Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	COSMIC_Gene_Freq	Algorithm
TRIM41	90933	hgsc.bcm.edu	37	5	180651182	180651187	+	In_Frame_Del	DEL	GGAGGA	GGAGGA	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	GGAGGA	GGAGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TRIM41	NM_201627	exon1	c.182_187del	p.61_63del	.	.	54.0	21.0	24.0	0.0	.	.	Atlas-Indel
CCDC105	126402	hgsc.bcm.edu	37	19	15133812	15133813	+	In_Frame_Ins	INS	-	-	TGCGCC	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CCDC105	NM_173482	exon7	c.1381_1382insTGCGCC	p.V461delinsVRL	.	.	64.0	12.0	29.0	0.0	.	.	Atlas-Indel
NEFH	4744	hgsc.bcm.edu	37	22	29885573	29885574	+	In_Frame_Ins	INS	-	-	CCTGAGAAGGCCAAGTCC	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	NEFH	NM_021076	exon4	c.1944_1945insCCTGAGAAGGCCAAGTCC	p.S648delinsSPEKAKS	.	.	152.0	19.0	46.0	0.0	.	.	Atlas-Indel
MYH11	4629	hgsc.bcm.edu	37	16	15808930	15808930	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	MYH11	NM_001040114	exon41	c.5644delG	p.G1882fs	.	.	19.0	19.0	0.0	0	.	.	Pindel,Atlas-Indel
C16orf3	750	hgsc.bcm.edu	37	16	90095597	90095598	+	In_Frame_Ins	INS	-	-	GGGGCAGGCTGC	rs71137702	alternate_allele	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	C16orf3	NM_001214	exon1	c.154_155insGCAGCCTGCCCC	p.I52delinsAACPI	.	.	59.0	13.0	38.0	0.0	GGGGCAGCCTACGGGGCAGGCTGC|1.000;|0.000	.	Atlas-Indel
C2orf62	375307	hgsc.bcm.edu	37	2	219222268	219222286	+	Frame_Shift_Del	DEL	CTACAGATGCTGTTCTTCT	CTACAGATGCTGTTCTTCT	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CTACAGATGCTGTTCTTCT	CTACAGATGCTGTTCTTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	C2orf62	NM_198559	exon3	c.129_147del	p.43_49del	.	.	41.0	16.0	37.0	0.0	.	.	Atlas-Indel
TCEB3C	162699	hgsc.bcm.edu	37	18	44555459	44555460	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TCEB3C	NM_145653	exon1	c.755_756insG	p.A252fs	.	.	280.0	17.0	76.0	0.0	.	.	Atlas-Indel
METTL2B	55798	hgsc.bcm.edu	37	7	128140983	128140984	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	METTL2B	NM_018396	exon8	c.943_944insT	p.V315fs	.	.	254.0	41.0	79.0	0.0	.	.	Atlas-Indel
CADM1	23705	hgsc.bcm.edu	37	11	115047284	115047285	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CADM1	NM_014333	exon10	c.1239_1240insG	p.G413fs	.	.	547.0	36.0	141.0	0.0	.	.	Atlas-Indel
TRMT1L	81627	hgsc.bcm.edu	37	1	185089286	185089287	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TRMT1L	NM_030934	exon15	c.2067_2068insT	p.L689fs	.	.	60.0	60.0	0.0	0	.	.	Pindel,Atlas-Indel
SMURF1	57154	hgsc.bcm.edu	37	7	98655111	98655111	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	SMURF1	NM_020429	exon4	c.268delC	p.Q90fs	.	.	56.0	56.0	0.0	0	.	.	Pindel,Atlas-Indel
BCAP29	55973	hgsc.bcm.edu	37	7	107254121	107254122	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	BCAP29	NM_001008405	exon7	c.713_714insA	p.L238fs	.	.	199.0	15.0	72.0	0.0	.	.	Atlas-Indel
APOB	338	hgsc.bcm.edu	37	2	21231993	21231994	+	Frame_Shift_Ins	INS	-	-	CTCTACC	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	APOB	NM_000384	exon26	c.7747_7748insGGTAGAG	p.Q2583fs	.	.	40.0	40.0	0.0	0	.	.	Pindel,Atlas-Indel
ITGA10	8515	hgsc.bcm.edu	37	1	145534989	145534990	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	ITGA10	NM_003637	exon15	c.1892_1893insG	p.V631fs	.	.	173.0	11.0	54.0	0.0	.	.	Atlas-Indel
DSPP	1834	hgsc.bcm.edu	37	4	88536644	88536652	+	In_Frame_Del	DEL	AGCAGTGAT	AGCAGTGAT	-	rs200486992		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	AGCAGTGAT	AGCAGTGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	DSPP	NM_014208	exon5	c.2829_2837del	p.943_946del	.	.	350.0	25.0	79.0	0.0	.	.	Atlas-Indel
SLCO1B3	28234	hgsc.bcm.edu	37	12	21028267	21028267	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	SLCO1B3	NM_019844	exon9	c.825delA	p.P275fs	.	.	12.0	12.0	0.0	0	.	.	Pindel
CTBP1-AS1	92070	hgsc.bcm.edu	37	4	1244521	1244523	+	RNA	DEL	ATC	ATC	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	ATC	ATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	.	.	.	.	.	.	24.0	24.0	0.0	0	.	.	Pindel
MUC6	4588	hgsc.bcm.edu	37	11	1017892	1017894	+	In_Frame_Del	DEL	CAT	CAT	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	MUC6	NM_005961	exon31	c.4908_4910del	p.1636_1637del	.	.	12.0	12.0	0.0	0	.	.	Pindel
ANO10	55129	hgsc.bcm.edu	37	3	43647212	43647213	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	ANO10	NM_001204833	exon2	c.133_134insA	p.D45fs	.	.	15.0	15.0	0.0	0	.	.	Pindel
C2orf62	375307	hgsc.bcm.edu	37	2	219222270	219222288	+	Frame_Shift_Del	DEL	ACAGATGCTGTTCTTCTCT	ACAGATGCTGTTCTTCTCT	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	ACAGATGCTGTTCTTCTCT	ACAGATGCTGTTCTTCTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	C2orf62	NM_198559	exon3	c.131_149del	p.44_50del	.	.	10.0	10.0	0.0	0	.	.	Pindel
GGTLC2	91227	hgsc.bcm.edu	37	22	22989321	22989321	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	GGTLC2	NM_199127	exon2	c.273delG	p.V91fs	.	.	12.0	12.0	0.0	0	.	.	Pindel
FRG1B	284802	hgsc.bcm.edu	37	20	29625932	29625935	+	RNA	DEL	GGCA	GGCA	-	rs144031280	alternate_allele	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	GGCA	GGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	FRG1B	.	.	.	.	.	.	10.0	10.0	0.0	0	.	.	Pindel
RAD51AP2	729475	hgsc.bcm.edu	37	2	17697199	17697199	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	RAD51AP2	NM_001099218	exon1	c.2485delT	p.Y829fs	.	.	13.0	13.0	0.0	0	.	.	Pindel
MLH3	27030	hgsc.bcm.edu	37	14	75483904	75483905	+	Frame_Shift_Ins	INS	-	-	CTATGGGAAGAAAGAATAACTTCAATTAGCAATATGA	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	MLH3	NM_001040108	exon13	c.4243_4244insTCATATTGCTAATTGAAGTTATTCTTTCTTCCCATAG	p.I1415_K1416delinsSYCX	.	.	23.0	23.0	0.0	0	.	.	Pindel
NQO1	1728	hgsc.bcm.edu	37	16	69748929	69748932	+	Frame_Shift_Del	DEL	GCTC	GCTC	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	GCTC	GCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	NQO1	NM_000903	exon4	c.353_356del	p.118_119del	.	.	14.0	14.0	0.0	0	.	.	Pindel
CYP20A1	57404	hgsc.bcm.edu	37	2	204150380	204150380	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CYP20A1	NM_177538	exon9	c.895delC	p.Q299fs	.	.	11.0	11.0	0.0	0	.	.	Pindel
KCTD3	51133	hgsc.bcm.edu	37	1	215747171	215747171	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	KCTD3	NM_016121	exon2	c.125delC	p.S42fs	.	.	21.0	21.0	0.0	0	.	.	Pindel
POLR2E	5434	hgsc.bcm.edu	37	19	1094065	1094117	+	Frame_Shift_Del	DEL	GGTCGTGGCACAGCTGCAGAGAGAAAGAACCAGCTGACCCCAGGGCAGAGAGA	GGTCGTGGCACAGCTGCAGAGAGAAAGAACCAGCTGACCCCAGGGCAGAGAGA	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	GGTCGTGGCACAGCTGCAGAGAGAAAGAACCAGCTGACCCCAGGGCAGAGAGA	GGTCGTGGCACAGCTGCAGAGAGAAAGAACCAGCTGACCCCAGGGCAGAGAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	POLR2E	NM_002695	exon2	c.58_71del	p.20_24del	.	.	11.0	11.0	0.0	0	.	.	Pindel
HESX1	8820	hgsc.bcm.edu	37	3	57232250	57232250	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	HESX1	NM_003865	exon4	c.534delT	p.N178fs	.	.	14.0	14.0	0.0	0	.	.	Pindel
ZC3H13	23091	hgsc.bcm.edu	37	13	46549613	46549614	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	ZC3H13	NM_015070	exon12	c.2273_2274del	p.758_758del	.	.	14.0	14.0	0.0	0	.	.	Pindel
ZFP106	64397	hgsc.bcm.edu	37	15	42742957	42742957	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	ZFP106	NM_022473	exon2	c.1445delC	p.S482fs	.	.	12.0	12.0	0.0	0	.	.	Pindel
OR51F1	256892	hgsc.bcm.edu	37	11	4790868	4790874	+	Frame_Shift_Del	DEL	TTTCACG	TTTCACG	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	TTTCACG	TTTCACG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	OR51F1	NM_001004752	exon1	c.275_281del	p.92_94del	.	.	14.0	14.0	0.0	0	.	.	Pindel
SYCP1	6847	hgsc.bcm.edu	37	1	115469133	115469134	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	SYCP1	NM_003176	exon23	c.1875_1876insA	p.L625fs	.	.	16.0	16.0	0.0	0	.	.	Pindel
RBMXL3	139804	hgsc.bcm.edu	37	X	114425207	114425208	+	In_Frame_Ins	INS	-	-	GGAGGCCGCTCGCCCGACACCCACAGT	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	NM_001145346	exon1	c.1203_1204insGGAGGCCGCTCGCCCGACACCCACAGT	p.S401delinsSGGRSPDTHS	.	.	10.0	10.0	0.0	0	.	.	Pindel
PCLO	27445	hgsc.bcm.edu	37	7	82595385	82595385	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PCLO	NM_014510	exon4	c.3720delG	p.K1240fs	.	.	11.0	11.0	0.0	0	.	.	Pindel
RBMX	27316	hgsc.bcm.edu	37	X	135960247	135960248	+	Splice_Site	INS	-	-	A	rs35488933		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	RBMX	NM_002139	exon5	c.217-2->T	.	.	.	10.0	10.0	0.0	0	.	.	Pindel
SPATA31C1	441452	hgsc.bcm.edu	37	9	90534192	90534193	+	In_Frame_Ins	INS	-	-	TCTTGTCTCCCAGCGTCA	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	NM_001145124	exon2	c.212_213insTCTTGTCTCCCAGCGTCA	p.H71delinsHLVSQRH	.	.	13.0	13.0	0.0	0	.	.	Pindel
SYCP3	50511	hgsc.bcm.edu	37	12	102122900	102122901	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	SYCP3	NM_001177949	exon8	c.644_645insA	p.I215fs	.	.	12.0	12.0	0.0	0	.	.	Pindel
METTL2B	55798	hgsc.bcm.edu	37	7	128140982	128140983	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	METTL2B	NM_018396	exon8	c.941_942del	p.314_314del	.	.	25.0	25.0	0.0	0	.	.	Pindel
NBN	4683	hgsc.bcm.edu	37	8	90965666	90965666	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	NBN	NM_002485	exon11	c.1652delG	p.R551fs	.	.	10.0	10.0	0.0	0	.	.	Pindel
SYCP1	6847	hgsc.bcm.edu	37	1	115527421	115527421	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	SYCP1	NM_003176	exon30	c.2634delT	p.S878fs	.	.	10.0	10.0	0.0	0	.	.	Pindel
ST18	9705	hgsc.bcm.edu	37	8	53062482	53062482	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	ST18	NM_014682	exon16	c.1863delT	p.N621fs	.	.	10.0	10.0	0.0	0	.	.	Pindel
PCP4L1	654790	hgsc.bcm.edu	37	1	161254154	161254156	+	In_Frame_Del	DEL	GGA	GGA	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	NM_001102566	exon3	c.89_91del	p.30_31del	.	.	12.0	12.0	0.0	0	.	.	Pindel
ANXA13	312	hgsc.bcm.edu	37	8	124707762	124707762	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	ANXA13	NM_001003954	exon7	c.575delT	p.I192fs	.	.	11.0	11.0	0.0	0	.	.	Pindel
DSPP	1834	hgsc.bcm.edu	37	4	88536764	88536781	+	In_Frame_Del	DEL	GATAGCAGTGACAGCAGT	GATAGCAGTGACAGCAGT	-	rs200486992	alternate_allele	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	GATAGCAGTGACAGCAGT	GATAGCAGTGACAGCAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	DSPP	NM_014208	exon5	c.2949_2966del	p.983_989del	.	.	14.0	14.0	0.0	0	.	.	Pindel
LARP7	51574	hgsc.bcm.edu	37	4	113570754	113570754	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	LARP7	NM_001267039	exon11	c.1226delT	p.L409X	.	.	10.0	10.0	0.0	0	.	.	Pindel
CCDC38	120935	hgsc.bcm.edu	37	12	96292432	96292432	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CCDC38	NM_182496	exon6	c.448delG	p.A150fs	.	.	10.0	10.0	0.0	0	.	.	Pindel
MUC4	4585	hgsc.bcm.edu	37	3	195512959	195513102	+	In_Frame_Del	DEL	GAAGCGTCGGTGACAGGAAGAGGGGTGGTGTCACCTGTGGATGCTGAGGAAGGGCTGGTGACAGGAAGAGGGATGGCCTGACCTGTGGATGCCGAGGAAACGTCGGTGACAGGAAGACGGGTGGTGTCATCTGTGGAAGCTGAA	GAAGCGTCGGTGACAGGAAGAGGGGTGGTGTCACCTGTGGATGCTGAGGAAGGGCTGGTGACAGGAAGAGGGATGGCCTGACCTGTGGATGCCGAGGAAACGTCGGTGACAGGAAGACGGGTGGTGTCATCTGTGGAAGCTGAA	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	GAAGCGTCGGTGACAGGAAGAGGGGTGGTGTCACCTGTGGATGCTGAGGAAGGGCTGGTGACAGGAAGAGGGATGGCCTGACCTGTGGATGCCGAGGAAACGTCGGTGACAGGAAGACGGGTGGTGTCATCTGTGGAAGCTGAA	GAAGCGTCGGTGACAGGAAGAGGGGTGGTGTCACCTGTGGATGCTGAGGAAGGGCTGGTGACAGGAAGAGGGATGGCCTGACCTGTGGATGCCGAGGAAACGTCGGTGACAGGAAGACGGGTGGTGTCATCTGTGGAAGCTGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	MUC4	NM_018406	exon2	c.5350_5493del	p.1784_1831del	.	.	11.0	11.0	0.0	0	.	.	Pindel
MUC6	4588	hgsc.bcm.edu	37	11	1016713	1016724	+	In_Frame_Del	DEL	TGTGGGTAGTGA	TGTGGGTAGTGA	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	TGTGGGTAGTGA	TGTGGGTAGTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	MUC6	NM_005961	exon31	c.6078_6089del	p.2026_2030del	.	.	10.0	10.0	0.0	0	.	.	Pindel
ATP1A4	480	hgsc.bcm.edu	37	1	160134106	160134106	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	ATP1A4	NM_144699	exon7	c.938delC	p.T313fs	.	.	13.0	13.0	0.0	0	.	.	Pindel
AHCTF1	25909	hgsc.bcm.edu	37	1	247007131	247007131	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	AHCTF1	NM_015446	exon34	c.6519delC	p.N2173fs	.	.	15.0	15.0	0.0	0	.	.	Pindel
IL7R	3575	hgsc.bcm.edu	37	5	35874637	35874637	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	IL7R	NM_002185	exon6	c.792delG	p.W264X	.	.	10.0	10.0	0.0	0	.	.	Pindel
CCDC73	493860	hgsc.bcm.edu	37	11	32635950	32635951	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CCDC73	NM_001008391	exon16	c.1914_1915insA	p.E638fs	.	.	12.0	12.0	0.0	0	.	.	Pindel
PDS5B	23047	hgsc.bcm.edu	37	13	33344887	33344888	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PDS5B	NM_015032	exon33	c.4160_4161insA	p.P1387fs	.	.	10.0	10.0	0.0	0	.	.	Pindel
MKI67	4288	hgsc.bcm.edu	37	10	129904535	129904535	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	MKI67	NM_002417	exon13	c.5570delT	p.I1857fs	.	.	17.0	17.0	0.0	0	.	.	Pindel
DYX1C1	161582	hgsc.bcm.edu	37	15	55759241	55759242	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	DYX1C1	NM_001033560	exon5	c.524_525insA	p.I175fs	.	.	17.0	17.0	0.0	0	.	.	Pindel
OR4C3	256144	hgsc.bcm.edu	37	11	48347124	48347144	+	In_Frame_Del	DEL	AAGTTGCCTGCACCAATACGT	AAGTTGCCTGCACCAATACGT	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	AAGTTGCCTGCACCAATACGT	AAGTTGCCTGCACCAATACGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	OR4C3	NM_001004702	exon1	c.631_651del	p.211_217del	.	.	10.0	10.0	0.0	0	.	.	Pindel
ERO1LB	56605	hgsc.bcm.edu	37	1	236393553	236393554	+	Splice_Site	DEL	GA	GA	-	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	ERO1LB	.	.	.	.	.	.	12.0	12.0	0.0	0	.	.	Pindel
SYNDIG1L	646658	hgsc.bcm.edu	37	14	74876039	74876039	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	SYNDIG1L	NM_001105579	exon2	c.G409A	p.E137K	CCTCTTCCTCCTG	.	88.0	54.0	72.0	0.0	.	.	Atlas-SNP
PLXNA1	5361	hgsc.bcm.edu	37	3	126733602	126733602	+	Silent	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PLXNA1	NM_032242	exon13	c.C2805A	p.A935A	TGACGCCCTGGTG	.	87.0	37.0	31.0	0.0	.	.	Atlas-SNP
GPR137B	7107	hgsc.bcm.edu	37	1	236368456	236368456	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	GPR137B	NM_003272	exon6	c.T997A	p.F333I	CATGGATTCAGTC	.	151.0	56.0	47.0	0.0	.	.	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47773060	47773060	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PCNT	NM_006031	exon10	c.A1499G	p.D500G	TGGAAGATTTAGA	.	92.0	25.0	56.0	0.0	.	.	Atlas-SNP
HYAL4	23553	hgsc.bcm.edu	37	7	123508467	123508467	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	HYAL4	NM_012269	exon3	c.C140A	p.P47H	GGAAACCTTTTAT	.	162.0	70.0	60.0	0.0	.	.	Atlas-SNP
CRNN	49860	hgsc.bcm.edu	37	1	152382699	152382699	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CRNN	NM_016190	exon3	c.G859A	p.A287T	TCTGAGCATGTCC	.	1688.0	90.0	184.0	0.0	.	.	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103390332	103390332	+	Missense_Mutation	SNP	C	C	T	rs200872789		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	NM_001146197	exon4	c.G12715A	p.E4239K	CAACTTCGTGATC	.	924.0	375.0	166.0	0.0	.	.	Atlas-SNP
CDK13	8621	hgsc.bcm.edu	37	7	40085553	40085553	+	Silent	SNP	T	T	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CDK13	NM_003718	exon6	c.T2472C	p.G824G	GGAGGGTCTGGAT	.	154.0	74.0	60.0	0.0	.	.	Atlas-SNP
PRR14L	253143	hgsc.bcm.edu	37	22	32111160	32111160	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PRR14L	NM_173566	exon4	c.A2665C	p.T889P	GAATGGTTTTGTT	.	438.0	208.0	123.0	0.0	.	.	Atlas-SNP
ZNF527	84503	hgsc.bcm.edu	37	19	37879212	37879212	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	ZNF527	NM_032453	exon5	c.G261T	p.W87C	AGACTGGGAGTCT	.	240.0	92.0	88.0	0.0	.	.	Atlas-SNP
APCDD1	147495	hgsc.bcm.edu	37	18	10471887	10471887	+	Silent	SNP	C	C	T	rs145453912	byfrequency;alternate_allele	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	APCDD1	NM_153000	exon3	c.C603T	p.A201A	CAAGGCCGTGAAC	.	69.0	26.0	30.0	0.0	C|1.000;G|0.000	.	Atlas-SNP
TRIM52	84851	hgsc.bcm.edu	37	5	180687440	180687440	+	Silent	SNP	T	T	C	rs80005177	byfrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TRIM52	NM_032765	exon1	c.A375G	p.E125E	TTCTTCTTCCTCC	.	180.0	23.0	56.0	0.0	T|0.991;C|0.009	.	Atlas-SNP
CUTC	51076	hgsc.bcm.edu	37	10	101503802	101503802	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CUTC	NM_015960	exon5	c.C412T	p.R138C	ATTTGCCGCCCTC	.	174.0	85.0	62.0	0.0	.	.	Atlas-SNP
TSC22D2	9819	hgsc.bcm.edu	37	3	150128513	150128513	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TSC22D2	NM_014779	exon1	c.C1376T	p.P459L	TGCCCCCGGCTAC	.	40.0	19.0	7.0	0.0	.	.	Atlas-SNP
DLG4	1742	hgsc.bcm.edu	37	17	7097812	7097812	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	DLG4	NM_001365	exon14	c.C1433T	p.A478V	AACAGGGCCCTGG	.	45.0	30.0	35.0	0.0	.	.	Atlas-SNP
LCP2	3937	hgsc.bcm.edu	37	5	169685155	169685155	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	LCP2	NM_005565	exon16	c.T986C	p.L329S	TGGGGCAAAGGTC	.	154.0	63.0	75.0	0.0	.	.	Atlas-SNP
SYCP1	6847	hgsc.bcm.edu	37	1	115524051	115524051	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	SYCP1	NM_003176	exon29	c.C2477T	p.S826L	TCACATCAGTTGA	.	215.0	96.0	74.0	0.0	.	.	Atlas-SNP
FLAD1	80308	hgsc.bcm.edu	37	1	154960711	154960711	+	Missense_Mutation	SNP	A	A	C	rs150372864	byfrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	FLAD1	NM_025207	exon2	c.A503C	p.N168T	TCTCCAACCGCTT	.	257.0	73.0	81.0	0.0	A|1.000;G|0.000;T|0.000	.	Atlas-SNP
SIMC1	375484	hgsc.bcm.edu	37	5	175772304	175772304	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	NM_198567	exon9	c.C1230A	p.F410L	GGCCTTCCGCAGC	.	191.0	81.0	73.0	0.0	.	.	Atlas-SNP
CDHR1	92211	hgsc.bcm.edu	37	10	85960359	85960359	+	Silent	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CDHR1	NM_001171971	exon6	c.C441T	p.D147D	TCAGGACATACCT	.	123.0	62.0	76.0	0.0	.	.	Atlas-SNP
HRC	3270	hgsc.bcm.edu	37	19	49657889	49657889	+	Silent	SNP	T	T	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	HRC	NM_002152	exon1	c.A606G	p.E202E	CTCCTCTTCCTCC	.	171.0	12.0	72.0	0.0	.	.	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507851	195507851	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	MUC4	NM_018406	exon2	c.G10600A	p.A3534T	GCGTGGCGTGACC	.	397.0	17.0	108.0	0.0	.	.	Atlas-SNP
PHTF2	57157	hgsc.bcm.edu	37	7	77569480	77569480	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PHTF2	NM_001127357	exon12	c.C1499A	p.S500X	CTGCTTCAGAACT	.	495.0	183.0	126.0	0.0	.	.	Atlas-SNP
ITPR3	3710	hgsc.bcm.edu	37	6	33657110	33657110	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	ITPR3	NM_002224	exon50	c.C6790A	p.L2264I	CGCCCCCTCATCG	.	75.0	32.0	57.0	0.0	.	.	Atlas-SNP
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39261945	39261945	+	Missense_Mutation	SNP	C	C	A	rs142970341	by1000genomes	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	NM_001146041	exon1	c.C305A	p.P102H	GCCAACCCACTTG	.	49.0	19.0	4.0	0.0	C|0.991;A|0.009	.	Atlas-SNP
CCDC57	284001	hgsc.bcm.edu	37	17	80115731	80115731	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CCDC57	NM_198082	exon14	c.C2134T	p.Q712X	CCACCTGCTTCCG	.	49.0	28.0	25.0	0.0	.	.	Atlas-SNP
OR5F1	338674	hgsc.bcm.edu	37	11	55761412	55761412	+	Silent	SNP	C	C	T	rs144082157	byfrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	OR5F1	NM_003697	exon1	c.G690A	p.S230S	CTCCCCCGAATGC	.	127.0	52.0	31.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
COX4I2	84701	hgsc.bcm.edu	37	20	30227827	30227827	+	Silent	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	COX4I2	NM_032609	exon3	c.C174T	p.N58N	ACTCAACGCTGAG	.	22.0	11.0	15.0	0.0	.	.	Atlas-SNP
MAGEC1	9947	hgsc.bcm.edu	37	X	140994346	140994346	+	Silent	SNP	C	C	T	rs60520741	byfrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	MAGEC1	NM_005462	exon4	c.C1156T	p.L386L	ACTTTACTGAGTC	.	713.0	37.0	105.0	0.0	C|0.992;G|0.008	.	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525411	248525411	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	OR2T4	NM_001004696	exon1	c.T529G	p.S177A	TTCCTGTCATCAG	.	1529.0	62.0	174.0	0.0	.	.	Atlas-SNP
EDNRA	1909	hgsc.bcm.edu	37	4	148457097	148457097	+	Silent	SNP	G	G	A	rs200693894		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	EDNRA	NM_001957	exon5	c.G816A	p.A272A	CACTGCGATCTTC	.	297.0	127.0	109.0	0.0	.	.	Atlas-SNP
PNMA3	29944	hgsc.bcm.edu	37	X	152225435	152225435	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PNMA3	NM_013364	exon2	c.A23G	p.D8G	TACAGGACTGGTG	.	117.0	104.0	40.0	0.0	.	.	Atlas-SNP
DHX37	57647	hgsc.bcm.edu	37	12	125453127	125453127	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	DHX37	NM_032656	exon10	c.G1361T	p.G454V	CACTCGCCACTGT	.	32.0	16.0	19.0	0.0	.	.	Atlas-SNP
CDO1	1036	hgsc.bcm.edu	37	5	115146946	115146946	+	Silent	SNP	T	T	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CDO1	NM_001801	exon3	c.A315G	p.T105T	AAATAATGTCTCC	.	302.0	120.0	106.0	0.0	.	.	Atlas-SNP
PTPN22	26191	hgsc.bcm.edu	37	1	114380291	114380291	+	Silent	SNP	A	A	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PTPN22	NM_015967	exon13	c.T1731C	p.Y577Y	ATTGTAATAAGAG	.	162.0	60.0	63.0	0.0	.	.	Atlas-SNP
GALNT4	8693	hgsc.bcm.edu	37	12	89916794	89916794	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	NM_003774	exon1	c.T1533G	p.N511K	CACATAATTTTTT	.	169.0	85.0	59.0	0.0	.	.	Atlas-SNP
OSCAR	126014	hgsc.bcm.edu	37	19	54602893	54602893	+	Splice_Site	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	OSCAR	NM_130771	exon4	c.71-1G>T	.	TGGCCACTAAGGG	.	117.0	50.0	44.0	0.0	.	.	Atlas-SNP
PABPC4L	132430	hgsc.bcm.edu	37	4	135121534	135121534	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	NM_001114734	exon2	c.G815T	p.G272V	GTTTTGCCATATT	.	195.0	87.0	62.0	0.0	.	.	Atlas-SNP
NOS1	4842	hgsc.bcm.edu	37	12	117768410	117768410	+	Silent	SNP	G	G	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	NOS1	NM_000620	exon2	c.C465T	p.P155P	ATTCCCGGGACCC	.	55.0	22.0	25.0	0.0	.	.	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	85043137	85043137	+	Silent	SNP	G	G	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	DNAH6	NM_001370	exon76	c.G12303A	p.K4101K	CTATAAGCCAAGC	.	228.0	85.0	75.0	0.0	.	.	Atlas-SNP
TRPC4AP	26133	hgsc.bcm.edu	37	20	33598060	33598060	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TRPC4AP	NM_015638	exon12	c.C1441G	p.L481V	CATTCAGCTCCTG	.	277.0	107.0	106.0	0.0	.	.	Atlas-SNP
TTC37	9652	hgsc.bcm.edu	37	5	94839530	94839530	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TTC37	NM_014639	exon31	c.G3205A	p.E1069K	TGCTCTCTTTATA	.	154.0	63.0	86.0	0.0	.	.	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525404	248525404	+	Silent	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	OR2T4	NM_001004696	exon1	c.C522T	p.L174L	GTGTCTCTTCCTG	.	1540.0	69.0	172.0	0.0	.	.	Atlas-SNP
SIMC1	375484	hgsc.bcm.edu	37	5	175772305	175772305	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	.	NM_198567	exon9	c.C1231A	p.R411S	GCCTTCCGCAGCC	.	193.0	80.0	72.0	0.0	.	.	Atlas-SNP
TMTC2	160335	hgsc.bcm.edu	37	12	83358835	83358835	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TMTC2	NM_152588	exon5	c.C1631G	p.A544G	GGTTTGCAGAAGC	.	498.0	193.0	131.0	0.0	.	.	Atlas-SNP
NRD1	4898	hgsc.bcm.edu	37	1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	rs62648104		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	NRD1	NM_002525	exon2	c.A449T	p.E150V	TCTTCCTCCACCT	.	298.0	18.0	111.0	0.0	T|0.024;A|0.976	.	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88776355	88776355	+	Silent	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CTU2	NM_001012759	exon3	c.C153T	p.F51F	CTGTTTCAAGGCC	.	102.0	44.0	62.0	0.0	.	.	Atlas-SNP
KRT33B	3884	hgsc.bcm.edu	37	17	39525703	39525703	+	Silent	SNP	G	G	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	KRT33B	NM_002279	exon1	c.C300T	p.C100C	GCTGGGGCACAGC	.	112.0	10.0	40.0	0.0	.	.	Atlas-SNP
HNRNPL	3191	hgsc.bcm.edu	37	19	39328060	39328060	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	HNRNPL	NM_001533	exon12	c.C1675G	p.L559V	AGCCCAGAGTCTC	.	172.0	68.0	69.0	0.0	.	.	Atlas-SNP
NRCAM	4897	hgsc.bcm.edu	37	7	107824934	107824934	+	Silent	SNP	G	G	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	NRCAM	NM_001037132	exon18	c.C2160T	p.R720R	CATCACGCGGAAG	.	106.0	39.0	42.0	0.0	.	.	Atlas-SNP
CHL1	10752	hgsc.bcm.edu	37	3	440785	440785	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CHL1	NM_006614	exon26	c.A3339T	p.L1113F	ACTATTATTAACT	.	456.0	196.0	120.0	0.0	.	.	Atlas-SNP
RYR2	6262	hgsc.bcm.edu	37	1	237774079	237774079	+	Silent	SNP	G	G	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	RYR2	NM_001035	exon36	c.G4701T	p.S1567S	TCTCTCGGCGGGA	.	181.0	52.0	67.0	0.0	.	.	Atlas-SNP
CYP39A1	51302	hgsc.bcm.edu	37	6	46607278	46607278	+	Silent	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CYP39A1	NM_016593	exon3	c.G441A	p.L147L	ATTCTCCAGTTGT	.	336.0	138.0	108.0	0.0	.	.	Atlas-SNP
PRB1	5542	hgsc.bcm.edu	37	12	11506288	11506288	+	Missense_Mutation	SNP	T	T	C	rs140825288		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PRB1	NM_199353	exon4	c.A350G	p.K117R	TGAGGTTTGTTGC	.	618.0	35.0	152.0	0.0	T|1.000;C|0.000	.	Atlas-SNP
TRIM52	84851	hgsc.bcm.edu	37	5	180687428	180687428	+	Silent	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	TRIM52	NM_032765	exon1	c.G387A	p.E129E	ATCTTCCTCTTCT	.	184.0	18.0	59.0	0.0	.	.	Atlas-SNP
CLEC4F	165530	hgsc.bcm.edu	37	2	71047619	71047619	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	CLEC4F	NM_173535	exon1	c.C37A	p.Q13K	CACACTGGTTATC	.	100.0	49.0	54.0	0.0	.	.	Atlas-SNP
LCA5L	150082	hgsc.bcm.edu	37	21	40800132	40800132	+	Silent	SNP	T	T	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	LCA5L	NM_152505	exon4	c.A288G	p.K96K	ATACTTTTTCTTC	.	303.0	123.0	109.0	0.0	.	.	Atlas-SNP
EFEMP2	30008	hgsc.bcm.edu	37	11	65638628	65638628	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	EFEMP2	NM_016938	exon4	c.G367T	p.D123Y	ACTCACCCACACA	.	58.0	20.0	23.0	0.0	.	.	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31255209	31255209	+	Silent	SNP	G	G	A	rs71447572		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	DDX11	NM_030653	exon22	c.G2235A	p.V745V	CCAGGTGGAGCAG	.	236.0	12.0	105.0	0.0	G|0.500;A|0.500	.	Atlas-SNP
RFC1	5981	hgsc.bcm.edu	37	4	39310299	39310299	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	RFC1	NM_002913	exon13	c.G1842T	p.W614C	TCGGAGCCAGCGT	.	563.0	248.0	141.0	0.0	.	.	Atlas-SNP
CTNNB1	1499	hgsc.bcm.edu	37	3	41266100	41266100	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	CTNNB1,gallbladder,other,-1	CTNNB1	NM_001098209	exon3	c.T97G	p.S33A	CTGGACTCTGGAA	.	238.0	105.0	89.0	0.0	.	.	Atlas-SNP
PCDHA3	56145	hgsc.bcm.edu	37	5	140182753	140182753	+	Silent	SNP	C	C	G	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PCDHA3	NM_031497	exon1	c.C1971G	p.P657P	TGAACCCTCATTG	.	106.0	48.0	50.0	0.0	.	.	Atlas-SNP
OR2L13	284521	hgsc.bcm.edu	37	1	248263611	248263611	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	OR2L13	NM_175911	exon3	c.G934T	p.E312X	CTGAAAGAATAAT	.	110.0	27.0	32.0	0.0	.	.	Atlas-SNP
FNDC3B	64778	hgsc.bcm.edu	37	3	172098773	172098773	+	Silent	SNP	T	T	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	FNDC3B	NM_001135095	exon25	c.T3193C	p.L1065L	ACACAGTTAGAAG	.	101.0	31.0	51.0	0.0	.	.	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678724	100678724	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	MUC17	NM_001040105	exon3	c.C4027A	p.P1343T	AGTATACCTGTCA	.	198.0	10.0	66.0	0.0	.	.	Atlas-SNP
FCGR3B	2215	hgsc.bcm.edu	37	1	161596059	161596059	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	FCGR3B	NM_001244753	exon4	c.T561G	p.F187L	ATGATGAAAATAC	.	199.0	160.0	100.0	0.0	.	.	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140563708	140563708	+	Missense_Mutation	SNP	G	G	A	rs17844651	byfrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	PCDHB16	NM_020957	exon1	c.G1574A	p.R525Q	CCCTGCGGGAGTT	.	117.0	17.0	39.0	0.0	G|0.567;A|0.433	.	Atlas-SNP
TNPO1	3842	hgsc.bcm.edu	37	5	72168474	72168474	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	TNPO1,NS,carcinoma,+1	TNPO1	NM_002270	exon7	c.C605T	p.A202V	CTCACGCTGTTGC	.	223.0	100.0	96.0	0.0	.	.	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016851	1016851	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	.	MUC6	NM_005961	exon31	c.A5950G	p.M1984V	CAGTCATAGGACC	.	1978.0	89.0	186.0	0.0	.	.	Atlas-SNP
