exon3	c.G316T	p.E106X	TTATTTCTTCAGA	.	PASS	Atlas-SNP
NOTCH2NL	388677	hgsc.bcm.edu	37	1	145248876	145248876	+	Missense_Mutation	SNP	A	A	G	rs61788900	bycluster	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	2062	334	2916	491	0.161979	0.168381	.	.	weak	NOTCH2NL_ENST00000362074,colon,carcinoma,0,2	NOTCH2NL	100	2	NM_203458	exon2	c.A20G	p.N7S	ACCACAATGGCAC	.	scavenged	Atlas-SNP
HIST1H2BD	3017	hgsc.bcm.edu	37	6	26158776	26158776	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	105	14	163	0	0.133333	0	.	.	none	.	HIST1H2BD	45	.	NM_021063	exon1	c.T379C	p.X127Q	TCCAAGTAACTTT	.	PASS	Atlas-SNP
CYP2F1	1572	hgsc.bcm.edu	37	19	41628014	41628014	+	Missense_Mutation	SNP	G	G	C	rs75405062	bycluster	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	34	7	41	11	0.205882	0.268293	G|0.250;C|0.750	0.750	weak	CYP2F1,NS,carcinoma,+2,1	CYP2F1	60	1	NM_000774	exon6	c.G798C	p.Q266H	CATCCAGTGCTTC	.	scavenged	Atlas-SNP
NBEA	26960	hgsc.bcm.edu	37	13	35729913	35729913	+	Silent	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	64	9	118	0	0.140625	0	.	.	none	.	NBEA	340	.	NM_015678	exon19	c.C2448A	p.I816I	TCAGATCTTGACA	.	PASS	Atlas-SNP
FBXL6	26233	hgsc.bcm.edu	37	8	145579967	145579967	+	Silent	SNP	T	T	C	rs77157066	bycluster;byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	54	6	50	5	0.111111	0.1	T|0.926;C|0.074	0.074	strong	FBXL6,colon,carcinoma,0,1	FBXL6	26	1	NM_012162	exon7	c.A1218G	p.P406P	CCGACATGGCAGA	.	scavenged	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	37	11	57971203	57971203	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	140	8	195	1	0.0571429	0.00512821	.	.	none	OR1S2,NS,carcinoma,0,3	OR1S2	119	3	NM_001004459	exon1	c.G451C	p.A151P	ACCTGGCCCGCAT	.	scavenged	Atlas-SNP
DCDC1	341019	hgsc.bcm.edu	37	11	31329373	31329373	+	Missense_Mutation	SNP	C	C	T	rs2761591	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	84	5	159	0	0.0595238	0	C|0.894;T|0.106	0.106	strong	DCDC1,NS,carcinoma,0,1	DCDC1	74	1	NM_181807	exon4	c.G247A	p.V83M	AATGCACGAGTCT	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	804886	804886	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	63	3	60	0	0.047619	0	.	.	none	PTBP1,larynx,carcinoma,-2,1	PTBP1	43	1	NM_031990	exon7	c.T664C	p.F222L	AACCAGTTCCAGG	.	scavenged	Atlas-SNP
AGGF1	55109	hgsc.bcm.edu	37	5	76332530	76332530	+	Silent	SNP	T	T	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	107	2	158	1	0.0186916	0.00632911	.	.	none	AGGF1,NS,carcinoma,+2,1	AGGF1	71	1	NM_018046	exon4	c.T666G	p.G222G	CACTGGTTTCTAT	.	scavenged	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190873379	190873379	+	Missense_Mutation	SNP	A	A	G	rs1803592		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	80	13	133	12	0.1625	0.0902256	.	.	weak	FRG1,arm,malignant_melanoma,0,1	FRG1	76	1	NM_004477	exon3	c.A196G	p.K66E	ATGGATAAGGGAA	.	scavenged	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52877609	52877609	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	138	13	118	0	0.0942029	0	.	.	none	.	ZNF880	45	.	NM_001145434	exon3	c.G197A	p.R66Q	ATCCCCGGAATCT	.	PASS	Atlas-SNP
PTPRQ	374462	hgsc.bcm.edu	37	12	81046571	81046571	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	117	5	145	0	0.042735	0	.	.	none	.	PTPRQ	119	.	NM_001145026	exon35	c.C5557G	p.P1853A	GATCTGCCTTGGA	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3089200	3089200	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	316	52	492	0	0.164557	0	.	.	none	.	MYOM1	192	.	NM_003803	exon29	c.G4109T	p.G1370V	CATTCACCAGTCA	.	PASS	Atlas-SNP
NKTR	4820	hgsc.bcm.edu	37	3	42674280	42674280	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	127	18	214	0	0.141732	0	.	.	none	.	NKTR	116	.	NM_005385	exon9	c.A738C	p.E246D	TTCAGAAGAGCCA	.	PASS	Atlas-SNP
PCDH15	65217	hgsc.bcm.edu	37	10	55626476	55626476	+	Silent	SNP	T	T	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	145	6	214	0	0.0413793	0	.	.	none	.	PCDH15	1715	.	NM_001142763	exon28	c.A3658C	p.R1220R	AGGATCTCCTCAT	.	PASS	Atlas-SNP
GYPA	2993	hgsc.bcm.edu	37	4	145041720	145041720	+	Missense_Mutation	SNP	A	A	G	rs7682260	bycluster;byfrequency;by2hit2allele	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	125	29	192	35	0.232	0.182292	A|0.519;G|0.481	0.481	strong	GYPA,NS,carcinoma,0,1	GYPA	27	1	NM_002099	exon2	c.T59C	p.L20S	GTACTTAATGCTG	.	scavenged	Atlas-SNP
CTNNA3	29119	hgsc.bcm.edu	37	10	67829199	67829199	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	150	16	260	0	0.106667	0	.	.	none	.	CTNNA3	401	.	NM_013266	exon15	c.C2026A	p.Q676K	CAACTTGCTCAGC	.	PASS	Atlas-SNP
VEZF1	7716	hgsc.bcm.edu	37	17	56056604	56056604	+	Silent	SNP	T	T	C	rs138088904	byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	111	13	158	2	0.117117	0.0126582	T|0.999;C|0.001	0.001	strong	VEZF1,colon,carcinoma,0,2	VEZF1	50	2	NM_007146	exon5	c.A1047G	p.Q349Q	TTGTTGTTGCTGC	.	scavenged	Atlas-SNP
FBXL6	26233	hgsc.bcm.edu	37	8	145579964	145579964	+	Silent	SNP	A	A	G	rs75159950	bycluster;byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	52	6	51	5	0.115385	0.0980392	A|0.928;G|0.072	0.072	strong	FBXL6,colon,carcinoma,0,1	FBXL6	26	1	NM_012162	exon7	c.T1221C	p.C407C	ACCCCGACATGGC	.	scavenged	Atlas-SNP
DLX4	1748	hgsc.bcm.edu	37	17	48051195	48051195	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	70	11	92	0	0.157143	0	.	.	none	.	DLX4	25	.	NM_138281	exon3	c.T611C	p.L204P	CCTCCCTCTGGGA	.	PASS	Atlas-SNP
NAA25	80018	hgsc.bcm.edu	37	12	112516526	112516526	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	153	10	219	0	0.0653595	0	.	.	none	.	NAA25	105	.	NM_024953	exon6	c.A497G	p.E166G	AGGTTTTCATCCT	.	PASS	Atlas-SNP
LRRC4	64101	hgsc.bcm.edu	37	7	127669744	127669744	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	110	17	135	0	0.154545	0	.	.	none	.	LRRC4	72	.	NM_022143	exon2	c.A950G	p.E317G	ATATACTCTCGAA	.	PASS	Atlas-SNP
LCP2	3937	hgsc.bcm.edu	37	5	169695446	169695446	+	Silent	SNP	C	C	T	rs2292254	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	9	7	8	1	0.777778	0.125	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
AGTR2	186	hgsc.bcm.edu	37	X	115304549	115304549	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	215	12	334	0	0.055814	0	.	.	none	.	AGTR2	62	.	NM_000686	exon3	c.G1016T	p.W339L	TTACTTGGCTCCA	.	PASS	Atlas-SNP
HIST2H2BE	8349	hgsc.bcm.edu	37	1	149857825	149857825	+	Silent	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	166	9	160	0	0.0542169	0	.	.	none	.	HIST2H2BE	33	.	NM_003528	exon1	c.C366T	p.Y122Y	GCTGGTGTACTTG	.	PASS	Atlas-SNP
PSG1	5669	hgsc.bcm.edu	37	19	43382402	43382402	+	Silent	SNP	G	G	A	rs17423717	bycluster;byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	114	7	159	2	0.0614035	0.0125786	G|0.996;A|0.004	0.004	strong	PSG1_ENST00000312439,NS,carcinoma,-1,4	PSG1	196	4	NM_001184826	exon2	c.C93T	p.P31P	AGTGGTGGGCAGG	.	scavenged	Atlas-SNP
PIK3C2G	5288	hgsc.bcm.edu	37	12	18491371	18491371	+	Silent	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	124	7	171	0	0.0564516	0	.	.	none	.	PIK3C2G	315	.	NM_004570	exon9	c.T1284C	p.Y428Y	CGTGTATAATATT	.	PASS	Atlas-SNP
ABCB5	340273	hgsc.bcm.edu	37	7	20683092	20683092	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	149	17	214	0	0.114094	0	.	.	none	.	ABCB5	357	.	NM_001163941	exon7	c.A515G	p.D172G	ACATTGACAAAAT	.	PASS	Atlas-SNP
MUC7	4589	hgsc.bcm.edu	37	4	71347060	71347060	+	Missense_Mutation	SNP	A	A	C	rs74904873	bycluster;byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	136	2	218	6	0.0147059	0.0275229	A|0.500;C|0.500	0.500	strong	MUC7,pharynx,carcinoma,0,1	MUC7	91	1	NM_001145007	exon4	c.A599C	p.Q200P	CTACACAAGCTCC	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506987	195506987	+	Missense_Mutation	SNP	T	T	C	rs200157887	byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	69	4	79	4	0.057971	0.0506329	T|0.816;C|0.185	0.185	strong	MUC4_ENST00000463781,extremity,malignant_melanoma,0,2	MUC4	1505	2	NM_018406	exon2	c.A11464G	p.T3822A	GGGTGGTGTCACC	.	scavenged	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274150	39274150	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	56	3	81	1	0.0535714	0.0123457	.	.	none	KRTAP4-11,NS,carcinoma,0,5	KRTAP4-11	94	5	NM_033059	exon1	c.A418T	p.S140C	AGATGCTGCAGCT	.	scavenged	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78923585	78923585	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	105	5	163	0	0.047619	0	.	.	none	.	PCSK5	329	.	NM_001190482	exon28	c.G3548C	p.C1183S	AGCCTTGTCATTC	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	37	2	109371681	109371681	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	594	7	840	0	0.0117845	0	.	.	none	RANBP2_ENST00000283195,NS,carcinoma,0,2	RANBP2	488	2	NM_006267	exon17	c.T2432G	p.L811R	CTTTACTGAAAAT	.	scavenged	Atlas-SNP
SPEN	23013	hgsc.bcm.edu	37	1	16255388	16255388	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	66	6	92	0	0.0909091	0	.	.	none	.	SPEN	374	.	NM_015001	exon11	c.G2653T	p.E885X	GTGAAAGAGAAAG	.	PASS	Atlas-SNP
NPAS3	64067	hgsc.bcm.edu	37	14	34270175	34270175	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	55	7	65	0	0.127273	0	.	.	none	.	NPAS3	266	.	NM_001164749	exon12	c.G2662A	p.A888T	GGCGGCGCAGTGA	.	PASS	Atlas-SNP
RGPD4	285190	hgsc.bcm.edu	37	2	108487901	108487901	+	Silent	SNP	A	A	G	rs7563250	bycluster	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	16	4	10	1	0.25	0.1	G|1.000;|0.000	1.000	weak	RGPD4,NS,carcinoma,0,1	RGPD4	112	1	NM_182588	exon20	c.A3441G	p.L1147L	GCGGTTAGCAGCA	.	scavenged	Atlas-SNP
DDIT4L	115265	hgsc.bcm.edu	37	4	101108876	101108876	+	Silent	SNP	T	T	C	rs56763427	bycluster;byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	210	82	354	166	0.390476	0.468927	T|0.913;C|0.087	0.087	strong	DDIT4L,NS,carcinoma,-1,1	DDIT4L	33	1	NM_145244	exon3	c.A540G	p.K180K	GTAAAGTTTTTTC	.	scavenged	Atlas-SNP
SLC5A9	200010	hgsc.bcm.edu	37	1	48688529	48688529	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	135	9	163	0	0.0666667	0	.	.	none	.	SLC5A9	82	.	NM_001135181	exon1	c.G121C	p.V41L	AGCGTGGTGGTCA	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37508026	37508026	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	160	12	216	0	0.075	0	.	.	none	.	ANKRD30A	448	.	NM_052997	exon34	c.A3218T	p.E1073V	AAAAGGAAAATAA	.	PASS	Atlas-SNP
EFNB1	1947	hgsc.bcm.edu	37	X	68058642	68058642	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	195	9	389	0	0.0461538	0	.	.	none	.	EFNB1	37	.	NM_004429	exon2	c.C311A	p.P104Q	ATAGGCCAGAGCA	.	PASS	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	37	8	77616927	77616927	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	118	2	165	0	0.0169492	0	.	.	none	ZFHX4,colon,carcinoma,0,3	ZFHX4	878	3	NM_024721	exon2	c.G604T	p.G202W	TCCCTCGGGAAAC	.	scavenged	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152768599	152768599	+	Silent	SNP	C	C	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	69	7	105	0	0.101449	0	.	.	none	.	SYNE1	3227	.	NM_033071	exon29	c.G3684C	p.L1228L	CTCTGACAGCAGC	.	PASS	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34825160	34825160	+	Missense_Mutation	SNP	C	C	T	rs201864059		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	105	9	152	0	0.0857143	0	.	.	weak	.	UHRF1BP1	102	.	NM_017754	exon12	c.C1486T	p.R496W	TGCAGTCGGAAAC	.	PASS	Atlas-SNP
APOBEC3B	9582	hgsc.bcm.edu	37	22	39382074	39382074	+	Silent	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	61	3	83	1	0.0491803	0.0120482	.	.	none	APOBEC3B,NS,carcinoma,+1,1	APOBEC3B	32	1	NM_004900	exon3	c.C432T	p.R144R	AGCCCGCGTGACG	.	scavenged	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	37	11	57971351	57971351	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	266	5	368	2	0.018797	0.00543478	.	.	none	OR1S2,NS,adenoma,-1,1	OR1S2	119	1	NM_001004459	exon1	c.C303G	p.N101K	TTGGCTGTTGGTT	.	scavenged	Atlas-SNP
PYY	5697	hgsc.bcm.edu	37	17	42030694	42030694	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	178	13	188	0	0.0730337	0	.	.	none	.	PYY	11	.	NM_004160	exon5	c.G158A	p.R53H	TAGTGGCGCAGGG	.	PASS	Atlas-SNP
AQP7	364	hgsc.bcm.edu	37	9	33385690	33385690	+	Missense_Mutation	SNP	G	G	T	rs139024279	bycluster;byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	24	7	22	1	0.291667	0.0454545	G|0.986;T|0.014	0.014	strong	AQP7,colon,carcinoma,0,1	AQP7	58	1	NM_001170	exon7	c.C700A	p.R234S	AGATGCGGGGGGG	.	scavenged	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230409	23230409	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	102	14	117	0	0.137255	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.G176A	p.S59N	GAAGCAGCCGATC	.	PASS	Atlas-SNP
OR4S1	256148	hgsc.bcm.edu	37	11	48328231	48328231	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	113	10	191	0	0.0884956	0	.	.	none	.	OR4S1	52	.	NM_001004725	exon1	c.C457T	p.H153Y	TTCCTGCATTCCA	.	PASS	Atlas-SNP
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651412	1651412	+	Silent	SNP	G	G	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	32	2	37	1	0.0625	0.027027	.	.	none	KRTAP5-5,NS,carcinoma,+1,2	KRTAP5-5	86	2	NM_001001480	exon1	c.G342C	p.G114G	TGGGGGGTCCAAG	.	scavenged	Atlas-SNP
KCNH1	3756	hgsc.bcm.edu	37	1	210856924	210856924	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	136	6	166	0	0.0441176	0	.	.	none	.	KCNH1	199	.	NM_172362	exon11	c.G2669A	p.R890H	TCCAGGCGCAAGT	.	PASS	Atlas-SNP
HNF4G	3174	hgsc.bcm.edu	37	8	76471075	76471075	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	89	9	117	0	0.101124	0	.	.	none	.	HNF4G	111	.	NM_004133	exon8	c.T896C	p.M299T	AGAACATGAGGTT	.	PASS	Atlas-SNP
AQP7	364	hgsc.bcm.edu	37	9	33385667	33385667	+	Silent	SNP	A	A	G	rs79779983	bycluster;byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	25	10	21	1	0.4	0.047619	A|0.710;G|0.290	0.290	strong	AQP7,colon,carcinoma,0,1	AQP7	58	1	NM_001170	exon7	c.T723C	p.G241G	GCCCCAACCAGCA	.	scavenged	Atlas-SNP
F7	2155	hgsc.bcm.edu	37	13	113773002	113773002	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	100	22	122	0	0.22	0	.	.	none	.	F7	49	.	NM_000131	exon9	c.A1081G	p.N361D	GTCCTCAACGTGC	.	PASS	Atlas-SNP
TSHZ3	57616	hgsc.bcm.edu	37	19	31768074	31768074	+	Silent	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	90	19	125	0	0.211111	0	.	.	none	.	TSHZ3	549	.	NM_020856	exon2	c.C2625T	p.D875D	GGCCCCGTCAATG	.	PASS	Atlas-SNP
H2AFV	94239	hgsc.bcm.edu	37	7	44874131	44874131	+	Missense_Mutation	SNP	A	A	G	rs114398265	bycluster	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	147	7	121	0	0.047619	0	A|0.999;G|0.001	0.001	weak	H2AFV,NS,carcinoma,0,1	H2AFV	14	1	NM_012412	exon5	c.T356C	p.I119T	TTTCCAATCAGAG	.	scavenged	Atlas-SNP
MPEG1	219972	hgsc.bcm.edu	37	11	58979509	58979509	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	117	11	119	0	0.0940171	0	.	.	none	.	MPEG1	72	.	NM_001039396	exon1	c.G830A	p.S277N	CCAATGCTCTGCA	.	PASS	Atlas-SNP
TRAM1L1	133022	hgsc.bcm.edu	37	4	118005633	118005633	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	179	18	225	0	0.100559	0	.	.	none	.	TRAM1L1	55	.	NM_152402	exon1	c.C917T	p.T306M	TGGATCGTGCAAC	.	PASS	Atlas-SNP
SPRR3	6707	hgsc.bcm.edu	37	1	152975715	152975715	+	Silent	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	67	13	59	0	0.19403	0	.	.	none	SPRR3,colon,carcinoma,0,3	SPRR3	45	3	NM_001097589	exon2	c.C219T	p.G73G	GCCAGGCTGTACC	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608843	26608843	+	Missense_Mutation	SNP	C	C	A	rs6667693	bycluster	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	23	9	26	5	0.391304	0.192308	C|0.500;A|0.500	0.500	weak	UBXN11,NS,carcinoma,0,1	UBXN11	54	1	NM_183008	exon16	c.G1510T	p.G504C	CGGGACCGGGACT	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508478	195508478	+	Missense_Mutation	SNP	G	G	C	rs76305071	bycluster;byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	81	4	97	1	0.0493827	0.0103093	G|0.990;C|0.010	0.010	strong	MUC4_ENST00000463781,NS,carcinoma,+2,3	MUC4	1505	3	NM_018406	exon2	c.C9973G	p.H3325D	TGGCGTGACCTGT	.	scavenged	Atlas-SNP
KCNB2	9312	hgsc.bcm.edu	37	8	73848718	73848718	+	Silent	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	174	2	244	1	0.0114943	0.00409836	.	.	none	KCNB2,right_upper_lobe,carcinoma,0,1	KCNB2	228	1	NM_004770	exon3	c.C1128T	p.T376T	GGCCACCATCACC	.	scavenged	Atlas-SNP
BMP1	649	hgsc.bcm.edu	37	8	22052356	22052356	+	Silent	SNP	G	G	A	rs11552824	alternate_allele	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	70	10	84	0	0.142857	0	.	.	alt	.	BMP1	131	.	NM_001199	exon12	c.G1563A	p.T521T	GAGCACGTCCAGC	.	PASS	Atlas-SNP
PAK2	5062	hgsc.bcm.edu	37	3	196530013	196530013	+	Silent	SNP	A	A	G	rs73205842	bycluster;byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	56	6	56	2	0.107143	0.0357143	A|0.970;G|0.030	0.030	strong	PAK2_ENST00000327134,rectum,carcinoma,0,2	PAK2	113	2	NM_002577	exon4	c.A414G	p.K138K	GCAGAAATATCTG	.	scavenged	Atlas-SNP
NPAT	4863	hgsc.bcm.edu	37	11	108044437	108044437	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	391	34	543	0	0.0869565	0	.	.	none	.	NPAT	124	.	NM_002519	exon13	c.A1274T	p.K425I	GCCTTTTTCTGTA	.	PASS	Atlas-SNP
CDH3	1001	hgsc.bcm.edu	37	16	68716273	68716273	+	Silent	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	63	8	76	0	0.126984	0	.	.	none	.	CDH3	68	.	NM_001793	exon9	c.C1065T	p.D355D	TCTGGACGCCCCC	.	PASS	Atlas-SNP
FRG2B	441581	hgsc.bcm.edu	37	10	135439015	135439015	+	Missense_Mutation	SNP	T	T	C	rs75470891	bycluster	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	298	7	397	7	0.0234899	0.0176322	C|1.000;|0.000	1.000	weak	FRG2B,NS,carcinoma,0,1	FRG2B	47	1	NM_001080998	exon4	c.A425G	p.D142G	TGGGCATCACAGG	.	scavenged	Atlas-SNP
CD36	948	hgsc.bcm.edu	37	7	80285936	80285936	+	Silent	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	126	22	156	0	0.174603	0	.	.	none	.	CD36	185	.	NM_001127444	exon2	c.C201A	p.I67I	TTGGATCTTTGAT	.	PASS	Atlas-SNP
UTS2B	257313	hgsc.bcm.edu	37	3	190999976	190999976	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	120	5	145	0	0.0416667	0	.	.	none	.	.	.	.	NM_198152	exon5	c.G3T	p.M1I	CTTGTTCATGTTA	.	PASS	Atlas-SNP
AQP7	364	hgsc.bcm.edu	37	9	33385808	33385808	+	Missense_Mutation	SNP	G	G	T	rs62542744	bycluster	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	30	6	26	0	0.2	0	.	.	weak	AQP7,colon,carcinoma,0,1	AQP7	58	1	NM_001170	exon7	c.C582A	p.N194K	TGGGTTGTTCTCC	.	scavenged	Atlas-SNP
TCHH	7062	hgsc.bcm.edu	37	1	152082269	152082269	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	211	7	214	2	0.0331754	0.00934579	.	.	none	TCHH,NS,malignant_melanoma,0,1	TCHH	275	1	NM_007113	exon3	c.G3424A	p.E1142K	CTTCCTCCCGATA	.	scavenged	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79328899	79328899	+	Silent	SNP	C	C	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	98	8	121	0	0.0816327	0	.	.	none	.	FRAS1	779	.	NM_001166133	exon31	c.C4212G	p.T1404T	AGCTACCCCCACC	.	PASS	Atlas-SNP
AQP7	364	hgsc.bcm.edu	37	9	33385815	33385815	+	Missense_Mutation	SNP	T	T	C	rs62542745	bycluster	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	33	6	26	1	0.181818	0.0384615	.	.	weak	AQP7,NS,carcinoma,0,1	AQP7	58	1	NM_001170	exon7	c.A575G	p.Q192R	TTCTCCTGGTCCG	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510910	195510910	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	213	14	319	8	0.0657277	0.0250784	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C7541A	p.P2514H	GTGACAGGTAGAG	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681303	100681303	+	Silent	SNP	T	T	C	rs143516283		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	60	6	88	6	0.1	0.0681818	.	.	weak	MUC17,rectum,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.T6606C	p.P2202P	ATCTCCTACAACT	.	scavenged	Atlas-SNP
DDC	1644	hgsc.bcm.edu	37	7	50531011	50531011	+	Missense_Mutation	SNP	G	G	A	rs147562019		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	165	14	218	0	0.0848485	0	G|1.000;A|0.000	0.000	weak	.	DDC	100	.	NM_001082971	exon14	c.C1361T	p.T454M	TCCACCGTGCGAG	.	PASS	Atlas-SNP
TRIM51	84767	hgsc.bcm.edu	37	11	55655597	55655597	+	Silent	SNP	A	A	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	274	15	412	11	0.0547445	0.026699	.	.	none	SPRYD5_ENST00000327733,NS,carcinoma,+2,2	.	.	2	NM_032681	exon4	c.A597G	p.E199E	CTTGGAAAGGCTG	.	scavenged	Atlas-SNP
TLX1	3195	hgsc.bcm.edu	37	10	102896618	102896618	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	124	18	144	0	0.145161	0	.	.	none	TLX1,NS,carcinoma,-1,1	TLX1	20	1	NM_005521	exon3	c.A941G	p.D314G	GGTCTGACGACTC	.	PASS	Atlas-SNP
ITPRIPL2	162073	hgsc.bcm.edu	37	16	19126812	19126812	+	Silent	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	44	4	54	0	0.0909091	0	.	.	none	.	ITPRIPL2	40	.	NM_001034841	exon1	c.G1029A	p.A343A	GCGTGCGGAGGCA	.	PASS	Atlas-SNP
BICC1	80114	hgsc.bcm.edu	37	10	60549152	60549152	+	Missense_Mutation	SNP	G	G	A	rs192860241	bycluster;by1000genomes	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	155	10	221	0	0.0645161	0	G|1.000;A|0.000	0.000	strong	BICC1,colon,carcinoma,+1,1	BICC1	121	1	NM_001080512	exon7	c.G731A	p.R244H	AACAGCGTTCCCG	.	PASS	Atlas-SNP
SLC6A14	11254	hgsc.bcm.edu	37	X	115588850	115588850	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	136	8	252	0	0.0588235	0	.	.	none	.	SLC6A14	56	.	NM_007231	exon13	c.G1690A	p.A564T	GGAGTTGCTTTAG	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017483	1017483	+	Missense_Mutation	SNP	T	T	G	rs79986665	bycluster	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	377	72	592	110	0.190981	0.185811	T|0.500;G|0.500	0.500	weak	MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.A5318C	p.H1773P	CTGGTGTGGTTGG	.	scavenged	Atlas-SNP
ATN1	1822	hgsc.bcm.edu	37	12	7045906	7045906	+	Silent	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	46	5	58	0	0.108696	0	.	.	none	.	ATN1	95	.	NM_001007026	exon5	c.G1476A	p.Q492Q	GCAGCAGCAGCAG	.	PASS	Atlas-SNP
TPPP	11076	hgsc.bcm.edu	37	5	678087	678087	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	257	8	265	5	0.0311284	0.0188679	.	.	none	TPPP,NS,carcinoma,0,1	TPPP	24	1	NM_007030	exon2	c.G89A	p.R30K	GACAGCCTCTTGG	.	scavenged	Atlas-SNP
MPEG1	219972	hgsc.bcm.edu	37	11	58978519	58978519	+	Missense_Mutation	SNP	G	G	A	rs376216311	alternate_allele	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	126	15	119	0	0.119048	0	.	.	alt	.	MPEG1	72	.	NM_001039396	exon1	c.C1820T	p.T607I	GTATTGGTGGCAG	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093286	1093286	+	Missense_Mutation	SNP	C	C	G	rs201333212	bycluster	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	9	3	11	1	0.333333	0.0909091	.	.	weak	MUC2_ENST00000441003,NS,carcinoma,0,6	MUC2	614	6	NM_002457	exon30	c.C5105G	p.T1702S	CCATCACCACCAC	.	scavenged	Atlas-SNP
PADI1	29943	hgsc.bcm.edu	37	1	17566209	17566209	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	128	14	203	0	0.109375	0	.	.	none	.	PADI1	77	.	NM_013358	exon14	c.C1563G	p.H521Q	AAAACACCAGGCA	.	PASS	Atlas-SNP
VIPR2	7434	hgsc.bcm.edu	37	7	158935181	158935181	+	Silent	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	190	21	264	0	0.110526	0	.	.	none	.	VIPR2	53	.	NM_003382	exon2	c.A108G	p.T36T	ACATTTTGTTTCT	.	PASS	Atlas-SNP
MPEG1	219972	hgsc.bcm.edu	37	11	58979544	58979544	+	Silent	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	133	12	128	0	0.0902256	0	.	.	none	.	MPEG1	72	.	NM_001039396	exon1	c.C795T	p.S265S	GAGGTAGCTCTTG	.	PASS	Atlas-SNP
KRTAP10-12	386685	hgsc.bcm.edu	37	21	46117576	46117576	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	64	4	88	0	0.0625	0	.	.	none	KRTAP10-12,rectum,carcinoma,0,2	KRTAP10-12	21	2	NM_198699	exon1	c.C460T	p.P154S	TGTGTGCCCGTCT	.	scavenged	Atlas-SNP
HS6ST2	90161	hgsc.bcm.edu	37	X	132091067	132091067	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	100	8	134	0	0.08	0	.	.	none	.	HS6ST2	89	.	NM_001077188	exon3	c.G716T	p.G239V	GTGGTGCCCCCGG	.	PASS	Atlas-SNP
TBC1D29	26083	hgsc.bcm.edu	37	17	28887667	28887667	+	Silent	SNP	T	T	C	rs78888987	bycluster;byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	44	6	56	1	0.136364	0.0178571	T|0.806;C|0.194	0.194	strong	TBC1D29,NS,carcinoma,0,1	TBC1D29	19	1	NM_015594	exon3	c.T111C	p.D37D	GTGGGATATGTAT	.	scavenged	Atlas-SNP
DRD5	1816	hgsc.bcm.edu	37	4	9784542	9784542	+	Missense_Mutation	SNP	A	A	C	rs2227851	bycluster	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	32	3	57	0	0.09375	0	A|0.989;C|0.011	0.011	weak	DRD5,colon,carcinoma,0,1	DRD5	119	1	NM_000798	exon1	c.A889C	p.T297P	CTCAAGACCCTGT	.	scavenged	Atlas-SNP
BTG1	694	hgsc.bcm.edu	37	12	92539203	92539203	+	Silent	SNP	G	G	A	rs369374957	alternate_allele	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	181	8	187	0	0.0441989	0	.	.	alt	BTG1,NS,lymphoid_neoplasm,0,3	BTG1	30	3	NM_001731	exon1	c.C109T	p.L37L	TCTGCAGCTGTCG	.	PASS	Atlas-SNP
KIF25	3834	hgsc.bcm.edu	37	6	168443315	168443315	+	Missense_Mutation	SNP	G	G	A	rs146787013	bycluster;byfrequency;by1000genomes	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	62	12	91	0	0.193548	0	G|0.993;A|0.007	0.007	strong	KIF25,NS,carcinoma,-2,1	KIF25	75	1	NM_030615	exon8	c.G904A	p.V302I	GCAGGCGTCCTGG	.	PASS	Atlas-SNP
PCDH17	27253	hgsc.bcm.edu	37	13	58209024	58209024	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	41	5	58	0	0.121951	0	.	.	none	.	PCDH17	304	.	NM_001040429	exon1	c.G2344A	p.V782I	ATGAACGTCATGA	.	PASS	Atlas-SNP
ITCH	83737	hgsc.bcm.edu	37	20	32996580	32996580	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	105	10	151	0	0.0952381	0	.	.	none	.	ITCH	73	.	NM_001257137	exon4	c.G194A	p.W65X	CCAAGTGGAAGCA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105411852	105411852	+	Silent	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	114	2	140	1	0.0175439	0.00714286	.	.	none	AHNAK2_ENST00000333244,NS,carcinoma,-1,1	AHNAK2	719	1	NM_138420	exon7	c.A9936G	p.K3312K	CTTGAATTTGGGC	.	scavenged	Atlas-SNP
SFR1	119392	hgsc.bcm.edu	37	10	105883796	105883796	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	203	24	297	0	0.118227	0	.	.	none	MEIR5,NS,carcinoma,-2,1	.	.	1	NM_001002759	exon3	c.G460A	p.A154T	TTAAACGCTGAAA	.	PASS	Atlas-SNP
TAB3	257397	hgsc.bcm.edu	37	X	30873153	30873153	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	170	22	243	0	0.129412	0	.	.	none	.	TAB3	82	.	NM_152787	exon6	c.C629A	p.P210Q	GCTCTTGGTACAG	.	PASS	Atlas-SNP
TBP	6908	hgsc.bcm.edu	37	6	170871058	170871058	+	Silent	SNP	G	G	A	rs113440919		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	33	4	39	1	0.121212	0.025641	G|0.500;A|0.500	0.500	weak	TBP,caecum,carcinoma,0,1	TBP	58	1	NM_003194	exon3	c.G234A	p.Q78Q	GCAGCAGCAGCAG	.	scavenged	Atlas-SNP
ELOVL6	79071	hgsc.bcm.edu	37	4	111119485	111119485	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	102	7	126	0	0.0686275	0	.	.	none	.	ELOVL6	27	.	NM_001130721	exon2	c.A7C	p.M3L	CTGACATGTTCAT	.	PASS	Atlas-SNP
CDH11	1009	hgsc.bcm.edu	37	16	64981740	64981740	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	162	15	190	0	0.0925926	0	.	.	none	.	CDH11	260	.	NM_001797	exon13	c.C2157A	p.D719E	GATGAAGTCATCG	.	PASS	Atlas-SNP
ITLN1	55600	hgsc.bcm.edu	37	1	160850422	160850422	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	91	22	132	0	0.241758	0	.	.	none	ITLN1,caecum,carcinoma,+1,1	ITLN1	45	1	NM_017625	exon6	c.G641A	p.G214D	GCGTCGCCAAAAT	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971108	45971108	+	Silent	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	75	4	86	3	0.0533333	0.0348837	.	.	none	KRTAP10-2,caecum,carcinoma,-1,1	KRTAP10-2	21	1	NM_198693	exon1	c.G234A	p.S78S	GCAGCACGAGGGC	.	scavenged	Atlas-SNP
NDUFV2	4729	hgsc.bcm.edu	37	18	9122638	9122638	+	Missense_Mutation	SNP	G	G	C	rs148158107	bycluster;byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	139	9	199	10	0.0647482	0.0502513	G|0.996;C|0.005	0.005	strong	NDUFV2,colon,carcinoma,+1,3	NDUFV2	17	3	NM_021074	exon5	c.G428C	p.R143P	TGCTTCGAAACTC	.	scavenged	Atlas-SNP
KLHDC4	54758	hgsc.bcm.edu	37	16	87748161	87748161	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	138	7	169	0	0.0507246	0	.	.	none	.	KLHDC4	45	.	NM_017566	exon8	c.G778A	p.D260N	CCTTGTCCACGTC	.	PASS	Atlas-SNP
INPP5B	3633	hgsc.bcm.edu	37	1	38355355	38355355	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	122	6	177	0	0.0491803	0	.	.	none	.	INPP5B	76	.	NM_005540	exon9	c.C671T	p.S224F	GTGGAGGAGCGAA	.	PASS	Atlas-SNP
XKR4	114786	hgsc.bcm.edu	37	8	56270333	56270333	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	134	4	210	0	0.0298507	0	.	.	none	XKR4,NS,carcinoma,+1,1	XKR4	104	1	NM_052898	exon2	c.A902C	p.D301A	ATGCGGATGTGAG	.	scavenged	Atlas-SNP
PRPF31	26121	hgsc.bcm.edu	37	19	54632434	54632434	+	Silent	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	51	8	53	0	0.156863	0	.	.	none	.	PRPF31	48	.	NM_015629	exon12	c.C1149A	p.I383I	CTAGATCGAGGAG	.	PASS	Atlas-SNP
CYBB	1536	hgsc.bcm.edu	37	X	37663373	37663373	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	196	24	324	0	0.122449	0	.	.	none	.	CYBB	62	.	NM_000397	exon9	c.A1141T	p.K381X	GCGTGGAAACTAC	.	PASS	Atlas-SNP
LYRM5	144363	hgsc.bcm.edu	37	12	25357062	25357062	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	194	26	260	0	0.134021	0	.	.	none	.	LYRM5	10	.	NM_001001660	exon3	c.A89C	p.D30A	GAGCAGACTATTT	.	PASS	Atlas-SNP
AMBRA1	55626	hgsc.bcm.edu	37	11	46419037	46419037	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	50	6	64	1	0.12	0.015625	.	.	none	AMBRA1_ENST00000458649,bladder,carcinoma,0,2	AMBRA1	201	2	NM_001267782	exon20	c.A3869G	p.D1290G	GCAGCGTCCCCCC	.	scavenged	Atlas-SNP
SORCS3	22986	hgsc.bcm.edu	37	10	106959775	106959775	+	Silent	SNP	C	C	T	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	81	9	91	0	0.111111	0	.	.	none	.	SORCS3	282	.	NM_014978	exon15	c.C2028T	p.S676S	CTTCAGCCTCCGC	.	PASS	Atlas-SNP
LCE1F	353137	hgsc.bcm.edu	37	1	152749039	152749039	+	Silent	SNP	T	T	C	rs202038292	byfrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	111	10	107	2	0.0900901	0.0186916	T|0.954;C|0.046	0.046	strong	LCE1F,NS,carcinoma,+2,1	LCE1F	42	1	NM_178354	exon1	c.T192C	p.G64G	TGGGGGTGGTGGC	.	scavenged	Atlas-SNP
ZNF496	84838	hgsc.bcm.edu	37	1	247492064	247492064	+	Silent	SNP	G	G	A	rs146066456	alternate_allele	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	93	5	102	0	0.0537634	0	G|1.000;T|0.000	.	alt	.	ZNF496	80	.	NM_032752	exon4	c.C495T	p.N165N	ATCCTGGTTCTTT	.	PASS	Atlas-SNP
IRS4	8471	hgsc.bcm.edu	37	X	107977810	107977810	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	76	7	103	0	0.0921053	0	.	.	none	.	IRS4	253	.	NM_003604	exon1	c.G1765T	p.G589W	CCCCCCCAGAGTT	.	PASS	Atlas-SNP
MYBL1	4603	hgsc.bcm.edu	37	8	67492515	67492515	+	Silent	SNP	A	A	G	novel		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	87	6	116	0	0.0689655	0	.	.	none	.	MYBL1	73	.	NM_001080416	exon9	c.T954C	p.T318T	CTCACTAGTGTGC	.	PASS	Atlas-SNP
