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
HYDIN	54768	hgsc.bcm.edu	37	16	70934989	70934989	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110.0	16.0	45.0	0.0	0.145455	0	.	.	none	.	HYDIN	788	.	NM_001270974	exon53	c.8967delC	p.I2989fs	.	.	PASS	Atlas-Indel
OR6A2	8590	hgsc.bcm.edu	37	11	6816750	6816751	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157.0	33.0	149.0	0.0	0.210191	0	.	.	none	.	OR6A2	68	.	NM_003696	exon1	c.190_191insT	p.L64fs	.	.	PASS	Atlas-Indel
FAM115C	285966	hgsc.bcm.edu	37	7	143417404	143417405	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87.0	16.0	106.0	0.0	0.183908	0	.	.	none	.	FAM115C	29	.	NM_173678	exon3	c.1251_1252del	p.417_418del	.	.	PASS	Atlas-Indel
FASTKD1	79675	hgsc.bcm.edu	37	2	170387132	170387133	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	222.0	69.0	190.0	0.0	0.311	.	.	.	none	.	FASTKD1	86	.	NM_024622	exon14	c.2407_2408insA	p.R803fs	.	.	PASS	Pindel,Atlas-Indel
FARP2	9855	hgsc.bcm.edu	37	2	242407679	242407680	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62.0	17.0	82.0	0.0	0.274	.	.	.	none	.	FARP2	92	.	NM_014808	exon18	c.2017_2018del	p.673_673del	.	.	PASS	Pindel,Atlas-Indel
NCL	4691	hgsc.bcm.edu	37	2	232325406	232325408	+	In_Frame_Del	DEL	TCA	TCA	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153.0	34.0	154.0	0.0	0.222	.	.	.	none	.	NCL	80	.	NM_005381	exon4	c.784_786del	p.262_262del	.	.	PASS	Pindel,Atlas-Indel
TET2	54790	hgsc.bcm.edu	37	4	106158509	106158510	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	272.0	55.0	250.0	0.0	0.202	.	.	.	none	TET2,NS,haematopoietic_neoplasm,0,1	TET2	1762	1	NM_017628	exon3	c.3410_3411insT	p.G1137fs	.	.	PASS	Pindel,Atlas-Indel
MUC4	4585	hgsc.bcm.edu	37	3	195505765	195505766	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68.0	10.0	91.0	0.0	0.147059	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.12686_12687insT	p.S4229fs	.	.	PASS	Atlas-Indel
ZNF660	285349	hgsc.bcm.edu	37	3	44636279	44636280	+	Frame_Shift_Del	DEL	AT	AT	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38.0	13.0	41.0	0.0	0.342	.	.	.	none	.	ZNF660	28	.	NM_173658	exon3	c.593_594del	p.198_198del	.	.	PASS	Pindel,Atlas-Indel
LDHAL6A	160287	hgsc.bcm.edu	37	11	18487252	18487253	+	Frame_Shift_Del	DEL	AC	AC	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179.0	56.0	152.0	0.0	0.313	.	.	.	none	.	LDHAL6A	35	.	NM_144972	exon3	c.312_313del	p.104_105del	.	.	PASS	Pindel,Atlas-Indel
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24329897	24329908	+	In_Frame_Del	DEL	AGCAGGAGCAGG	AGCAGGAGCAGG	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AGCAGGAGCAGG	AGCAGGAGCAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153.0	38.0	101.0	0.0	0.248366	0	.	.	none	.	.	.	.	NM_001136233	exon1	c.1526_1537del	p.509_513del	.	.	PASS	Atlas-Indel
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305774	39305775	+	In_Frame_Ins	INS	-	-	TGGCAGCAGCTGGGG	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31.0	17.0	22.0	0.0	0.548387	0	.	.	none	KRTAP4-5,NS,carcinoma,0,1	KRTAP4-5	34	1	NM_033188	exon1	c.246_247insCCCCAGCTGCTGCCA	p.Q82delinsHPSCCQ	.	.	PASS	Atlas-Indel
HYDIN	54768	hgsc.bcm.edu	37	16	70934990	70934991	+	In_Frame_Ins	INS	-	-	CCC	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108.0	16.0	47.0	0.0	0.148148	0	.	.	none	.	HYDIN	788	.	NM_001270974	exon53	c.8965_8966insGGG	p.I2989delinsGI	.	.	PASS	Atlas-Indel
CTAGE5	4253	hgsc.bcm.edu	37	14	39784005	39784008	+	Splice_Site	DEL	TATA	TATA	-	rs75318507	bycluster;by1000genomes;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TATA	TATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131.0	79.0	116.0	0.0	0.603053	0	.	.	alt	.	CTAGE5	75	.	.	.	.	.	.	.	PASS	Atlas-Indel
PCDH9	5101	hgsc.bcm.edu	37	13	67802190	67802190	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154.0	12.0	103.0	0.0	0.0779221	0	.	.	none	.	PCDH9	252	.	NM_020403	exon2	c.384delA	p.I128fs	.	.	PASS	Atlas-Indel
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382374	24382388	+	In_Frame_Del	DEL	TGCTGCTGCTGCTGC	TGCTGCTGCTGCTGC	-	rs371342199	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGCTGCTGCTGCTGC	TGCTGCTGCTGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195.0	52.0	131.0	0.0	0.266667	0	.	.	alt	.	.	.	.	NM_001136234	exon1	c.1496_1510del	p.499_504del	.	.	PASS	Atlas-Indel
MROH2B	133558	hgsc.bcm.edu	37	5	41064591	41064598	+	Frame_Shift_Del	DEL	TTCATCCT	TTCATCCT	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTCATCCT	TTCATCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36.0	13.0	46.0	0.0	0.361	.	.	.	none	.	.	.	.	NM_173489	exon5	c.437_444del	p.146_148del	.	.	PASS	Pindel,Atlas-Indel
UHRF2	115426	hgsc.bcm.edu	37	9	6413513	6413513	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75.0	14.0	87.0	0.0	0.186667	0	.	.	none	.	UHRF2	50	.	NM_152896	exon1	c.22delA	p.I8fs	.	.	PASS	Atlas-Indel
TSR1	55720	hgsc.bcm.edu	37	17	2237939	2237941	+	In_Frame_Del	DEL	CCA	CCA	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87.0	29.0	110.0	0.0	0.333	.	.	.	none	.	TSR1	57	.	NM_018128	exon5	c.807_809del	p.269_270del	.	.	PASS	Pindel,Atlas-Indel
GCC2	9648	hgsc.bcm.edu	37	2	109087929	109087931	+	In_Frame_Del	DEL	AAG	AAG	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83.0	24.0	109.0	0.0	0.289	.	.	.	none	.	GCC2	129	.	NM_181453	exon6	c.2143_2145del	p.715_715del	.	.	PASS	Pindel,Atlas-Indel
TET2	54790	hgsc.bcm.edu	37	4	106196525	106196525	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76.0	13.0	96.0	0.0	0.171	.	.	.	none	.	TET2	1762	.	NM_001127208	exon11	c.4857delT	p.P1619fs	.	.	PASS	Pindel,Atlas-Indel
KIAA0586	9786	hgsc.bcm.edu	37	14	58899157	58899157	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152.0	56.0	170.0	0.0	0.368	.	.	.	none	.	KIAA0586	180	.	NM_001244189	exon5	c.427delA	p.R143fs	.	.	PASS	Pindel,Atlas-Indel
IGLL5	100423062	hgsc.bcm.edu	37	22	23230370	23230370	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45.0	10.0	144.0	0.0	0.222	.	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.136delC	p.Q46fs	.	.	PASS	Pindel,Atlas-Indel
MUC4	4585	hgsc.bcm.edu	37	3	195505762	195505763	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68.0	10.0	88.0	0.0	0.147059	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-2,4	MUC4	1505	4	NM_018406	exon2	c.12689_12690del	p.4230_4230del	.	.	PASS	Atlas-Indel
ZNF543	125919	hgsc.bcm.edu	37	19	57839629	57839630	+	In_Frame_Ins	INS	-	-	GCG	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47.0	20.0	55.0	0.0	0.426	.	.	.	none	.	ZNF543	61	.	NM_213598	exon4	c.799_800insGCG	p.R267delinsSG	.	.	PASS	Pindel,Atlas-Indel
DDN	23109	hgsc.bcm.edu	37	12	49391394	49391395	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52.0	11.0	41.0	0.0	0.212	.	.	.	none	.	DDN	54	.	NM_015086	exon2	c.1265_1266insG	p.A422fs	.	.	PASS	Pindel,Atlas-Indel
ZNF623	9831	hgsc.bcm.edu	37	8	144733650	144733654	+	Frame_Shift_Del	DEL	ATAAA	ATAAA	-	rs202122969	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	ATAAA	ATAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143.0	57.0	145.0	0.0	0.399	.	ATAAA|0.993;-|0.007	0.007	strong	.	ZNF623	63	.	NM_014789	exon1	c.1607_1611del	p.536_537del	.	.	PASS	Pindel,Atlas-Indel
MCCC1	56922	hgsc.bcm.edu	37	3	182755074	182755074	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131.0	39.0	122.0	0.0	0.298	.	.	.	none	.	MCCC1	87	.	NM_020166	exon13	c.1527delC	p.C509fs	.	.	PASS	Pindel,Atlas-Indel
SLC23A1	9963	hgsc.bcm.edu	37	5	138715033	138715034	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99.0	16.0	85.0	0.0	0.162	.	.	.	none	.	SLC23A1	51	.	NM_152685	exon9	c.948_949insG	p.G316fs	.	.	PASS	Pindel,Atlas-Indel
RFC4	5984	hgsc.bcm.edu	37	3	186508121	186508122	+	Frame_Shift_Del	DEL	CA	CA	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112.0	24.0	134.0	0.0	0.214	.	.	.	none	RFC4,NS,carcinoma,+2,2	RFC4	54	2	NM_002916	exon9	c.876_877del	p.292_293del	.	.	PASS	Pindel,Atlas-Indel
C16orf88	400506	hgsc.bcm.edu	37	16	19725766	19725767	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36.0	18.0	45.0	0.0	0.500	.	.	.	none	.	C16orf88	41	.	NM_001012991	exon2	c.592_593insG	p.Q198fs	.	.	PASS	Pindel,Atlas-Indel
B2M	567	hgsc.bcm.edu	37	15	45007888	45007891	+	Frame_Shift_Del	DEL	TAGT	TAGT	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TAGT	TAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51.0	17.0	71.0	0.0	0.333	.	.	.	none	.	B2M	99	.	NM_004048	exon2	c.334_337del	p.112_113del	.	.	PASS	Pindel
NUDT17	200035	hgsc.bcm.edu	37	1	145586672	145586679	+	Frame_Shift_Del	DEL	TTTTACAC	TTTTACAC	-	rs201063949	by1000genomes;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTTTACAC	TTTTACAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84.0	21.0	116.0	0.0	0.250	.	-|0.017;TTTTA|0.983	0.017	alt	.	NUDT17	25	.	NM_001012758	exon8	c.898_905del	p.300_302del	.	.	PASS	Pindel
C14orf23	387978	hgsc.bcm.edu	37	14	29261305	29261306	+	RNA	INS	-	-	AACAAAC	rs200251419	by1000genomes;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67.0	12.0	86.0	0.0	0.179	.	-|0.668;AAC|0.332	.	alt	.	C14orf23	5	.	.	.	.	.	.	.	PASS	Pindel
STK17B	9262	hgsc.bcm.edu	37	2	197004468	197004575	+	In_Frame_Del	DEL	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68.0	15.0	84.0	0.0	0.221	.	.	.	none	.	STK17B	28	.	NM_004226	exon7	c.657_713del	p.219_238del	.	.	PASS	Pindel
SLC12A9	56996	hgsc.bcm.edu	37	7	100464136	100464136	+	Missense_Mutation	SNP	G	G	A	rs374047787		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52.0	20.0	26.0	0.0	0.384615	0	.	.	weak	.	SLC12A9	81	.	NM_020246	exon14	c.G2654A	p.R885H	ACCCCCGCTACCT	.	PASS	Atlas-SNP
MN1	4330	hgsc.bcm.edu	37	22	28192809	28192809	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96.0	30.0	81.0	0.0	0.3125	0	.	.	none	.	MN1	122	.	NM_002430	exon1	c.C3723T	p.D1241D	CTTGTCGTCGTCC	.	PASS	Atlas-SNP
CLCA2	9635	hgsc.bcm.edu	37	1	86913384	86913384	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89.0	20.0	76.0	0.0	0.224719	0	.	.	none	.	CLCA2	102	.	NM_006536	exon11	c.T1907A	p.L636H	CCATTCTTAATGC	.	PASS	Atlas-SNP
RRP8	23378	hgsc.bcm.edu	37	11	6622218	6622218	+	Missense_Mutation	SNP	G	G	A	rs17834692	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91.0	39.0	60.0	0.0	0.428571	0	G|0.986;A|0.014	0.014	strong	.	RRP8	40	.	NM_015324	exon4	c.C985T	p.P329S	GCACAGGGTTCCG	.	PASS	Atlas-SNP
ALDH3A2	224	hgsc.bcm.edu	37	17	19575096	19575096	+	Missense_Mutation	SNP	C	C	T	rs61737992	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104.0	50.0	102.0	0.0	0.480769	0	C|0.996;T|0.004	0.004	strong	.	ALDH3A2	41	.	NM_001031806	exon9	c.C1270T	p.P424S	CAGCGTCCCTGTT	.	PASS	Atlas-SNP
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20739922	20739922	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87.0	47.0	61.0	0.0	0.54023	0	.	.	none	.	GOLGA6L6	37	.	NM_001145004	exon8	c.C1828T	p.Q610X	CCTCCTGCTTCCA	.	PASS	Atlas-SNP
ND6	0	hgsc.bcm.edu	37	MT	14149	14149	+	Silent	SNP	C	C	T	rs28357668	bycluster;byfrequency;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	19.0	19.0	12.0	0.0	1	0	A|0.995;G|0.005	.	alt	.	.	.	.	ENST00000361681	exon1	c.G525A	p.X175X	ACATAACCTATTC	.	PASS	Atlas-SNP
SFMBT2	57713	hgsc.bcm.edu	37	10	7412243	7412243	+	Silent	SNP	G	G	A	rs142871492	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	32.0	119.0	0.0	0.438356	0	G|0.997;A|0.003	0.003	strong	.	SFMBT2	209	.	NM_001029880	exon3	c.C195T	p.H65H	ACATACGTGTTTG	.	PASS	Atlas-SNP
ACP6	51205	hgsc.bcm.edu	37	1	147131611	147131611	+	Missense_Mutation	SNP	C	C	T	rs144959805	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124.0	61.0	69.0	0.0	0.491935	0	C|0.999;T|0.001	0.001	strong	.	ACP6	36	.	NM_016361	exon3	c.G379A	p.V127M	TGCCCACCTTGGT	.	PASS	Atlas-SNP
CEACAM1	634	hgsc.bcm.edu	37	19	43031318	43031318	+	Missense_Mutation	SNP	G	G	A	rs199627333		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	313.0	13.0	275.0	0.0	0.0415335	0	.	.	weak	.	CEACAM1	43	.	NM_001184816	exon2	c.C299T	p.T100I	TATATTGTCTCTC	.	PASS	Atlas-SNP
CYP3A4	1576	hgsc.bcm.edu	37	7	99358598	99358598	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	252.0	105.0	276.0	0.0	0.416667	0	.	.	none	.	CYP3A4	56	.	NM_017460	exon12	c.C1260T	p.S420S	CTTCTTGCTGAAT	.	PASS	Atlas-SNP
ANKRD36	375248	hgsc.bcm.edu	37	2	97790211	97790211	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178.0	9.0	153.0	1.0	0.0505618	0.00653595	.	.	none	ANKRD36_ENST00000420699,extremity,malignant_melanoma,0,2	ANKRD36	170	2	NM_001164315	exon5	c.A608T	p.H203L	TCATACATGCTGT	.	scavenged	Atlas-SNP
CDH8	1006	hgsc.bcm.edu	37	16	61935317	61935317	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98.0	20.0	87.0	0.0	0.204082	0	.	.	none	CDH8,NS,carcinoma,0,1	CDH8	273	1	NM_001796	exon3	c.G313T	p.A105S	TCCCAGCTCCATC	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43557637	43557637	+	Silent	SNP	C	C	T	rs200233807	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	205.0	127.0	131.0	0.0	0.619512	0	C|0.999;T|0.001	0.001	strong	.	UMODL1	186	.	NM_173568	exon21	c.C4248T	p.A1416A	AACAGCCACCCTT	.	PASS	Atlas-SNP
CENPB	1059	hgsc.bcm.edu	37	20	3766137	3766137	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	35.0	88.0	0.0	0.479452	0	.	.	none	.	CENPB	24	.	NM_001810	exon1	c.C994A	p.Q332K	TCACCTGCTGGAC	.	PASS	Atlas-SNP
AMER1	139285	hgsc.bcm.edu	37	X	63412987	63412987	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123.0	51.0	73.0	0.0	0.414634	0	.	.	none	.	.	.	.	NM_152424	exon2	c.T180C	p.F60F	GCCACCAAAGAGT	.	PASS	Atlas-SNP
FCF1	51077	hgsc.bcm.edu	37	14	75190002	75190002	+	Missense_Mutation	SNP	T	T	C	rs41309250	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122.0	67.0	115.0	0.0	0.54918	0	T|0.995;C|0.005	0.005	strong	.	FCF1	15	.	NM_015962	exon5	c.T320C	p.M107T	GTGTAATGGCTGA	.	PASS	Atlas-SNP
UPP2	151531	hgsc.bcm.edu	37	2	158991346	158991346	+	Missense_Mutation	SNP	C	C	T	rs144945330	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91.0	20.0	138.0	0.0	0.21978	0	C|0.999;T|0.001	0.001	strong	.	UPP2	60	.	NM_001135098	exon9	c.C1069T	p.R357W	CAGCAACGGCCTC	.	PASS	Atlas-SNP
LRP1	4035	hgsc.bcm.edu	37	12	57603636	57603636	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49.0	18.0	47.0	0.0	0.367347	0	.	.	none	.	LRP1	428	.	NM_002332	exon80	c.C12424T	p.H4142Y	CATCAGCACAAGC	.	PASS	Atlas-SNP
CCND3	896	hgsc.bcm.edu	37	6	41909273	41909273	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72.0	22.0	104.0	0.0	0.305556	0	.	.	none	.	CCND3	40	.	NM_001760	exon1	c.G115A	p.V39I	GGGGTACGTAGCG	.	PASS	Atlas-SNP
ANKRD1	27063	hgsc.bcm.edu	37	10	92679979	92679979	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147.0	71.0	144.0	0.0	0.482993	0	.	.	none	.	ANKRD1	50	.	NM_014391	exon2	c.C154G	p.P52A	TCACAGGGTGGGC	.	PASS	Atlas-SNP
ZFAND2B	130617	hgsc.bcm.edu	37	2	220072382	220072382	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82.0	28.0	80.0	0.0	0.341463	0	.	.	none	ZFAND2B_ENST00000444522,NS,carcinoma,-1,2	ZFAND2B	28	2	NM_138802	exon3	c.C163T	p.P55S	CAGGTACCTGTGT	.	PASS	Atlas-SNP
ZNF646	9726	hgsc.bcm.edu	37	16	31090221	31090221	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91.0	4.0	83.0	0.0	0.043956	0	.	.	none	.	ZNF646	133	.	NM_014699	exon2	c.C2576T	p.S859F	TTGACTCTCTGCC	.	PASS	Atlas-SNP
STAB1	23166	hgsc.bcm.edu	37	3	52557136	52557136	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54.0	5.0	61.0	0.0	0.0925926	0	.	.	none	.	STAB1	178	.	NM_015136	exon63	c.T7006G	p.S2336A	AACTTCTCCACCT	.	PASS	Atlas-SNP
FHIT	2272	hgsc.bcm.edu	37	3	60522657	60522657	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59.0	13.0	42.0	0.0	0.220339	0	.	.	none	.	FHIT	44	.	NM_002012	exon5	c.T39G	p.S13S	CACTACAGAGGGC	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	3019696	3019696	+	Silent	SNP	G	G	A	rs145598896	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45.0	18.0	40.0	0.0	0.4	0	G|0.999;A|0.001	0.001	strong	.	CSMD1	1469	.	NM_033225	exon38	c.C5829T	p.P1943P	GTACCCGGGCTCG	.	PASS	Atlas-SNP
BIRC6	57448	hgsc.bcm.edu	37	2	32774473	32774473	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	258.0	72.0	237.0	0.0	0.27907	0	.	.	none	.	BIRC6	838	.	NM_016252	exon65	c.C13069T	p.P4357S	GCCCTTCCTTCTG	.	PASS	Atlas-SNP
CCDC54	84692	hgsc.bcm.edu	37	3	107096926	107096926	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	215.0	50.0	207.0	0.0	0.232558	0	.	.	none	.	CCDC54	56	.	NM_032600	exon1	c.A492C	p.K164N	GGGTAAAGAAATC	.	PASS	Atlas-SNP
SMTNL1	219537	hgsc.bcm.edu	37	11	57317522	57317522	+	Silent	SNP	A	A	G	rs117673759	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112.0	50.0	115.0	0.0	0.446429	0	A|0.999;G|0.001	0.001	strong	.	SMTNL1	68	.	NM_001105565	exon7	c.A1422G	p.T474T	CTACACATACATC	.	PASS	Atlas-SNP
CTAGE5	4253	hgsc.bcm.edu	37	14	39790149	39790149	+	Missense_Mutation	SNP	C	C	G	rs36060072	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100.0	52.0	86.0	0.0	0.52	0	G|0.005;C|0.995	0.005	strong	.	CTAGE5	75	.	NM_001247989	exon19	c.C1576G	p.P526A	TATGGTCCCTCAC	.	PASS	Atlas-SNP
ZBBX	79740	hgsc.bcm.edu	37	3	167023485	167023485	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169.0	37.0	202.0	0.0	0.218935	0	.	.	none	.	ZBBX	299	.	NM_024687	exon17	c.C1671A	p.S557R	CAGATTGCTCAAT	.	PASS	Atlas-SNP
PCDHGB3	56102	hgsc.bcm.edu	37	5	140751891	140751891	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27.0	9.0	35.0	0.0	0.333333	0	.	.	none	.	PCDHGB3	168	.	NM_018924	exon1	c.G1930A	p.V644I	CTGCTGGTCACTG	.	PASS	Atlas-SNP
PRR22	163154	hgsc.bcm.edu	37	19	5783840	5783840	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36.0	14.0	19.0	0.0	0.388889	0	.	.	none	.	PRR22	25	.	NM_001134316	exon3	c.C418G	p.P140A	ACTGGGGCCCCCC	.	PASS	Atlas-SNP
TANK	10010	hgsc.bcm.edu	37	2	162036195	162036195	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100.0	41.0	136.0	0.0	0.41	0	.	.	none	.	TANK	35	.	NM_004180	exon2	c.C22T	p.Q8X	GGCGAGCAACTCA	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129813567	129813567	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	39.0	90.0	0.0	0.534247	0	.	.	none	.	LAMA2	481	.	NM_000426	exon58	c.T8183A	p.V2728D	AAATAGTTATCCA	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77075631	77075631	+	Silent	SNP	C	C	T	rs3744182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72.0	23.0	84.0	0.0	0.319444	0	C|0.878;T|0.122	0.122	strong	ENGASE,NS,carcinoma,+2,2	ENGASE	55	2	NM_001042573	exon4	c.C477T	p.D159D	CATCGACGTCTTT	.	PASS	Atlas-SNP
HUNK	30811	hgsc.bcm.edu	37	21	33368191	33368191	+	Missense_Mutation	SNP	G	G	C	rs138721520	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180.0	106.0	162.0	0.0	0.588889	0	G|0.998;C|0.002	0.002	strong	.	HUNK	74	.	NM_014586	exon10	c.G1416C	p.M472I	GCTTATGACACAG	.	PASS	Atlas-SNP
HAGHL	84264	hgsc.bcm.edu	37	16	777590	777590	+	Silent	SNP	C	C	T	rs143758903	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96.0	45.0	92.0	0.0	0.46875	0	C|0.999;T|0.001	0.001	strong	.	HAGHL	18	.	NM_032304	exon1	c.C81T	p.A27A	GGTGGCCGTGGAC	.	PASS	Atlas-SNP
CD48	962	hgsc.bcm.edu	37	1	160681535	160681535	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	265.0	53.0	275.0	0.0	0.2	0	.	.	none	.	CD48	31	.	NM_001256030	exon1	c.G19A	p.D7N	ACGAATCCCAACC	.	PASS	Atlas-SNP
PAX5	5079	hgsc.bcm.edu	37	9	37033992	37033992	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89.0	41.0	61.0	0.0	0.460674	0	.	.	none	.	PAX5	250	.	NM_016734	exon1	c.A37G	p.S13G	TCCTGCTGGTCCG	.	PASS	Atlas-SNP
RFTN2	130132	hgsc.bcm.edu	37	2	198498595	198498595	+	Missense_Mutation	SNP	C	C	T	rs139323535	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170.0	85.0	173.0	0.0	0.5	0	C|0.998;T|0.002	0.002	strong	RFTN2,NS,carcinoma,0,2	RFTN2	68	2	NM_144629	exon4	c.G565A	p.G189S	CTGAACCGTGTCT	.	PASS	Atlas-SNP
C2orf53	339779	hgsc.bcm.edu	37	2	27360773	27360773	+	Missense_Mutation	SNP	G	G	A	rs61741796	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43.0	20.0	47.0	0.0	0.465116	0	G|0.993;A|0.007	0.007	strong	.	C2orf53	45	.	NM_178553	exon3	c.C425T	p.P142L	TGGCAAGGTGAGT	.	PASS	Atlas-SNP
MCMDC2	157777	hgsc.bcm.edu	37	8	67786817	67786817	+	Missense_Mutation	SNP	C	C	T	rs116671744	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117.0	50.0	120.0	0.0	0.42735	0	C|0.970;T|0.030	0.030	strong	.	MCMDC2	84	.	NM_173518	exon4	c.C281T	p.T94M	CTGAAACGCAAGT	.	PASS	Atlas-SNP
TOX3	27324	hgsc.bcm.edu	37	16	52484278	52484278	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113.0	33.0	97.0	0.0	0.292035	0	.	.	none	.	TOX3	121	.	NM_001080430	exon4	c.C589T	p.H197Y	ATGTGTGAGGCAT	.	PASS	Atlas-SNP
SYMPK	8189	hgsc.bcm.edu	37	19	46320218	46320218	+	Silent	SNP	G	G	A	rs140350780	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92.0	47.0	110.0	0.0	0.51087	0	G|0.997;A|0.003	0.003	strong	.	SYMPK	104	.	NM_004819	exon24	c.C3096T	p.P1032P	CACCTTGGGGTAC	.	PASS	Atlas-SNP
KHDRBS1	10657	hgsc.bcm.edu	37	1	32479924	32479924	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84.0	28.0	73.0	0.0	0.333333	0	.	.	none	.	KHDRBS1	34	.	NM_006559	exon1	c.G328A	p.E110K	ATGGCCGAGAAGG	.	PASS	Atlas-SNP
ATAD3B	83858	hgsc.bcm.edu	37	1	1425644	1425644	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101.0	50.0	92.0	0.0	0.49505	0	.	.	none	.	ATAD3B	68	.	NM_031921	exon14	c.C1345G	p.L449V	TTCATGCTGGTCC	.	PASS	Atlas-SNP
USP35	57558	hgsc.bcm.edu	37	11	77911745	77911745	+	Missense_Mutation	SNP	C	C	T	rs147270370	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119.0	95.0	95.0	0.0	0.798319	0	C|0.996;T|0.004	0.004	strong	USP35_ENST00000263311,rectum,carcinoma,-1,2	USP35	179	2	NM_020798	exon6	c.C1088T	p.S363L	AGGACTCGAACTC	.	PASS	Atlas-SNP
SAMD9L	219285	hgsc.bcm.edu	37	7	92761064	92761064	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75.0	17.0	63.0	0.0	0.226667	0	.	.	none	.	SAMD9L	227	.	NM_152703	exon5	c.A4221C	p.K1407N	TTGTTTTTTTAGC	.	PASS	Atlas-SNP
OR10A5	144124	hgsc.bcm.edu	37	11	6867588	6867588	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	224.0	12.0	243.0	0.0	0.0535714	0	.	.	none	.	OR10A5	48	.	NM_178168	exon1	c.T675C	p.A225A	TGCTGCTATCCTC	.	PASS	Atlas-SNP
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744062	31744062	+	Missense_Mutation	SNP	C	C	A	rs150635388	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110.0	65.0	105.0	0.0	0.590909	0	C|0.999;A|0.001	0.001	strong	KRTAP13-2,NS,carcinoma,0,1	KRTAP13-2	29	1	NM_181621	exon1	c.G470T	p.C157F	GACTGGCAGCTCC	.	PASS	Atlas-SNP
KIAA0196	9897	hgsc.bcm.edu	37	8	126056088	126056088	+	Silent	SNP	C	C	T	rs369339497		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137.0	70.0	112.0	0.0	0.510949	0	.	.	weak	KIAA0196,NS,carcinoma,0,1	KIAA0196	90	1	NM_014846	exon23	c.G2829A	p.A943A	GAGATACGCAGTC	.	PASS	Atlas-SNP
GALNT14	79623	hgsc.bcm.edu	37	2	31348076	31348076	+	Missense_Mutation	SNP	G	G	A	rs41280621	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36.0	15.0	37.0	0.0	0.416667	0	G|0.994;A|0.006	0.006	strong	.	GALNT14	103	.	NM_001253826	exon2	c.C173T	p.A58V	TGAGGCGCCCAAG	.	PASS	Atlas-SNP
TRAPPC12	51112	hgsc.bcm.edu	37	2	3391458	3391458	+	Missense_Mutation	SNP	G	G	A	rs200941005	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46.0	34.0	43.0	0.0	0.73913	0	G|0.998;A|0.002	0.002	strong	.	.	.	.	NM_016030	exon2	c.G64A	p.A22T	CAGCTCGCGCCTC	.	PASS	Atlas-SNP
MAMDC2	256691	hgsc.bcm.edu	37	9	72723204	72723204	+	Missense_Mutation	SNP	G	G	A	rs139498917	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125.0	63.0	149.0	0.0	0.504	0	G|0.999;A|0.001	0.001	strong	.	MAMDC2	55	.	NM_153267	exon3	c.G226A	p.E76K	CAGGCTGAGGAAT	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19500088	19500088	+	Silent	SNP	A	A	G	rs41273197	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112.0	59.0	78.0	0.0	0.526786	0	A|0.995;G|0.005	0.005	strong	.	UBR4	415	.	NM_020765	exon23	c.T3010C	p.L1004L	GTATCAAGAAGTA	.	PASS	Atlas-SNP
CWF19L2	143884	hgsc.bcm.edu	37	11	107309826	107309826	+	Silent	SNP	C	C	T	rs201136952	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32.0	8.0	44.0	0.0	0.25	0	C|1.000;T|0.000	0.000	strong	CWF19L2_ENST00000282251,NS,carcinoma,0,2	CWF19L2	135	2	NM_152434	exon6	c.G654A	p.S218S	AGTAATCGATGAC	.	PASS	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34789443	34789443	+	Missense_Mutation	SNP	C	C	G	rs369670668		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114.0	14.0	115.0	0.0	0.122807	0	.	.	weak	.	UHRF1BP1	102	.	NM_017754	exon2	c.C58G	p.L20V	AAGAATCTTTCCC	.	PASS	Atlas-SNP
PVRL1	5818	hgsc.bcm.edu	37	11	119549473	119549473	+	Missense_Mutation	SNP	C	C	T	rs200377205	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40.0	9.0	34.0	0.0	0.225	0	C|0.996;T|0.005	0.005	weak	.	PVRL1	133	.	NM_002855	exon2	c.G82A	p.V28I	AGTGGACGCCTGG	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132504639	132504639	+	Silent	SNP	C	C	T	rs147615479	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48.0	30.0	57.0	0.0	0.625	0	C|0.994;T|0.006	0.006	strong	.	EP400	370	.	NM_015409	exon22	c.C4323T	p.T1441T	TCGCACCGTGGCT	.	PASS	Atlas-SNP
STPG2	285555	hgsc.bcm.edu	37	4	98902403	98902403	+	Missense_Mutation	SNP	T	T	C	rs76740552	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92.0	56.0	134.0	0.0	0.608696	0	T|0.994;C|0.006	0.006	strong	.	.	.	.	NM_174952	exon6	c.A679G	p.K227E	AAGACTTGAGAGC	.	PASS	Atlas-SNP
GRHL2	79977	hgsc.bcm.edu	37	8	102570830	102570830	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119.0	33.0	101.0	0.0	0.277311	0	.	.	none	GRHL2,right_lower_lobe,carcinoma,0,1	GRHL2	68	1	NM_024915	exon4	c.G468A	p.T156T	AATCACGGTGGTG	.	PASS	Atlas-SNP
TIAM2	26230	hgsc.bcm.edu	37	6	155458562	155458562	+	Silent	SNP	C	C	T	rs374521659		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86.0	33.0	89.0	0.0	0.383721	0	.	.	weak	.	TIAM2	161	.	NM_012454	exon4	c.C1446T	p.T482T	AGAAACCGCCGAG	.	PASS	Atlas-SNP
FCRL3	115352	hgsc.bcm.edu	37	1	157670258	157670258	+	Missense_Mutation	SNP	G	G	C	rs201961888	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132.0	43.0	163.0	0.0	0.325758	0	G|1.000;C|0.000	0.000	strong	.	FCRL3	163	.	NM_052939	exon2	c.C22G	p.L8V	GGATCAGCAGCAG	.	PASS	Atlas-SNP
SLC16A11	162515	hgsc.bcm.edu	37	17	6946357	6946357	+	Missense_Mutation	SNP	C	C	A	rs75636181	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28.0	17.0	68.0	0.0	0.607143	0	C|0.967;A|0.033	0.033	strong	SLC16A11,NS,carcinoma,0,1	SLC16A11	25	1	NM_153357	exon2	c.G310T	p.A104S	GGCGGGCCCCCCA	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144943384	144943384	+	Silent	SNP	G	G	A	rs189024404	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48.0	30.0	37.0	0.0	0.625	0	G|0.988;A|0.012	0.012	strong	.	EPPK1	199	.	NM_031308	exon1	c.C4038T	p.L1346L	TGGCACGAGCCCC	.	PASS	Atlas-SNP
ZBTB20	26137	hgsc.bcm.edu	37	3	114058008	114058008	+	Silent	SNP	G	G	T	rs139619357	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104.0	45.0	126.0	0.0	0.432692	0	G|0.999;T|0.001	0.001	strong	.	ZBTB20	157	.	NM_001164342	exon5	c.C2070A	p.T690T	AGGGGGGGTCCCA	.	PASS	Atlas-SNP
TSHZ3	57616	hgsc.bcm.edu	37	19	31770506	31770506	+	Missense_Mutation	SNP	C	C	T	rs111618794	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41.0	19.0	71.0	0.0	0.463415	0	C|0.998;T|0.002	0.002	strong	TSHZ3_ENST00000240587,NS,carcinoma,+2,1	TSHZ3	549	1	NM_020856	exon2	c.G193A	p.A65T	ACTCGGCGGCCGG	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17367354	17367354	+	Silent	SNP	G	G	A	rs141680124	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54.0	31.0	60.0	0.0	0.574074	0	G|0.992;A|0.008	0.008	strong	.	USHBP1	85	.	NM_031941	exon9	c.C1396T	p.L466L	TCCCCAGAATGGC	.	PASS	Atlas-SNP
SPOCK1	6695	hgsc.bcm.edu	37	5	136834138	136834138	+	Missense_Mutation	SNP	T	T	C	rs111393448	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41.0	20.0	44.0	0.0	0.487805	0	T|0.991;C|0.009	0.009	strong	.	SPOCK1	58	.	NM_004598	exon2	c.A110G	p.N37S	AGGAAATTGCCGT	.	PASS	Atlas-SNP
USP7	7874	hgsc.bcm.edu	37	16	8989511	8989511	+	Silent	SNP	C	C	T	rs61731196	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84.0	38.0	94.0	0.0	0.452381	0	C|0.994;T|0.006	0.006	strong	.	USP7	116	.	NM_003470	exon27	c.G2907A	p.T969T	TCGAAACGTCCGG	.	PASS	Atlas-SNP
MTERFD2	130916	hgsc.bcm.edu	37	2	242039210	242039210	+	Missense_Mutation	SNP	G	G	A	rs143756138	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93.0	42.0	79.0	0.0	0.451613	0	G|0.999;A|0.001	0.001	strong	.	MTERFD2	33	.	NM_182501	exon2	c.C121T	p.R41C	GTTTGCGCAACAA	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124417973	124417973	+	Silent	SNP	C	C	T	rs56219209	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57.0	27.0	43.0	0.0	0.473684	0	C|0.985;T|0.015	0.015	strong	.	DNAH10	888	.	NM_207437	exon76	c.C13038T	p.N4346N	GAAGAACGGCTGG	.	PASS	Atlas-SNP
VPS9D1	9605	hgsc.bcm.edu	37	16	89783205	89783205	+	Silent	SNP	G	G	A	rs118114589	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52.0	29.0	60.0	0.0	0.557692	0	G|0.988;A|0.012	0.012	strong	.	.	.	.	NM_004913	exon3	c.C201T	p.D67D	GGAGGTGTCGGGG	.	PASS	Atlas-SNP
OR51E1	143503	hgsc.bcm.edu	37	11	4674343	4674343	+	Missense_Mutation	SNP	G	G	A	rs139501861	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138.0	74.0	143.0	1.0	0.536232	0.00699301	G|0.996;A|0.004	0.004	strong	OR51E1,caecum,carcinoma,-1,1	OR51E1	67	1	NM_152430	exon2	c.G587A	p.R196Q	ATATCCGGGTCAA	.	scavenged	Atlas-SNP
NPC2	10577	hgsc.bcm.edu	37	14	74951269	74951269	+	Missense_Mutation	SNP	T	T	C	rs142075589	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47.0	25.0	46.0	0.0	0.531915	0	T|1.000;C|0.000	0.000	strong	.	NPC2	9	.	NM_006432	exon3	c.A212G	p.K71R	ACGGCCTTGCTGC	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74303550	74303550	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97.0	4.0	129.0	0.0	0.0412371	0	.	.	none	.	QRICH2	143	.	NM_032134	exon1	c.C32T	p.A11V	ACCCTGGCAAAGC	.	PASS	Atlas-SNP
ZNF311	282890	hgsc.bcm.edu	37	6	28963861	28963861	+	Silent	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107.0	79.0	91.0	0.0	0.738318	0	.	.	none	.	ZNF311	59	.	NM_001010877	exon7	c.C918G	p.T306T	ACACTGGGTGCAA	.	PASS	Atlas-SNP
EPHA1	2041	hgsc.bcm.edu	37	7	143088584	143088584	+	Missense_Mutation	SNP	C	C	T	rs139482378	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104.0	52.0	121.0	0.0	0.5	0	C|0.999;T|0.001	0.001	strong	EPHA1,NS,carcinoma,-1,1	EPHA1	193	1	NM_005232	exon18	c.G2897A	p.R966H	AGAATGCGCTTCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505746	195505746	+	Silent	SNP	T	T	G	rs369426870		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70.0	21.0	90.0	0.0	0.3	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.A12705C	p.T4235T	GTGACCTGTGGAT	.	PASS	Atlas-SNP
HIST1H4I	8294	hgsc.bcm.edu	37	6	27107302	27107302	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141.0	93.0	116.0	0.0	0.659574	0	.	.	none	.	HIST1H4I	26	.	NM_003495	exon1	c.C215G	p.T72S	CCGTGACCTACAC	.	PASS	Atlas-SNP
C5orf20	140947	hgsc.bcm.edu	37	5	134782443	134782443	+	Missense_Mutation	SNP	T	T	C	rs113429044	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58.0	24.0	65.0	0.0	0.413793	0	T|0.902;C|0.098	0.098	strong	.	C5orf20	16	.	NM_130848	exon1	c.A356G	p.K119R	CCTGTCTTCCTTC	.	PASS	Atlas-SNP
HNF1A	6927	hgsc.bcm.edu	37	12	121435342	121435342	+	Silent	SNP	C	C	T	rs2259820	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117.0	116.0	70.0	0.0	0.991453	0	C|0.718;T|0.282	0.282	strong	.	HNF1A	302	.	NM_000545	exon7	c.C1375T	p.L459L	ACCACCCTGCAGC	.	PASS	Atlas-SNP
CRISPLD2	83716	hgsc.bcm.edu	37	16	84900645	84900645	+	Missense_Mutation	SNP	G	G	A	rs149615348	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54.0	24.0	79.0	0.0	0.444444	0	G|0.994;A|0.006	0.006	strong	.	CRISPLD2	36	.	NM_031476	exon7	c.G852A	p.M284I	CTACATGAGTGAG	.	PASS	Atlas-SNP
ATL2	64225	hgsc.bcm.edu	37	2	38537579	38537579	+	Missense_Mutation	SNP	T	T	C	rs34873284	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97.0	58.0	107.0	0.0	0.597938	0	T|0.967;C|0.033	0.033	strong	.	ATL2	49	.	NM_001135673	exon8	c.A815G	p.N272S	TGTTGATTTTGTT	.	PASS	Atlas-SNP
KLHDC4	54758	hgsc.bcm.edu	37	16	87782322	87782322	+	Missense_Mutation	SNP	G	G	C	rs3751727	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70.0	28.0	51.0	0.0	0.4	0	G|0.974;C|0.026	0.026	strong	.	KLHDC4	45	.	NM_001184856	exon5	c.C463G	p.L155V	CCCAGAGATCCTT	.	PASS	Atlas-SNP
MYH13	8735	hgsc.bcm.edu	37	17	10222310	10222310	+	Missense_Mutation	SNP	G	G	A	rs200861648	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138.0	56.0	155.0	0.0	0.405797	0	G|1.000;A|0.000	0.000	strong	MYH13_ENST00000252172,right_upper_lobe,carcinoma,0,2	MYH13	533	2	NM_003802	exon27	c.C3535T	p.R1179C	CCCTGCGCATTTT	.	PASS	Atlas-SNP
CCDC158	339965	hgsc.bcm.edu	37	4	77255210	77255210	+	Silent	SNP	C	C	T	rs113022439	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140.0	140.0	138.0	0.0	1	0	C|0.984;T|0.016	0.016	strong	.	CCDC158	114	.	NM_001042784	exon18	c.G2775A	p.K925K	CTCTGTCTTGCTC	.	PASS	Atlas-SNP
HMBOX1	79618	hgsc.bcm.edu	37	8	28827928	28827928	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87.0	4.0	52.0	0.0	0.045977	0	.	.	none	.	HMBOX1	34	.	NM_024567	exon4	c.A392T	p.K131M	ATGGAAAGATGTC	.	PASS	Atlas-SNP
TFDP3	51270	hgsc.bcm.edu	37	X	132351703	132351703	+	Missense_Mutation	SNP	C	C	A	rs35745873	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84.0	28.0	71.0	0.0	0.333333	0	C|0.978;A|0.022	0.022	strong	.	TFDP3	92	.	NM_016521	exon1	c.G585T	p.Q195H	ACAGTTCTGAGCC	.	PASS	Atlas-SNP
KEAP1	9817	hgsc.bcm.edu	37	19	10602344	10602344	+	Missense_Mutation	SNP	G	G	A	rs147613351	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98.0	43.0	115.0	0.0	0.438776	0	G|1.000;A|0.000	0.000	strong	.	KEAP1	182	.	NM_012289	exon3	c.C1234T	p.P412S	TACGGGGCACGCT	.	PASS	Atlas-SNP
PRSS3	5646	hgsc.bcm.edu	37	9	33799103	33799103	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	210.0	9.0	176.0	0.0	0.0428571	0	.	.	none	.	PRSS3	79	.	NM_007343	exon5	c.G840A	p.K280K	CTGGAAGAACAGG	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88500957	88500957	+	Missense_Mutation	SNP	C	C	T	rs76389306	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74.0	35.0	74.0	0.0	0.472973	0	C|0.998;T|0.002	0.002	strong	.	ZNF469	121	.	NM_001127464	exon2	c.C6995T	p.P2332L	CAGGGCCGGACTC	.	PASS	Atlas-SNP
MSGN1	343930	hgsc.bcm.edu	37	2	17998001	17998001	+	Silent	SNP	C	C	T	rs201149255	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77.0	33.0	67.0	0.0	0.428571	0	C|0.999;T|0.001	0.001	strong	MSGN1,NS,carcinoma,+1,1	MSGN1	39	1	NM_001105569	exon1	c.C216T	p.G72G	GCACGGCGGGGCC	.	PASS	Atlas-SNP
DUSP8	1850	hgsc.bcm.edu	37	11	1580173	1580173	+	Silent	SNP	C	C	A	rs17854342	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119.0	34.0	119.0	0.0	0.285714	0	.	.	alt	.	DUSP8	22	.	NM_004420	exon4	c.G483T	p.L161L	GCGGGTCAGGCCC	.	PASS	Atlas-SNP
MROH1	727957	hgsc.bcm.edu	37	8	145223239	145223239	+	Missense_Mutation	SNP	C	C	T	rs374952645		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36.0	9.0	31.0	0.0	0.25	0	.	.	weak	.	.	.	.	NM_001099280	exon4	c.C64T	p.P22S	AAGGACCCCCTGG	.	PASS	Atlas-SNP
CLRN3	119467	hgsc.bcm.edu	37	10	129690837	129690837	+	Missense_Mutation	SNP	G	G	T	rs35890579	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79.0	38.0	50.0	0.0	0.481013	0	G|0.966;T|0.034	0.034	strong	.	CLRN3	27	.	NM_152311	exon1	c.C212A	p.P71Q	TTCTTTGGTTCTG	.	PASS	Atlas-SNP
PKP3	11187	hgsc.bcm.edu	37	11	403658	403658	+	Missense_Mutation	SNP	G	G	C	rs147657735	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28.0	17.0	26.0	0.0	0.607143	0	G|0.999;C|0.001	0.001	strong	PKP3,NS,lymphoid_neoplasm,0,1	PKP3	36	1	NM_007183	exon10	c.G1964C	p.R655P	AGGAGCGTATTCT	.	PASS	Atlas-SNP
AVIL	10677	hgsc.bcm.edu	37	12	58204648	58204648	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132.0	6.0	91.0	0.0	0.0454545	0	.	.	none	.	AVIL	60	.	NM_006576	exon5	c.T509C	p.V170A	ATGATGACTTTCC	.	PASS	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	37	3	121251922	121251922	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	237.0	66.0	228.0	0.0	0.278481	0	.	.	none	.	POLQ	273	.	NM_199420	exon6	c.T875C	p.L292P	TCCAAAAGCGGTA	.	PASS	Atlas-SNP
MYH9	4627	hgsc.bcm.edu	37	22	36690158	36690158	+	Missense_Mutation	SNP	C	C	T	rs147031322		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49.0	20.0	48.0	0.0	0.408163	0	C|1.000;T|0.000	0.000	weak	MYH9,rectum,carcinoma,0,1	MYH9	225	1	NM_002473	exon28	c.G3817A	p.D1273N	CCTTGTCGGCCAG	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44890654	44890654	+	Missense_Mutation	SNP	C	C	T	rs149238831	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100.0	15.0	108.0	0.0	0.15	0	C|0.995;T|0.005	0.005	strong	.	ZNF285	86	.	NM_152354	exon4	c.G1753A	p.E585K	TCTGCTCATGTAG	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152882648	152882648	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79.0	11.0	82.0	0.0	0.139241	0	.	.	none	.	IVL	100	.	NM_005547	exon2	c.A375C	p.E125D	GGAAGAAGAGAAG	.	PASS	Atlas-SNP
FNDC8	54752	hgsc.bcm.edu	37	17	33454198	33454198	+	Missense_Mutation	SNP	G	G	T	rs147725468	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84.0	49.0	61.0	0.0	0.583333	0	G|0.999;T|0.001	0.001	strong	.	FNDC8	28	.	NM_017559	exon2	c.G347T	p.G116V	TGGAGGGGGAGCT	.	PASS	Atlas-SNP
IL10RA	3587	hgsc.bcm.edu	37	11	117869878	117869878	+	Missense_Mutation	SNP	C	C	T	rs2229114	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116.0	107.0	96.0	0.0	0.922414	0	C|0.969;T|0.031	0.031	strong	.	IL10RA	46	.	NM_001558	exon7	c.C1259T	p.S420L	GTGGCTCGGCCTT	.	PASS	Atlas-SNP
SPTLC3	55304	hgsc.bcm.edu	37	20	13145471	13145471	+	Missense_Mutation	SNP	G	G	A	rs200308499	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94.0	28.0	89.0	0.0	0.297872	0	.	.	weak	.	SPTLC3	78	.	NM_018327	exon12	c.G1616A	p.R539H	CAGCACGTCCTGA	.	PASS	Atlas-SNP
RICTOR	253260	hgsc.bcm.edu	37	5	38944635	38944635	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	4.0	60.0	0.0	0.0547945	0	.	.	none	RICTOR,colon,carcinoma,0,1	RICTOR	182	1	NM_152756	exon36	c.G4826A	p.R1609H	AGTATACGGCACA	.	PASS	Atlas-SNP
B3GNT5	84002	hgsc.bcm.edu	37	3	182988131	182988131	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156.0	69.0	168.0	0.0	0.442308	0	.	.	none	.	B3GNT5	26	.	NM_032047	exon2	c.A545G	p.Y182C	ATACCTATTGTCC	.	PASS	Atlas-SNP
ERBB4	2066	hgsc.bcm.edu	37	2	212251864	212251864	+	Silent	SNP	T	T	C	rs3748962	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189.0	92.0	165.0	0.0	0.486772	0	T|0.756;C|0.244	0.244	strong	.	ERBB4	480	.	NM_005235	exon27	c.A3195G	p.V1065V	TCGGTATACAAAC	.	PASS	Atlas-SNP
FHOD1	29109	hgsc.bcm.edu	37	16	67281172	67281172	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	11.0	6.0	16.0	0.0	0.545455	0	.	.	none	.	FHOD1	86	.	NM_013241	exon1	c.G142A	p.A48T	GCAGCGCCCCGTC	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495200	134495200	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76.0	5.0	72.0	0.0	0.0657895	0	.	.	none	.	SGK1	387	.	NM_001143676	exon5	c.C456G	p.I152M	CTTCAAGATGGAC	.	PASS	Atlas-SNP
SNAP25	6616	hgsc.bcm.edu	37	20	10258375	10258375	+	Splice_Site	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20.0	5.0	40.0	0.0	0.25	0	.	.	none	.	SNAP25	79	.	NM_130811	exon3	c.114+1G>A	.	GAAGAGGTAAGAA	.	PASS	Atlas-SNP
STAT3	6774	hgsc.bcm.edu	37	17	40475330	40475330	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102.0	33.0	87.0	0.0	0.323529	0	.	.	none	STAT3,NS,lymphoid_neoplasm,0,1	STAT3	268	1	NM_003150	exon19	c.G1696T	p.D566Y	TATTGTCCAGCCA	.	PASS	Atlas-SNP
MRPL45	84311	hgsc.bcm.edu	37	17	36453167	36453167	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67.0	20.0	51.0	0.0	0.298507	0	.	.	none	.	MRPL45	27	.	NM_032351	exon1	c.T18C	p.P6P	CATACCTCAAGGG	.	PASS	Atlas-SNP
HSP90AA1	3320	hgsc.bcm.edu	37	14	102552201	102552201	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155.0	40.0	136.0	0.0	0.258065	0	.	.	none	.	HSP90AA1	65	.	NM_001017963	exon4	c.T789C	p.A263A	CAAATAAGCAGAA	.	PASS	Atlas-SNP
PTPRD	5789	hgsc.bcm.edu	37	9	8449782	8449782	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189.0	57.0	228.0	0.0	0.301587	0	.	.	none	.	PTPRD	1348	.	NM_002839	exon34	c.C3931T	p.P1311S	GTGAAGGGATCTC	.	PASS	Atlas-SNP
TAS1R2	80834	hgsc.bcm.edu	37	1	19175944	19175944	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92.0	4.0	86.0	0.0	0.0434783	0	.	.	none	.	TAS1R2	134	.	NM_152232	exon4	c.G1358A	p.W453X	CATTGCCACTGGA	.	PASS	Atlas-SNP
OR2W5	441932	hgsc.bcm.edu	37	1	247655102	247655102	+	Missense_Mutation	SNP	G	G	A	rs143904230	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94.0	60.0	76.0	0.0	0.638298	0	G|0.989;A|0.011	0.011	strong	.	OR2W5	97	.	NM_001004698	exon1	c.G673A	p.G225S	AGCCGCGGTGCTG	.	PASS	Atlas-SNP
NOS1	4842	hgsc.bcm.edu	37	12	117672544	117672544	+	Missense_Mutation	SNP	G	G	A	rs375069851		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68.0	26.0	72.0	0.0	0.382353	0	.	.	weak	NOS1,caecum,carcinoma,0,2	NOS1	240	2	NM_001204218	exon22	c.C3163T	p.R1055C	GGAGACGCACGAA	.	PASS	Atlas-SNP
BST1	683	hgsc.bcm.edu	37	4	15720553	15720553	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79.0	38.0	82.0	0.0	0.481013	0	.	.	none	.	BST1	30	.	NM_004334	exon7	c.T728C	p.M243T	GCAGCATGAAAGT	.	PASS	Atlas-SNP
PAIP2B	400961	hgsc.bcm.edu	37	2	71415619	71415619	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80.0	54.0	143.0	0.0	0.675	0	.	.	none	.	PAIP2B	7	.	NM_020459	exon4	c.A362G	p.E121G	TACTTCTCTCCTG	.	PASS	Atlas-SNP
OR4K17	390436	hgsc.bcm.edu	37	14	20585769	20585769	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	205.0	95.0	267.0	0.0	0.463415	0	.	.	none	.	OR4K17	58	.	NM_001004715	exon1	c.C204T	p.V68V	TGTGGTCACAGTT	.	PASS	Atlas-SNP
MRGPRG	386746	hgsc.bcm.edu	37	11	3239366	3239366	+	Silent	SNP	G	G	A	rs145777944	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87.0	49.0	93.0	0.0	0.563218	0	G|1.000;A|0.000	0.000	strong	.	MRGPRG	6	.	NM_001164377	exon1	c.C678T	p.F226F	CAGCAGGAAGTTC	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138946	37138946	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55.0	8.0	53.0	0.0	0.145455	0	.	.	none	.	PIM1	71	.	NM_001243186	exon4	c.G559A	p.V187M	AAGAAGGTGAGCT	.	PASS	Atlas-SNP
HIST1H2AE	3012	hgsc.bcm.edu	37	6	26217245	26217245	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81.0	25.0	89.0	0.0	0.308642	0	.	.	none	.	HIST1H2AE	25	.	NM_021052	exon1	c.G43A	p.A15T	GCAAAAGCTAAAA	.	PASS	Atlas-SNP
CACNA1F	778	hgsc.bcm.edu	37	X	49081230	49081230	+	Missense_Mutation	SNP	C	C	T	rs141010716	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69.0	47.0	55.0	0.0	0.681159	0	C|0.997;T|0.003	0.003	strong	.	CACNA1F	218	.	NM_005183	exon14	c.G1903A	p.V635I	TGGTGACCTTAAA	.	PASS	Atlas-SNP
GRIK4	2900	hgsc.bcm.edu	37	11	120531044	120531044	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51.0	20.0	34.0	0.0	0.392157	0	.	.	none	GRIK4,colon,NS,0,1	GRIK4	149	1	NM_014619	exon1	c.C17T	p.A6V	TCTCGGCGCCTTT	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11009703	11009703	+	Missense_Mutation	SNP	C	C	T	rs1281012	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54.0	29.0	61.0	0.0	0.537037	0	C|0.907;T|0.093	0.093	strong	.	C1orf127	134	.	NM_001170754	exon11	c.G1268A	p.R423Q	GAAGGCCGGTGCA	.	PASS	Atlas-SNP
EPS8	2059	hgsc.bcm.edu	37	12	15776095	15776095	+	Silent	SNP	C	C	T	rs1126786	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129.0	63.0	119.0	0.0	0.488372	0	T|0.130;G|0.153;C|0.674;A|0.042	0.130	strong	.	EPS8	70	.	NM_004447	exon20	c.G2352A	p.L784L	TACCTCCAATGCA	.	PASS	Atlas-SNP
SLFN5	162394	hgsc.bcm.edu	37	17	33592323	33592323	+	Missense_Mutation	SNP	C	C	G	rs113644060	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140.0	64.0	127.0	0.0	0.457143	0	C|0.975;G|0.025	0.025	strong	.	SLFN5	92	.	NM_144975	exon5	c.C2092G	p.P698A	CTCCCCCCTCCCT	.	PASS	Atlas-SNP
CD27	939	hgsc.bcm.edu	37	12	6554263	6554263	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25.0	9.0	37.0	0.0	0.36	0	.	.	none	.	CD27	17	.	NM_001242	exon1	c.T2C	p.M1T	GGACCATGGCACG	.	PASS	Atlas-SNP
CLCNKA	1187	hgsc.bcm.edu	37	1	16355287	16355287	+	Missense_Mutation	SNP	C	C	G	rs45588635	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	60.0	79.0	0.0	0.983607	0	C|0.981;G|0.019	0.019	strong	.	CLCNKA	56	.	NM_004070	exon11	c.C1000G	p.L334V	ACCTTGCTTCTCG	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130104153	130104153	+	Missense_Mutation	SNP	G	G	A	rs149308947	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56.0	23.0	75.0	0.0	0.410714	0	G|1.000;A|0.000	0.000	strong	.	COL6A5	205	.	NM_153264	exon5	c.G1807A	p.D603N	AACTTTGATGCTT	.	PASS	Atlas-SNP
GPC6	10082	hgsc.bcm.edu	37	13	94482567	94482567	+	Missense_Mutation	SNP	G	G	A	rs369251626		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127.0	77.0	94.0	0.0	0.606299	0	.	.	weak	.	GPC6	102	.	NM_005708	exon3	c.G480A	p.M160I	GGAAATGCTCAAT	.	PASS	Atlas-SNP
CSF1R	1436	hgsc.bcm.edu	37	5	149460355	149460355	+	Silent	SNP	G	G	A	rs41287102	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151.0	70.0	149.0	0.0	0.463576	0	G|0.994;A|0.006	0.006	strong	.	CSF1R	250	.	NM_005211	exon3	c.C282T	p.S94S	GGCGGCGCTGCCT	.	PASS	Atlas-SNP
ZNF341	84905	hgsc.bcm.edu	37	20	32376748	32376748	+	Silent	SNP	C	C	T	rs34260449	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142.0	75.0	180.0	0.0	0.528169	0	C|0.985;T|0.015	0.015	strong	.	ZNF341	73	.	NM_032819	exon13	c.C1911T	p.H637H	GATCCACGAGCCC	.	PASS	Atlas-SNP
CDCA4	55038	hgsc.bcm.edu	37	14	105478159	105478159	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80.0	33.0	57.0	0.0	0.4125	0	.	.	none	.	CDCA4	18	.	NM_017955	exon2	c.G108A	p.S36S	CAGGAGCGACTGC	.	PASS	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54161756	54161756	+	Missense_Mutation	SNP	T	T	C	rs146618010	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53.0	22.0	65.0	0.0	0.415094	0	T|1.000;C|0.000	0.000	weak	.	PSME4	247	.	NM_014614	exon8	c.A943G	p.I315V	CGGTGATCCATAT	.	PASS	Atlas-SNP
PLXNB3	5365	hgsc.bcm.edu	37	X	153043896	153043896	+	Silent	SNP	G	G	A	rs144872102	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76.0	47.0	62.0	0.0	0.618421	0	G|0.999;A|0.001	0.001	strong	.	PLXNB3	208	.	NM_001163257	exon35	c.G5589A	p.E1863E	CCAGGAGATGAAC	.	PASS	Atlas-SNP
WDR72	256764	hgsc.bcm.edu	37	15	54007512	54007512	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223.0	64.0	223.0	0.0	0.286996	0	.	.	none	.	WDR72	177	.	NM_182758	exon5	c.G392T	p.G131V	TATTCTCCACAAC	.	PASS	Atlas-SNP
ARID4A	5926	hgsc.bcm.edu	37	14	58831258	58831258	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85.0	16.0	87.0	0.0	0.188235	0	.	.	none	.	ARID4A	222	.	NM_002892	exon20	c.A2451C	p.A817A	TGAAGCAGGAAGT	.	PASS	Atlas-SNP
CHML	1122	hgsc.bcm.edu	37	1	241797585	241797585	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90.0	47.0	86.0	0.0	0.522222	0	.	.	none	.	CHML	82	.	NM_001821	exon1	c.G1484C	p.C495S	GAAGAACATAATT	.	PASS	Atlas-SNP
ATRNL1	26033	hgsc.bcm.edu	37	10	117061434	117061434	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107.0	24.0	97.0	0.0	0.224299	0	.	.	none	.	ATRNL1	219	.	NM_207303	exon17	c.C2699T	p.T900I	ACTGTACAAGCAA	.	PASS	Atlas-SNP
WHSC1	7468	hgsc.bcm.edu	37	4	1957774	1957774	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93.0	4.0	109.0	0.0	0.0430108	0	.	.	none	.	WHSC1	180	.	NM_133335	exon15	c.G2740A	p.E914K	AAGCACGAGATTG	.	PASS	Atlas-SNP
ZNRF3	84133	hgsc.bcm.edu	37	22	29445817	29445817	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86.0	27.0	110.0	0.0	0.313953	0	.	.	none	.	ZNRF3	75	.	NM_001206998	exon8	c.G1648A	p.D550N	GGCAGCGACAGCA	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56505175	56505175	+	Silent	SNP	T	T	A	rs113432929	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132.0	70.0	136.0	0.0	0.530303	0	T|0.997;A|0.003	0.003	strong	.	DST	1427	.	NM_001723	exon4	c.A645T	p.S215S	CATCCCTGATGAC	.	PASS	Atlas-SNP
ZNF81	347344	hgsc.bcm.edu	37	X	47774599	47774599	+	Missense_Mutation	SNP	C	C	T	rs186251256	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	279.0	197.0	198.0	0.0	0.706093	0	C|0.992;T|0.008	0.008	strong	.	ZNF81	60	.	NM_007137	exon5	c.C554T	p.S185L	TTCTTTCACAGAA	.	PASS	Atlas-SNP
RANBP6	26953	hgsc.bcm.edu	37	9	6012347	6012347	+	Silent	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79.0	29.0	81.0	0.0	0.367089	0	.	.	none	.	RANBP6	127	.	NM_012416	exon1	c.A3261T	p.V1087V	TTGTGATACACAT	.	PASS	Atlas-SNP
PCDHGA4	56111	hgsc.bcm.edu	37	5	140735361	140735361	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72.0	31.0	80.0	0.0	0.430556	0	.	.	none	.	PCDHGA4	150	.	NM_018917	exon1	c.C594T	p.R198R	GGAACGCGCTCTA	.	PASS	Atlas-SNP
CXCL14	9547	hgsc.bcm.edu	37	5	134914455	134914455	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23.0	7.0	52.0	0.0	0.304348	0	.	.	none	.	CXCL14	13	.	NM_004887	exon1	c.C50T	p.A17V	GCGGCCGCCAGGA	.	PASS	Atlas-SNP
C6orf118	168090	hgsc.bcm.edu	37	6	165715405	165715405	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29.0	9.0	28.0	0.0	0.310345	0	.	.	none	.	C6orf118	116	.	NM_144980	exon2	c.G406A	p.A136T	GAGAGGCCTGGGG	.	PASS	Atlas-SNP
MGA	23269	hgsc.bcm.edu	37	15	41988709	41988709	+	Missense_Mutation	SNP	A	A	G	rs199666635	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40.0	28.0	63.0	0.0	0.7	0	.	.	weak	.	MGA	264	.	NM_001080541	exon3	c.A1501G	p.M501V	TCTTCTATGTTGG	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	37	16	11001256	11001256	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105.0	41.0	121.0	0.0	0.390476	0	.	.	none	.	CIITA	92	.	NM_000246	exon11	c.C1907T	p.T636M	CCTCCACGCTCAC	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38690860	38690860	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107.0	30.0	90.0	0.0	0.280374	0	.	.	none	.	DNAH8	1239	.	NM_001206927	exon2	c.C275T	p.P92L	CGCGACCGGTTCA	.	PASS	Atlas-SNP
CAND1	55832	hgsc.bcm.edu	37	12	67699536	67699536	+	Silent	SNP	G	G	A	rs17781675	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56.0	22.0	58.0	0.0	0.392857	0	G|0.959;A|0.041	0.041	strong	.	CAND1	100	.	NM_018448	exon10	c.G2088A	p.E696E	AGATGAGCTCCCA	.	PASS	Atlas-SNP
FMR1	2332	hgsc.bcm.edu	37	X	146993715	146993715	+	Silent	SNP	G	G	T	rs111485627	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123.0	27.0	89.0	0.0	0.219512	0	C|0.000;G|0.987;T|0.013	0.013	strong	.	FMR1	93	.	NM_002024	exon1	c.G18T	p.V6V	GGTGGTGGAAGTG	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132528724	132528724	+	Silent	SNP	C	C	T	rs61944617	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74.0	43.0	70.0	0.0	0.581081	0	C|0.996;T|0.004	0.004	strong	.	EP400	370	.	NM_015409	exon35	c.C6453T	p.D2151D	TCAGGACGCAGTG	.	PASS	Atlas-SNP
TCF12	6938	hgsc.bcm.edu	37	15	57565432	57565432	+	Silent	SNP	C	C	T	rs77034126	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121.0	61.0	127.0	0.0	0.504132	0	C|0.996;T|0.004	0.004	strong	.	TCF12	242	.	NM_207036	exon19	c.C1950T	p.V650V	GGCAGTCATCCTT	.	PASS	Atlas-SNP
SLCO1B1	10599	hgsc.bcm.edu	37	12	21358837	21358837	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94.0	22.0	91.0	0.0	0.234043	0	.	.	none	SLCO1B1,right_lower_lobe,carcinoma,+1,1	SLCO1B1	151	1	NM_006446	exon11	c.T1367G	p.L456R	TACCACTTTCTTA	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	37	8	55538741	55538741	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44.0	17.0	53.0	0.0	0.386364	0	.	.	none	.	RP1	429	.	NM_006269	exon4	c.A2299G	p.N767D	ACTCAAAATTCCA	.	PASS	Atlas-SNP
ESRRB	2103	hgsc.bcm.edu	37	14	76966275	76966275	+	Missense_Mutation	SNP	T	T	C	rs188462546	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91.0	50.0	97.0	0.0	0.549451	0	T|0.994;C|0.006	0.006	strong	.	ESRRB	114	.	NM_004452	exon10	c.T1366C	p.F456L	TGCCCCTTCCAAT	.	PASS	Atlas-SNP
TIGD1	200765	hgsc.bcm.edu	37	2	233413842	233413842	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20.0	9.0	17.0	0.0	0.45	0	.	.	none	.	TIGD1	17	.	NM_145702	exon1	c.A751G	p.T251A	ATTTAGTATAATT	.	PASS	Atlas-SNP
ALAD	210	hgsc.bcm.edu	37	9	116152915	116152915	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29.0	16.0	40.0	0.0	0.551724	0	.	.	none	.	ALAD	36	.	NM_000031	exon6	c.C439T	p.R147C	GCTGGCGGCTCTC	.	PASS	Atlas-SNP
COL1A1	1277	hgsc.bcm.edu	37	17	48269167	48269167	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38.0	3.0	29.0	0.0	0.0789474	0	.	.	none	COL1A1,NS,carcinoma,-2,2	COL1A1	158	2	NM_000088	exon31	c.C2109T	p.P703P	GTTGCCGGGAGCA	.	scavenged	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	37	14	102482399	102482399	+	Silent	SNP	C	C	T	rs17541158	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47.0	23.0	36.0	0.0	0.489362	0	C|0.972;T|0.028	0.028	strong	.	DYNC1H1	395	.	NM_001376	exon36	c.C7449T	p.I2483I	GCAGATCGAGCAG	.	PASS	Atlas-SNP
GNB2	2783	hgsc.bcm.edu	37	7	100273936	100273936	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98.0	10.0	109.0	0.0	0.102041	0	.	.	none	.	GNB2	29	.	NM_005273	exon2	c.C48T	p.N16N	CCGGAACCAGATC	.	PASS	Atlas-SNP
FAM65B	9750	hgsc.bcm.edu	37	6	24843183	24843183	+	Silent	SNP	A	A	G	rs145837095	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87.0	68.0	72.0	0.0	0.781609	0	A|0.998;G|0.002	0.002	strong	FAM65B_ENST00000259698,NS,carcinoma,-1,2	FAM65B	134	2	NM_014722	exon14	c.T1827C	p.N609N	AAGCCCATTAAAA	.	PASS	Atlas-SNP
GEMIN2	8487	hgsc.bcm.edu	37	14	39587220	39587220	+	Silent	SNP	C	C	A	rs150986614	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51.0	21.0	40.0	0.0	0.411765	0	C|0.997;A|0.003	0.003	strong	.	.	.	.	NM_003616	exon3	c.C273A	p.P91P	CCAACCCGCCCCT	.	PASS	Atlas-SNP
LARGE	9215	hgsc.bcm.edu	37	22	34000460	34000460	+	Silent	SNP	G	G	A	rs36002910	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104.0	67.0	86.0	0.0	0.644231	0	G|0.979;A|0.021	0.021	strong	.	LARGE	98	.	NM_004737	exon6	c.C576T	p.P192P	CACAGCGGGCACC	.	PASS	Atlas-SNP
FAM129B	64855	hgsc.bcm.edu	37	9	130270782	130270782	+	Silent	SNP	G	G	A	rs11545937	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41.0	17.0	47.0	0.0	0.414634	0	G|0.957;C|0.000;A|0.043	0.043	strong	.	FAM129B	84	.	NM_022833	exon11	c.C1353T	p.L451L	GTGCAGGAGGGTC	.	PASS	Atlas-SNP
LMOD3	56203	hgsc.bcm.edu	37	3	69168747	69168747	+	Silent	SNP	A	A	G	rs115972674	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57.0	31.0	72.0	0.0	0.54386	0	A|0.979;G|0.021	0.021	strong	.	LMOD3	92	.	NM_198271	exon2	c.T759C	p.P253P	CATGTCAGGATCA	.	PASS	Atlas-SNP
OR2T27	403239	hgsc.bcm.edu	37	1	248813470	248813470	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91.0	27.0	84.0	0.0	0.296703	0	.	.	none	.	OR2T27	52	.	NM_001001824	exon1	c.C716T	p.A239V	CAGGTGGCCACAG	.	PASS	Atlas-SNP
OR4E2	26686	hgsc.bcm.edu	37	14	22133692	22133692	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196.0	95.0	210.0	0.0	0.484694	0	.	.	none	.	OR4E2	44	.	NM_001001912	exon1	c.C396A	p.Y132X	CCACTACCCCAAT	.	PASS	Atlas-SNP
CCDC85A	114800	hgsc.bcm.edu	37	2	56603044	56603044	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189.0	45.0	177.0	0.0	0.238095	0	.	.	none	.	CCDC85A	70	.	NM_001080433	exon5	c.C1546T	p.P516S	CAGCAGCCTGAAC	.	PASS	Atlas-SNP
ECSIT	51295	hgsc.bcm.edu	37	19	11617020	11617020	+	Silent	SNP	T	T	G	rs34645543	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44.0	26.0	32.0	0.0	0.590909	0	T|0.999;G|0.001	0.001	strong	.	ECSIT	32	.	NM_016581	exon8	c.A1275C	p.R425R	CTGCTGTCGCTGC	.	PASS	Atlas-SNP
TMOD1	7111	hgsc.bcm.edu	37	9	100331188	100331188	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97.0	50.0	102.0	0.0	0.515464	0	.	.	none	.	TMOD1	29	.	NM_001166116	exon8	c.A739T	p.M247L	GCTGAGATGCTCA	.	PASS	Atlas-SNP
ZNF597	146434	hgsc.bcm.edu	37	16	3486738	3486738	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38.0	9.0	43.0	0.0	0.236842	0	.	.	none	.	ZNF597	41	.	NM_152457	exon4	c.G961T	p.D321Y	CAGAGTCCTCGTC	.	PASS	Atlas-SNP
SPATA31D4	389761	hgsc.bcm.edu	37	9	84547771	84547771	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109.0	45.0	119.0	0.0	0.412844	0	.	.	none	.	.	.	.	NM_001145197	exon4	c.A2695C	p.M899L	CAAAAGATGTTGG	.	PASS	Atlas-SNP
PTPRZ1	5803	hgsc.bcm.edu	37	7	121659234	121659234	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173.0	9.0	172.0	0.0	0.0520231	0	.	.	none	.	PTPRZ1	605	.	NM_002851	exon13	c.G4900A	p.E1634K	GAATCCGAGAAGA	.	PASS	Atlas-SNP
WFIKKN1	117166	hgsc.bcm.edu	37	16	683547	683547	+	Silent	SNP	G	G	A	rs148648187	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	7.0	5.0	13.0	0.0	0.714286	0	G|0.994;A|0.006	0.006	strong	.	WFIKKN1	30	.	NM_053284	exon2	c.G1137A	p.P379P	CAGCCCGCTGCTG	.	PASS	Atlas-SNP
OR2J3	442186	hgsc.bcm.edu	37	6	29080267	29080267	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	295.0	17.0	318.0	0.0	0.0576271	0	.	.	none	.	OR2J3	53	.	NM_001005216	exon1	c.G600A	p.L200L	TGAGCTGACCCTC	.	PASS	Atlas-SNP
OR9G9	504191	hgsc.bcm.edu	37	11	56468431	56468431	+	Missense_Mutation	SNP	G	G	A	rs141836537	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143.0	22.0	167.0	0.0	0.153846	0	G|1.000;A|0.000	0.000	weak	.	.	.	.	NM_001013358	exon1	c.G568A	p.E190K	TGTGGCGAGAAGG	.	PASS	Atlas-SNP
GPRC5C	55890	hgsc.bcm.edu	37	17	72436078	72436078	+	Missense_Mutation	SNP	G	G	A	rs148895616	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29.0	15.0	40.0	0.0	0.517241	0	G|0.999;A|0.001	0.001	strong	.	GPRC5C	92	.	NM_022036	exon2	c.G298A	p.A100T	CTGGAGGCCGTGG	.	PASS	Atlas-SNP
HCFC1	3054	hgsc.bcm.edu	37	X	153227753	153227753	+	Silent	SNP	G	G	C	rs372516617		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48.0	10.0	26.0	0.0	0.208333	0	.	.	weak	.	HCFC1	284	.	NM_005334	exon5	c.C717G	p.T239T	CGTCAGGGTGTCT	.	PASS	Atlas-SNP
TRERF1	55809	hgsc.bcm.edu	37	6	42236973	42236973	+	Missense_Mutation	SNP	C	C	T	rs61756353	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90.0	19.0	59.0	0.0	0.211111	0	C|0.997;T|0.003	0.003	strong	.	TRERF1	124	.	NM_033502	exon5	c.G356A	p.G119D	TGGTAGCCATCAG	.	PASS	Atlas-SNP
FAM102A	399665	hgsc.bcm.edu	37	9	130742413	130742413	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66.0	15.0	65.0	0.0	0.227273	0	.	.	none	.	FAM102A	32	.	NM_001035254	exon1	c.G4A	p.A2T	AGAAAGCCATGAG	.	PASS	Atlas-SNP
CNGB1	1258	hgsc.bcm.edu	37	16	58001086	58001086	+	Silent	SNP	C	C	T	rs61997250	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46.0	20.0	56.0	0.0	0.434783	0	C|0.981;T|0.019	0.019	strong	.	CNGB1	105	.	NM_001297	exon2	c.G105A	p.A35A	CACCTCCGCCTCC	.	PASS	Atlas-SNP
S100A7	6278	hgsc.bcm.edu	37	1	153431435	153431435	+	Missense_Mutation	SNP	T	T	G	rs72708760	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160.0	77.0	177.0	0.0	0.48125	0	T|0.997;G|0.003	0.003	strong	.	S100A7	23	.	NM_002963	exon2	c.A55C	p.K19Q	TGTATTTGTGAAA	.	PASS	Atlas-SNP
C1orf101	257044	hgsc.bcm.edu	37	1	244715882	244715882	+	Silent	SNP	A	A	G	rs34510134	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	194.0	86.0	227.0	0.0	0.443299	0	A|0.933;G|0.067	0.067	strong	.	C1orf101	158	.	NM_173807	exon9	c.A795G	p.S265S	TGATTCATTCAAA	.	PASS	Atlas-SNP
NEK5	341676	hgsc.bcm.edu	37	13	52661569	52661569	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126.0	65.0	82.0	0.0	0.515873	0	.	.	none	.	NEK5	189	.	NM_199289	exon15	c.G1297A	p.E433K	TTGGCTCGGCAGA	.	PASS	Atlas-SNP
SFSWAP	6433	hgsc.bcm.edu	37	12	132239988	132239988	+	Silent	SNP	G	G	A	rs139034136	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28.0	10.0	33.0	0.0	0.357143	0	G|0.999;A|0.001	0.001	strong	.	SFSWAP	69	.	NM_001261411	exon10	c.G1512A	p.Q504Q	GAAGCAGTTCTTC	.	PASS	Atlas-SNP
ALS2CR8	79800	hgsc.bcm.edu	37	2	203847044	203847044	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170.0	52.0	139.0	0.0	0.305882	0	.	.	none	.	ALS2CR8	56	.	NM_024744	exon16	c.G1939A	p.E647K	ATGGACGAGCTGG	.	PASS	Atlas-SNP
ENPP2	5168	hgsc.bcm.edu	37	8	120569870	120569870	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106.0	5.0	108.0	0.0	0.0471698	0	.	.	none	.	ENPP2	254	.	NM_006209	exon26	c.G2639A	p.R880H	ATGTCACGCACCC	.	PASS	Atlas-SNP
ZNF652	22834	hgsc.bcm.edu	37	17	47394825	47394825	+	Missense_Mutation	SNP	G	G	C	rs181916483	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	211.0	108.0	226.0	1.0	0.511848	0.00442478	G|0.998;C|0.002	0.002	strong	ZNF652,NS,haematopoietic_neoplasm,0,3	ZNF652	54	3	NM_001145365	exon2	c.C263G	p.S88C	ACGTCAGACACTG	.	PASS	Atlas-SNP
INTS6	26512	hgsc.bcm.edu	37	13	51950198	51950198	+	Missense_Mutation	SNP	T	T	C	rs144918317	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87.0	26.0	67.0	0.0	0.298851	0	T|0.999;C|0.001	0.001	strong	.	INTS6	72	.	NM_012141	exon13	c.A1715G	p.K572R	TGTCCTTTCAGAA	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1056183	1056183	+	Missense_Mutation	SNP	C	C	T	rs144562001	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39.0	20.0	36.0	0.0	0.512821	0	C|0.999;G|0.000;T|0.000	0.000	strong	.	ABCA7	174	.	NM_019112	exon32	c.C4357T	p.R1453C	CTCGACCGTGTCC	.	PASS	Atlas-SNP
RIN2	54453	hgsc.bcm.edu	37	20	19955473	19955473	+	Silent	SNP	C	C	T	rs41306763	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105.0	53.0	61.0	0.0	0.504762	0	C|0.990;T|0.010	0.010	strong	.	RIN2	126	.	NM_001242581	exon8	c.C951T	p.A317A	CGGGGCCCTGTGC	.	PASS	Atlas-SNP
GALNT8	26290	hgsc.bcm.edu	37	12	4835923	4835923	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52.0	14.0	53.0	0.0	0.269231	0	.	.	none	.	GALNT8	89	.	NM_017417	exon2	c.A437C	p.K146T	TCCGGAAGTTTGG	.	PASS	Atlas-SNP
SCAF11	9169	hgsc.bcm.edu	37	12	46320944	46320944	+	Missense_Mutation	SNP	C	C	T	rs28930670	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147.0	72.0	155.0	0.0	0.489796	0	C|0.978;T|0.022	0.022	strong	.	SCAF11	145	.	NM_004719	exon11	c.G2540A	p.R847H	TGAGAACGGGATT	.	PASS	Atlas-SNP
SLC9A8	23315	hgsc.bcm.edu	37	20	48503306	48503306	+	Silent	SNP	G	G	A	rs73125686	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105.0	55.0	64.0	0.0	0.52381	0	G|0.996;A|0.004	0.004	strong	.	SLC9A8	63	.	NM_001260491	exon15	c.G1557A	p.S519S	GGAGTCGGAGCAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512439	195512439	+	Silent	SNP	G	G	A	rs112365404	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148.0	34.0	125.0	0.0	0.22973	0	G|0.990;A|0.010	0.010	strong	.	MUC4	1505	.	NM_018406	exon2	c.C6012T	p.T2004T	AGTGTCGGTGACC	.	PASS	Atlas-SNP
HIRA	7290	hgsc.bcm.edu	37	22	19385570	19385570	+	Silent	SNP	T	T	C	rs373432911		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86.0	49.0	77.0	0.0	0.569767	0	.	.	weak	.	HIRA	100	.	NM_003325	exon6	c.A438G	p.L146L	TGAGGCTAGCCAG	.	PASS	Atlas-SNP
PCDH10	57575	hgsc.bcm.edu	37	4	134072185	134072185	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39.0	9.0	48.0	0.0	0.230769	0	.	.	none	.	PCDH10	290	.	NM_032961	exon1	c.C890T	p.A297V	CCCGGGCGCGGGA	.	PASS	Atlas-SNP
SPATA31D1	389763	hgsc.bcm.edu	37	9	84605777	84605777	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170.0	84.0	152.0	0.0	0.494118	0	.	.	none	.	.	.	.	NM_001001670	exon4	c.G392A	p.R131Q	TCTGTCGGGTGTG	.	PASS	Atlas-SNP
CCDC178	374864	hgsc.bcm.edu	37	18	30825388	30825388	+	Missense_Mutation	SNP	G	G	A	rs146565345	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54.0	22.0	52.0	0.0	0.407407	0	G|0.998;A|0.002	0.002	strong	C18orf34_ENST00000383096,NS,carcinoma,0,2	.	.	2	NM_001105528	exon14	c.C1414T	p.R472W	TTTTCCGTATGCT	.	PASS	Atlas-SNP
CCAR1	55749	hgsc.bcm.edu	37	10	70513614	70513614	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109.0	55.0	122.0	0.0	0.504587	0	.	.	none	.	CCAR1	118	.	NM_018237	exon11	c.G1124T	p.S375I	GTCCCAGTTGTGA	.	PASS	Atlas-SNP
LRRIQ3	127255	hgsc.bcm.edu	37	1	74648375	74648375	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83.0	26.0	68.0	0.0	0.313253	0	.	.	none	.	LRRIQ3	146	.	NM_001105659	exon3	c.T420C	p.Y140Y	ATGTCTATATCCT	.	PASS	Atlas-SNP
ABHD5	51099	hgsc.bcm.edu	37	3	43743773	43743773	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63.0	20.0	81.0	0.0	0.31746	0	.	.	none	ABHD5,NS,carcinoma,-1,1	ABHD5	33	1	NM_016006	exon3	c.A200C	p.K67T	CACTGAAGTTCTC	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33726303	33726303	+	Silent	SNP	C	C	T	rs200555493	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141.0	63.0	95.0	0.0	0.446809	0	C|0.998;T|0.002	0.002	weak	.	URB1	176	.	NM_014825	exon18	c.G2355A	p.A785A	GACTACCGCACTG	.	PASS	Atlas-SNP
ALDH7A1	501	hgsc.bcm.edu	37	5	125928395	125928395	+	Silent	SNP	A	A	G	rs60720055	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96.0	51.0	106.0	0.0	0.53125	0	A|0.941;G|0.059	0.059	strong	.	ALDH7A1	57	.	NM_001202404	exon3	c.T354C	p.T118T	CTTTACAGTTTCT	.	PASS	Atlas-SNP
ZPLD1	131368	hgsc.bcm.edu	37	3	102171858	102171858	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118.0	44.0	143.0	0.0	0.372881	0	.	.	none	.	ZPLD1	82	.	NM_175056	exon3	c.C250A	p.L84M	ACAGATCTGGCAC	.	PASS	Atlas-SNP
FOXA2	3170	hgsc.bcm.edu	37	20	22563684	22563684	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68.0	27.0	83.0	0.0	0.397059	0	.	.	none	.	FOXA2	48	.	NM_021784	exon2	c.G196A	p.A66T	AGCCCGCGCTCAT	.	PASS	Atlas-SNP
CALHM3	119395	hgsc.bcm.edu	37	10	105233301	105233301	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54.0	28.0	88.0	0.0	0.518519	0	.	.	none	.	CALHM3	46	.	NM_001129742	exon3	c.C704T	p.A235V	TCCCGCGCATGCT	.	PASS	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197427584	197427584	+	Silent	SNP	G	G	A	rs368476866		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132.0	63.0	97.0	0.0	0.477273	0	.	.	weak	.	KIAA0226	136	.	NM_014687	exon7	c.C1161T	p.S387S	GAAGCTGGACCTG	.	PASS	Atlas-SNP
ATAD3C	219293	hgsc.bcm.edu	37	1	1403848	1403848	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172.0	80.0	196.0	0.0	0.465116	0	.	.	none	.	ATAD3C	23	.	NM_001039211	exon12	c.C1174G	p.Q392E	CACCAGCAGATGA	.	PASS	Atlas-SNP
CDK5R2	8941	hgsc.bcm.edu	37	2	219824731	219824731	+	Silent	SNP	G	G	C	rs78141300	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22.0	12.0	26.0	0.0	0.545455	0	G|0.972;C|0.028	0.028	strong	.	CDK5R2	17	.	NM_003936	exon1	c.G189C	p.A63A	CTCGGCGCTCACC	.	PASS	Atlas-SNP
MCM6	4175	hgsc.bcm.edu	37	2	136602196	136602196	+	Silent	SNP	G	G	A	rs4988270	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54.0	10.0	48.0	0.0	0.185185	0	G|0.997;A|0.003	0.003	strong	.	MCM6	64	.	NM_005915	exon16	c.C2268T	p.I756I	TGATTCGATTTCC	.	PASS	Atlas-SNP
TXNDC11	51061	hgsc.bcm.edu	37	16	11785486	11785486	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62.0	33.0	46.0	0.0	0.532258	0	.	.	none	.	TXNDC11	75	.	NM_015914	exon8	c.C1560T	p.I520I	AGAGTCGATGAAG	.	PASS	Atlas-SNP
PRRT3	285368	hgsc.bcm.edu	37	3	9989028	9989028	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17.0	5.0	6.0	0.0	0.294118	0	.	.	none	.	PRRT3	35	.	NM_207351	exon4	c.C1829T	p.A610V	ACGGCCGCGCCCC	.	PASS	Atlas-SNP
TRAK1	22906	hgsc.bcm.edu	37	3	42251321	42251321	+	Missense_Mutation	SNP	C	C	T	rs375255978		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60.0	24.0	55.0	0.0	0.4	0	.	.	weak	.	TRAK1	188	.	NM_001265608	exon14	c.C1807T	p.P603S	CTGGACCCCCGGC	.	PASS	Atlas-SNP
ADAMTS13	11093	hgsc.bcm.edu	37	9	136320665	136320665	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35.0	19.0	47.0	0.0	0.542857	0	.	.	none	.	ADAMTS13	113	.	NM_139025	exon25	c.T3508C	p.S1170P	CTCTTCTCCCCGG	.	PASS	Atlas-SNP
DAGLA	747	hgsc.bcm.edu	37	11	61511794	61511794	+	Missense_Mutation	SNP	C	C	G	rs117050893	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50.0	21.0	54.0	0.0	0.42	0	C|0.994;G|0.006	0.006	strong	.	DAGLA	109	.	NM_006133	exon20	c.C2962G	p.L988V	ATCTCACTCTCGC	.	PASS	Atlas-SNP
UBOX5	22888	hgsc.bcm.edu	37	20	3102636	3102636	+	Missense_Mutation	SNP	G	G	C	rs148731933	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54.0	27.0	49.0	0.0	0.5	0	G|1.000;C|0.000	0.000	strong	UBOX5,NS,carcinoma,+2,1	UBOX5	47	1	NM_014948	exon3	c.C649G	p.L217V	GAGGCAGGTTCTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506159	195506159	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26.0	19.0	80.0	0.0	0.730769	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.C12292G	p.P4098A	TGAGAGGAAGAGG	.	PASS	Atlas-SNP
NLRP12	91662	hgsc.bcm.edu	37	19	54313944	54313944	+	Missense_Mutation	SNP	A	A	C	rs142063194	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51.0	27.0	51.0	0.0	0.529412	0	A|0.991;C|0.009	0.009	strong	.	NLRP12	236	.	NM_144687	exon3	c.C969G	p.S323R	GTTAAGAAGCAGC	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420416	58420416	+	Silent	SNP	G	G	A	rs150518835	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80.0	25.0	79.0	0.0	0.3125	0	G|0.984;A|0.016	0.016	strong	.	ZNF417	44	.	NM_152475	exon3	c.C1230T	p.C410C	TTCCTTGCACTCA	.	PASS	Atlas-SNP
FAM208A	23272	hgsc.bcm.edu	37	3	56667896	56667896	+	Missense_Mutation	SNP	G	G	T	rs200904014	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67.0	36.0	97.0	0.0	0.537313	0	G|0.999;T|0.001	0.001	strong	.	FAM208A	113	.	NM_001112736	exon18	c.C2923A	p.Q975K	GAAACTGGTAATC	.	PASS	Atlas-SNP
ZNF763	284390	hgsc.bcm.edu	37	19	12087921	12087921	+	Silent	SNP	G	G	C	rs376310072	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96.0	9.0	137.0	1.0	0.09375	0.00729927	.	.	alt	ZNF763,NS,carcinoma,+1,2	ZNF763	31	2	NM_001012753	exon2	c.G81C	p.S27S	TATTTCGCAGAGG	.	scavenged	Atlas-SNP
KIAA0947	23379	hgsc.bcm.edu	37	5	5441314	5441314	+	Missense_Mutation	SNP	A	A	G	rs72646675	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	203.0	93.0	201.0	0.0	0.458128	0	A|0.999;G|0.001	0.001	strong	.	KIAA0947	301	.	NM_015325	exon5	c.A287G	p.K96R	CTTTAAAAGCAGA	.	PASS	Atlas-SNP
TSC22D1	8848	hgsc.bcm.edu	37	13	45149973	45149973	+	Missense_Mutation	SNP	G	G	A	rs140514784	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	202.0	151.0	128.0	0.0	0.747525	0	G|0.999;A|0.001	0.001	strong	.	TSC22D1	88	.	NM_183422	exon1	c.C238T	p.P80S	GAGGCGGAGGCTG	.	PASS	Atlas-SNP
TET3	200424	hgsc.bcm.edu	37	2	74320089	74320089	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144.0	74.0	202.0	0.0	0.513889	0	.	.	none	.	TET3	101	.	NM_144993	exon6	c.C2695T	p.R899X	TACAAGCGACTGG	.	PASS	Atlas-SNP
AGAP6	414189	hgsc.bcm.edu	37	10	51769058	51769058	+	Silent	SNP	G	G	A	rs200123722	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112.0	40.0	156.0	0.0	0.357143	0	G|0.985;A|0.015	0.015	strong	AGAP6,NS,carcinoma,+1,1	AGAP6	53	1	NM_001077665	exon8	c.G1173A	p.P391P	CAACCCGCCCCCC	.	scavenged	Atlas-SNP
WNT9B	7484	hgsc.bcm.edu	37	17	44953637	44953637	+	Silent	SNP	G	G	A	rs62071993	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120.0	60.0	106.0	0.0	0.5	0	G|0.997;A|0.003	0.003	strong	.	WNT9B	37	.	NM_003396	exon4	c.G627A	p.T209T	GACCACGTGTAAG	.	PASS	Atlas-SNP
USP42	84132	hgsc.bcm.edu	37	7	6194379	6194379	+	Missense_Mutation	SNP	G	G	C	rs112550268	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28.0	20.0	28.0	0.0	0.714286	0	G|0.992;C|0.008	0.008	strong	.	USP42	138	.	NM_032172	exon15	c.G3194C	p.R1065T	ATGACAGGTACGC	.	PASS	Atlas-SNP
METTL25	84190	hgsc.bcm.edu	37	12	82780676	82780676	+	Silent	SNP	A	A	G	rs56337649	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89.0	52.0	69.0	0.0	0.58427	0	A|0.969;G|0.031	0.031	strong	.	.	.	.	NM_032230	exon2	c.A354G	p.Q118Q	TGTACAAAACTTG	.	PASS	Atlas-SNP
C1orf210	149466	hgsc.bcm.edu	37	1	43748923	43748923	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	392.0	16.0	350.0	0.0	0.0408163	0	.	.	none	.	C1orf210	9	.	NM_182517	exon2	c.A19C	p.T7P	ACTCACTTTTGTT	.	PASS	Atlas-SNP
ITGB2	3689	hgsc.bcm.edu	37	21	46330667	46330667	+	Silent	SNP	G	G	A	rs5030667	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74.0	28.0	80.0	0.0	0.378378	0	G|0.975;A|0.025	0.025	strong	.	ITGB2	107	.	NM_000211	exon2	c.C31T	p.L11L	CCACCAGGGCGAG	.	PASS	Atlas-SNP
PIGG	54872	hgsc.bcm.edu	37	4	509850	509850	+	Silent	SNP	T	T	C	rs11726338	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80.0	27.0	86.0	0.0	0.3375	0	T|0.972;C|0.028	0.028	strong	.	PIGG	86	.	NM_017733	exon6	c.T990C	p.S330S	AGACAGTGTAGGG	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144945535	144945535	+	Silent	SNP	G	G	A	rs73715515	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60.0	22.0	62.0	0.0	0.366667	0	G|0.977;A|0.023	0.023	strong	.	EPPK1	199	.	NM_031308	exon1	c.C1887T	p.A629A	GCATCGGGCCTCA	.	PASS	Atlas-SNP
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465449	39465449	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71.0	18.0	91.0	0.0	0.253521	0	.	.	none	.	KRTAP16-1	12	.	NM_001146182	exon1	c.C57T	p.C19C	AGTGGAGCAGAGA	.	PASS	Atlas-SNP
CYP2S1	29785	hgsc.bcm.edu	37	19	41703793	41703793	+	Silent	SNP	G	G	A	rs57266494	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52.0	22.0	46.0	0.0	0.423077	0	G|0.975;A|0.025	0.025	strong	.	CYP2S1	47	.	NM_030622	exon3	c.G453A	p.A151A	CCAGGCGGAGGCC	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495725	134495725	+	Splice_Site	SNP	C	C	G	rs186450029	by1000genomes;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41.0	11.0	67.0	0.0	0.268293	0	C|1.000;T|0.000	.	alt	SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,4	SGK1	387	4	NM_005627	exon3	c.77-1G>C	.	TGAAAGCTGTGGA	.	PASS	Atlas-SNP
SAPCD2	89958	hgsc.bcm.edu	37	9	139959231	139959231	+	Silent	SNP	G	G	A	rs140919217	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112.0	59.0	114.0	0.0	0.526786	0	G|0.995;A|0.005	0.005	strong	.	.	.	.	NM_178448	exon6	c.C1065T	p.T355T	CTTCTCGGTCACC	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124345721	124345721	+	Silent	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93.0	49.0	76.0	0.0	0.526882	0	.	.	none	.	DMBT1	677	.	NM_007329	exon16	c.G1605T	p.L535L	GCAGCTGGGCTGT	.	PASS	Atlas-SNP
ARRDC2	27106	hgsc.bcm.edu	37	19	18121454	18121454	+	Silent	SNP	G	G	C	rs147293119	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48.0	25.0	34.0	0.0	0.520833	0	G|0.998;C|0.002	0.002	strong	.	ARRDC2	60	.	NM_015683	exon7	c.G1086C	p.P362P	GCTTCCGCAGGAC	.	PASS	Atlas-SNP
TTLL3	26140	hgsc.bcm.edu	37	3	9874914	9874914	+	Nonsense_Mutation	SNP	C	C	T	rs115917139	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	37.0	82.0	0.0	0.606557	0	C|0.975;T|0.025	0.025	strong	.	TTLL3	51	.	NM_001025930	exon11	c.C2110T	p.R704X	ACCCAGCGAGGCT	.	PASS	Atlas-SNP
HCN1	348980	hgsc.bcm.edu	37	5	45396654	45396654	+	Silent	SNP	G	G	A	rs369683016		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157.0	43.0	157.0	0.0	0.273885	0	.	.	weak	.	HCN1	298	.	NM_021072	exon4	c.C1170T	p.V390V	ATGGCCGACAAAC	.	PASS	Atlas-SNP
KCNC4	3749	hgsc.bcm.edu	37	1	110766185	110766185	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81.0	42.0	110.0	0.0	0.518519	0	.	.	none	.	KCNC4	113	.	NM_001039574	exon2	c.C1278T	p.G426G	CATTGGCTTCTGG	.	PASS	Atlas-SNP
PABPC3	5042	hgsc.bcm.edu	37	13	25670627	25670627	+	Silent	SNP	A	A	G	rs369126872	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151.0	85.0	137.0	0.0	0.562914	0	.	.	alt	.	PABPC3	129	.	NM_030979	exon1	c.A291G	p.G97G	AAGTGGAGTGGGC	.	PASS	Atlas-SNP
DGKQ	1609	hgsc.bcm.edu	37	4	956309	956309	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57.0	6.0	72.0	0.0	0.105263	0	.	.	none	.	DGKQ	29	.	NM_001347	exon18	c.G2128A	p.V710M	TGAGCACGGCGTC	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103388764	103388764	+	Silent	SNP	T	T	C	rs113711522	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	290.0	206.0	385.0	0.0	0.710345	0	T|0.996;C|0.004	0.004	strong	.	.	.	.	NM_001146197	exon4	c.A14283G	p.V4761V	TGTTTGTACTCTG	.	PASS	Atlas-SNP
IRF1	3659	hgsc.bcm.edu	37	5	131825088	131825088	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48.0	19.0	69.0	0.0	0.395833	0	.	.	none	.	IRF1	26	.	NM_002198	exon2	c.A83C	p.N28T	ACTTTATTAATCC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1281932	1281932	+	Silent	SNP	C	C	T	rs61734215	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106.0	49.0	137.0	0.0	0.462264	0	C|0.992;T|0.008	0.008	strong	.	MUC5B	473	.	NM_002458	exon48	c.C17043T	p.C5681C	CTTCTGCGAGGGC	.	PASS	Atlas-SNP
MTRR	4552	hgsc.bcm.edu	37	5	7873566	7873566	+	Silent	SNP	C	C	G	rs41282641	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80.0	37.0	94.0	0.0	0.4625	0	C|0.997;G|0.003	0.003	strong	.	MTRR	74	.	NM_024010	exon3	c.C291G	p.R97R	AGCCCGCAAGTTT	.	PASS	Atlas-SNP
PROKR1	10887	hgsc.bcm.edu	37	2	68882661	68882661	+	Missense_Mutation	SNP	A	A	G	rs34715748	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41.0	25.0	79.0	0.0	0.609756	0	A|0.960;G|0.040	0.040	strong	PROKR1,NS,carcinoma,0,1	PROKR1	69	1	NM_138964	exon2	c.A1135G	p.I379V	AAGACAATTGGGA	.	PASS	Atlas-SNP
LTB	4050	hgsc.bcm.edu	37	6	31549599	31549599	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84.0	46.0	70.0	0.0	0.547619	0	.	.	none	.	LTB	19	.	NM_002341	exon2	c.A200G	p.Q67R	AGTCCTTGCTGGG	.	PASS	Atlas-SNP
BTG1	694	hgsc.bcm.edu	37	12	92539223	92539223	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151.0	48.0	140.0	0.0	0.317881	0	.	.	none	.	BTG1	30	.	NM_001731	exon1	c.G89A	p.G30E	GTGAGCCCCTTGG	.	PASS	Atlas-SNP
CREB3	10488	hgsc.bcm.edu	37	9	35733116	35733116	+	Missense_Mutation	SNP	C	C	T	rs200166825	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	250.0	135.0	263.0	0.0	0.54	0	C|0.999;T|0.001	0.001	weak	.	CREB3	24	.	NM_006368	exon2	c.C253T	p.R85W	CTCCCACGGGAAA	.	PASS	Atlas-SNP
POM121L2	94026	hgsc.bcm.edu	37	6	27278838	27278838	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135.0	32.0	157.0	0.0	0.237037	0	.	.	none	.	POM121L2	61	.	NM_033482	exon1	c.A1112C	p.N371T	TCTGTGTTGACCT	.	PASS	Atlas-SNP
PHF15	23338	hgsc.bcm.edu	37	5	133901934	133901934	+	Silent	SNP	C	C	T	rs148155246	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84.0	43.0	114.0	0.0	0.511905	0	C|0.997;T|0.003	0.003	strong	.	PHF15	60	.	NM_015288	exon9	c.C1098T	p.D366D	CAGTGACGGGGGC	.	PASS	Atlas-SNP
ISG20	3669	hgsc.bcm.edu	37	15	89182736	89182736	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64.0	16.0	58.0	0.0	0.25	0	.	.	none	.	ISG20	17	.	NM_002201	exon2	c.G139A	p.G47R	CCTGAGGGAGAGA	.	PASS	Atlas-SNP
NRXN1	9378	hgsc.bcm.edu	37	2	51255307	51255307	+	Silent	SNP	G	G	T	rs55640811	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38.0	22.0	37.0	0.0	0.578947	0	.	.	weak	.	NRXN1	1118	.	NM_004801	exon2	c.C105A	p.G35G	CTCGGCGCCCGGA	.	PASS	Atlas-SNP
VASN	114990	hgsc.bcm.edu	37	16	4431373	4431373	+	Silent	SNP	G	G	C	rs740374	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24.0	15.0	27.0	0.0	0.625	0	G|0.986;C|0.014	0.014	strong	.	VASN	21	.	NM_138440	exon2	c.G495C	p.P165P	GCCCCCGCTGCGC	.	PASS	Atlas-SNP
RTN3	10313	hgsc.bcm.edu	37	11	63487033	63487033	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86.0	21.0	87.0	0.0	0.244186	0	.	.	none	.	RTN3	104	.	NM_001265589	exon3	c.T1059C	p.D353D	GACCGATAAATCT	.	PASS	Atlas-SNP
PBX1	5087	hgsc.bcm.edu	37	1	164761924	164761924	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51.0	13.0	58.0	0.0	0.254902	0	.	.	none	.	PBX1	60	.	NM_001204963	exon3	c.A459C	p.K153N	AGCCAAACTCTCA	.	PASS	Atlas-SNP
HAVCR1	26762	hgsc.bcm.edu	37	5	156482296	156482296	+	Missense_Mutation	SNP	C	C	G	rs56084311	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133.0	71.0	112.0	0.0	0.533835	0	C|0.992;G|0.008	0.008	strong	HAVCR1,NS,carcinoma,+1,1	HAVCR1	84	1	NM_001099414	exon3	c.G295C	p.D99H	CACTGTCAGACAC	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56549518	56549518	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133.0	24.0	127.0	0.0	0.180451	0	.	.	none	.	NLRP5	217	.	NM_153447	exon10	c.A2743G	p.S915G	CCTCTCAGTGATG	.	PASS	Atlas-SNP
ITIH6	347365	hgsc.bcm.edu	37	X	54783779	54783779	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94.0	7.0	55.0	0.0	0.0744681	0	.	.	none	.	.	.	.	NM_198510	exon8	c.A2728G	p.S910G	TGGAACTTGAGAT	.	PASS	Atlas-SNP
MAP3K1	4214	hgsc.bcm.edu	37	5	56178615	56178615	+	Silent	SNP	A	A	C	rs55912465	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47.0	28.0	55.0	0.0	0.595745	0	A|0.993;C|0.007	0.007	strong	.	MAP3K1	355	.	NM_005921	exon14	c.A3588C	p.S1196S	AATGTCAGCGTCT	.	PASS	Atlas-SNP
BTG2	7832	hgsc.bcm.edu	37	1	203274835	203274835	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110.0	31.0	124.0	0.0	0.281818	0	.	.	none	.	BTG2	16	.	NM_006763	exon1	c.G101A	p.R34K	AGCAGAGGCTTAA	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495155	134495155	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	12.0	76.0	1.0	0.196721	0.0131579	.	.	none	SGK1_ENST00000528577,NS,lymphoid_neoplasm,-2,5	SGK1	387	5	NM_001143676	exon5	c.C501T	p.N167N	AGAAGGGTTGGCA	.	scavenged	Atlas-SNP
FAM65B	9750	hgsc.bcm.edu	37	6	24839461	24839461	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118.0	38.0	120.0	0.0	0.322034	0	.	.	none	.	FAM65B	134	.	NM_014722	exon15	c.A1960C	p.S654R	TGAGACTTAAACT	.	PASS	Atlas-SNP
UHRF2	115426	hgsc.bcm.edu	37	9	6413498	6413498	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70.0	13.0	73.0	0.0	0.185714	0	.	.	none	.	UHRF2	50	.	NM_152896	exon1	c.T8A	p.I3K	TGTGGATACAGGT	.	PASS	Atlas-SNP
OPA1	4976	hgsc.bcm.edu	37	3	193332566	193332566	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158.0	8.0	155.0	0.0	0.0506329	0	.	.	none	.	OPA1	79	.	NM_130832	exon2	c.A87G	p.P29P	TTTACCACTACAA	.	PASS	Atlas-SNP
SQSTM1	8878	hgsc.bcm.edu	37	5	179263542	179263542	+	Silent	SNP	C	C	T	rs374985304		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70.0	30.0	81.0	0.0	0.428571	0	.	.	weak	SQSTM1,NS,carcinoma,0,1	SQSTM1	30	1	NM_003900	exon8	c.C1272T	p.I424I	TGACATCGGAGCG	.	PASS	Atlas-SNP
MYO1C	4641	hgsc.bcm.edu	37	17	1382889	1382889	+	Silent	SNP	G	G	A	rs146685153		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123.0	57.0	138.0	0.0	0.463415	0	G|1.000;A|0.000	0.000	weak	.	MYO1C	57	.	NM_001080779	exon8	c.C1017T	p.T339T	CACCCTGGTCAGA	.	PASS	Atlas-SNP
PTPRQ	374462	hgsc.bcm.edu	37	12	80865948	80865948	+	Silent	SNP	A	A	G	rs61729291	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116.0	53.0	120.0	0.0	0.456897	0	A|0.969;G|0.031	0.031	strong	.	PTPRQ	119	.	NM_001145026	exon5	c.A588G	p.T196T	ATTTACAATGTAT	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152532702	152532702	+	Missense_Mutation	SNP	T	T	C	rs35763277	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55.0	34.0	64.0	0.0	0.618182	0	T|0.988;C|0.012	0.012	strong	.	SYNE1	3227	.	NM_182961	exon124	c.A22516G	p.S7506G	GACGACTGAACAT	.	PASS	Atlas-SNP
MMP24	10893	hgsc.bcm.edu	37	20	33855126	33855126	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97.0	4.0	85.0	0.0	0.0412371	0	.	.	none	.	MMP24	35	.	NM_006690	exon6	c.C1098T	p.L366L	GCCCCTCGGGGAC	.	PASS	Atlas-SNP
FLAD1	80308	hgsc.bcm.edu	37	1	154956487	154956487	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103.0	31.0	102.0	0.0	0.300971	0	.	.	none	.	FLAD1	52	.	NM_025207	exon1	c.C317A	p.S106Y	AACTTTCTCCGGG	.	PASS	Atlas-SNP
C3orf17	25871	hgsc.bcm.edu	37	3	112724619	112724619	+	Missense_Mutation	SNP	A	A	G	rs7628368	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116.0	65.0	129.0	0.0	0.560345	0	A|0.949;G|0.051	0.051	strong	C3orf17,lymph_node,lymphoid_neoplasm,0,1	C3orf17	37	1	NM_015412	exon9	c.T1468C	p.S490P	AGTGTGAGAGTCT	.	PASS	Atlas-SNP
TRIM45	80263	hgsc.bcm.edu	37	1	117659283	117659283	+	Missense_Mutation	SNP	C	C	T	rs61758105	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	40.0	80.0	0.0	0.547945	0	C|0.989;T|0.011	0.011	strong	.	TRIM45	55	.	NM_025188	exon3	c.G1307A	p.G436E	TTGTCTCCTCCCC	.	PASS	Atlas-SNP
MTNR1A	4543	hgsc.bcm.edu	37	4	187455399	187455399	+	Missense_Mutation	SNP	C	C	T	rs28383653	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69.0	33.0	71.0	0.0	0.478261	0	C|0.988;T|0.012	0.012	strong	.	MTNR1A	46	.	NM_005958	exon2	c.G497A	p.G166E	AGAGTCCCTGCAC	.	PASS	Atlas-SNP
SLC26A7	115111	hgsc.bcm.edu	37	8	92330561	92330561	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86.0	10.0	101.0	0.0	0.116279	0	.	.	none	.	SLC26A7	207	.	NM_134266	exon5	c.T595C	p.L199L	TATCTCTTGGGAA	.	PASS	Atlas-SNP
DNAJC13	23317	hgsc.bcm.edu	37	3	132221139	132221139	+	Missense_Mutation	SNP	C	C	T	rs55825559	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115.0	59.0	125.0	0.0	0.513043	0	C|0.981;T|0.019	0.019	strong	.	DNAJC13	253	.	NM_015268	exon40	c.C4543T	p.P1515S	AGTATTCCCCGCG	.	PASS	Atlas-SNP
ASXL3	80816	hgsc.bcm.edu	37	18	31326554	31326554	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20.0	7.0	21.0	0.0	0.35	0	.	.	none	ASXL3_ENST00000269197,NS,carcinoma,-1,1	ASXL3	405	1	NM_030632	exon12	c.C6742T	p.R2248X	GTTGTACGATAAG	.	PASS	Atlas-SNP
SLC12A3	6559	hgsc.bcm.edu	37	16	56904075	56904075	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80.0	4.0	90.0	0.0	0.05	0	.	.	none	.	SLC12A3	99	.	NM_001126108	exon5	c.C669T	p.F223F	CATTTTCGCTTTC	.	PASS	Atlas-SNP
INPP5B	3633	hgsc.bcm.edu	37	1	38343863	38343863	+	Silent	SNP	G	G	A	rs141357169	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92.0	37.0	118.0	0.0	0.402174	0	G|0.997;A|0.003	0.003	strong	.	INPP5B	76	.	NM_005540	exon16	c.C1674T	p.I558I	TACCCCGATGTCA	.	PASS	Atlas-SNP
BRD4	23476	hgsc.bcm.edu	37	19	15349962	15349962	+	Silent	SNP	G	G	A	rs118000160	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104.0	55.0	116.0	0.0	0.528846	0	G|0.997;A|0.003	0.003	strong	.	BRD4	172	.	NM_058243	exon18	c.C3690T	p.A1230A	CCGAGCGGCGCGG	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	37	16	11000862	11000862	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41.0	19.0	33.0	0.0	0.463415	0	.	.	none	.	CIITA	92	.	NM_000246	exon11	c.G1513T	p.E505X	GAGCTGGAAGCGC	.	PASS	Atlas-SNP
DCST2	127579	hgsc.bcm.edu	37	1	155004092	155004092	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165.0	78.0	161.0	0.0	0.472727	0	.	.	none	.	DCST2	80	.	NM_144622	exon4	c.G697A	p.V233M	TGAGCACGTAACA	.	PASS	Atlas-SNP
ZNF451	26036	hgsc.bcm.edu	37	6	56966040	56966040	+	Silent	SNP	T	T	C	rs188982073	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53.0	28.0	56.0	0.0	0.528302	0	T|0.999;C|0.001	0.001	strong	.	ZNF451	181	.	NM_001257273	exon4	c.T826C	p.L276L	GTGACATTACAAT	.	PASS	Atlas-SNP
MAFG	4097	hgsc.bcm.edu	37	17	79880565	79880565	+	Silent	SNP	G	G	A	rs61752690	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	12.0	7.0	14.0	0.0	0.583333	0	A|0.002;G|0.998	0.002	strong	.	MAFG	9	.	NM_032711	exon3	c.C405T	p.A135A	CAGGCCGGCGGCA	.	PASS	Atlas-SNP
R3HDM1	23518	hgsc.bcm.edu	37	2	136467080	136467080	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	206.0	87.0	253.0	0.0	0.42233	0	.	.	none	.	R3HDM1	84	.	NM_015361	exon21	c.A2432T	p.Q811L	GTTCCCAGCAGCT	.	PASS	Atlas-SNP
FGL1	2267	hgsc.bcm.edu	37	8	17731876	17731876	+	Silent	SNP	A	A	G	rs34871936	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102.0	45.0	115.0	0.0	0.441176	0	A|0.990;G|0.010	0.010	strong	.	FGL1	31	.	NM_201553	exon5	c.T399C	p.F133F	CCTGTTAAAGTTT	.	PASS	Atlas-SNP
GNGT1	2792	hgsc.bcm.edu	37	7	93540153	93540153	+	Missense_Mutation	SNP	G	G	A	rs17243826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101.0	39.0	97.0	0.0	0.386139	0	A|0.023;C|0.029;G|0.948	0.023	strong	.	GNGT1	12	.	NM_021955	exon3	c.G148A	p.E50K	TCTGGCGAGGATC	.	PASS	Atlas-SNP
IRF1	3659	hgsc.bcm.edu	37	5	131825083	131825083	+	Splice_Site	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49.0	21.0	66.0	0.0	0.428571	0	.	.	none	.	IRF1	26	.	NM_002198	exon3	c.87+1G>T	.	CACTCACTTTATT	.	PASS	Atlas-SNP
SGIP1	84251	hgsc.bcm.edu	37	1	67148009	67148009	+	Silent	SNP	G	G	A	rs61798708	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106.0	45.0	109.0	0.0	0.424528	0	G|0.994;A|0.006	0.006	strong	.	SGIP1	272	.	NM_032291	exon15	c.G1272A	p.S424S	GGTTTCGTCCCCC	.	PASS	Atlas-SNP
VWA5B2	90113	hgsc.bcm.edu	37	3	183958706	183958706	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60.0	15.0	79.0	0.0	0.25	0	.	.	none	.	VWA5B2	47	.	NM_138345	exon16	c.G2868A	p.V956V	GCAGGTGTGCAGC	.	PASS	Atlas-SNP
USH1C	10083	hgsc.bcm.edu	37	11	17552707	17552707	+	Silent	SNP	C	C	A	rs41282942	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75.0	36.0	65.0	0.0	0.48	0	C|0.998;A|0.002	0.002	strong	.	USH1C	157	.	NM_005709	exon4	c.G381T	p.G127G	CTGGAGCCCGACG	.	PASS	Atlas-SNP
AMBRA1	55626	hgsc.bcm.edu	37	11	46456444	46456444	+	Silent	SNP	G	G	A	rs61999319	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176.0	101.0	161.0	0.0	0.573864	0	G|0.985;A|0.015	0.015	strong	.	AMBRA1	201	.	NM_001267782	exon15	c.C2785T	p.L929L	GGGCCAGGGAGTA	.	PASS	Atlas-SNP
EVPL	2125	hgsc.bcm.edu	37	17	74003525	74003525	+	Missense_Mutation	SNP	C	C	T	rs141706835	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66.0	33.0	68.0	0.0	0.5	0	C|1.000;T|0.000	0.000	weak	EVPL,colon,carcinoma,0,1	EVPL	155	1	NM_001988	exon22	c.G5761A	p.V1921I	TCTGGACGGCCTC	.	PASS	Atlas-SNP
COL2A1	1280	hgsc.bcm.edu	37	12	48381394	48381394	+	Silent	SNP	G	G	A	rs150865922	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28.0	12.0	30.0	0.0	0.428571	0	G|0.997;A|0.003	0.003	strong	.	COL2A1	368	.	NM_001844	exon19	c.C1221T	p.S407S	ACTTACGGAGGCA	.	PASS	Atlas-SNP
BCAN	63827	hgsc.bcm.edu	37	1	156616814	156616814	+	Missense_Mutation	SNP	C	C	G	rs115373136	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47.0	22.0	62.0	0.0	0.468085	0	C|0.989;G|0.011	0.011	strong	.	BCAN	174	.	NM_198427	exon3	c.C313G	p.R105G	GCCTACCGGTTCC	.	PASS	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	37	7	2984153	2984153	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63.0	25.0	45.0	0.0	0.396825	0	.	.	none	CARD11,colon,carcinoma,+1,4	CARD11	339	4	NM_032415	exon5	c.G377A	p.G126D	GTGAGGCCCTCGT	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152668211	152668211	+	Missense_Mutation	SNP	A	A	G	rs111449472	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104.0	42.0	116.0	0.0	0.403846	0	A|0.990;G|0.010	0.010	strong	.	SYNE1	3227	.	NM_182961	exon73	c.T12061C	p.C4021R	TGCTGCAGATCGC	.	PASS	Atlas-SNP
FHAD1	114827	hgsc.bcm.edu	37	1	15679393	15679393	+	Silent	SNP	G	G	A	rs35368057	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85.0	33.0	86.0	0.0	0.388235	0	G|0.991;A|0.009	0.009	strong	.	FHAD1	78	.	NM_052929	exon19	c.G2409A	p.A803A	CATTGCGTACGAG	.	PASS	Atlas-SNP
HIST1H2AK	8330	hgsc.bcm.edu	37	6	27805865	27805865	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128.0	50.0	121.0	0.0	0.390625	0	.	.	none	.	HIST1H2AK	28	.	NM_003510	exon1	c.C253T	p.Q85X	CCAGCTGCAAGTG	.	PASS	Atlas-SNP
SLC6A11	6538	hgsc.bcm.edu	37	3	10960057	10960057	+	Missense_Mutation	SNP	G	G	A	rs376135284		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100.0	42.0	111.0	0.0	0.42	0	.	.	weak	.	SLC6A11	87	.	NM_014229	exon8	c.G1039A	p.V347M	AGCTTCGTGGCTG	.	PASS	Atlas-SNP
WDR65	149465	hgsc.bcm.edu	37	1	43680952	43680952	+	Silent	SNP	C	C	T	rs74422853	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113.0	61.0	123.0	0.0	0.539823	0	C|0.989;T|0.011	0.011	strong	.	WDR65	76	.	NM_001195831	exon12	c.C1956T	p.F652F	TCAGTTCCTGCTG	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14740229	14740229	+	Silent	SNP	G	G	A	rs187325866	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64.0	32.0	42.0	0.0	0.5	0	G|0.999;A|0.001	0.001	strong	.	FREM1	261	.	NM_144966	exon37	c.C6258T	p.Y2086Y	GCCCAGGTATCTA	.	PASS	Atlas-SNP
CAPRIN2	65981	hgsc.bcm.edu	37	12	30881884	30881884	+	Missense_Mutation	SNP	G	G	A	rs374198235	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155.0	92.0	161.0	0.0	0.593548	0	.	.	alt	.	CAPRIN2	109	.	NM_023925	exon8	c.C1480T	p.P494S	GCTTTGGTGTCTC	.	PASS	Atlas-SNP
ZNF414	84330	hgsc.bcm.edu	37	19	8576390	8576390	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103.0	57.0	100.0	0.0	0.553398	0	.	.	none	.	ZNF414	25	.	NM_032370	exon6	c.G905A	p.G302D	GAGCCGCCCTGGG	.	PASS	Atlas-SNP
DACT1	51339	hgsc.bcm.edu	37	14	59113721	59113721	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30.0	13.0	50.0	0.0	0.433333	0	.	.	none	.	DACT1	119	.	NM_016651	exon4	c.C2380G	p.Q794E	CCCATTCAAACGG	.	PASS	Atlas-SNP
FAM22G	441457	hgsc.bcm.edu	37	9	99701002	99701002	+	Silent	SNP	C	C	T	rs76993010		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	360.0	124.0	315.0	0.0	0.344444	0	T|1.000;|0.000	1.000	weak	.	FAM22G	66	.	NM_001170741	exon7	c.C1797T	p.L599L	GGGTCTCCCTGGA	.	PASS	Atlas-SNP
DAO	1610	hgsc.bcm.edu	37	12	109293183	109293183	+	Missense_Mutation	SNP	T	T	G	rs113854555	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52.0	14.0	33.0	0.0	0.269231	0	T|0.500;C|0.500	.	alt	.	DAO	58	.	NM_001917	exon10	c.T844G	p.F282V	ACTGGCTTCCGGC	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134664628	134664628	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43.0	12.0	43.0	0.0	0.27907	0	.	.	none	.	TTC40	100	.	NM_001200049	exon40	c.T5756C	p.V1919A	AGGCCGACGGAAG	.	PASS	Atlas-SNP
KIAA1033	23325	hgsc.bcm.edu	37	12	105550565	105550565	+	Silent	SNP	C	C	T	rs35149056	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86.0	38.0	71.0	0.0	0.44186	0	C|0.946;T|0.054	0.054	strong	.	KIAA1033	83	.	NM_015275	exon27	c.C2820T	p.A940A	CAATGCCATTAGG	.	PASS	Atlas-SNP
TIAM2	26230	hgsc.bcm.edu	37	6	155575639	155575639	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175.0	94.0	144.0	0.0	0.537143	0	.	.	none	TIAM2,NS,carcinoma,+1,1	TIAM2	161	1	NM_012454	exon25	c.C4400T	p.P1467L	AATTACCACTGGA	.	PASS	Atlas-SNP
RAPGEF3	10411	hgsc.bcm.edu	37	12	48143315	48143315	+	Missense_Mutation	SNP	A	A	G	rs145878042	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14.0	5.0	20.0	0.0	0.357143	0	A|0.993;G|0.007	0.007	strong	.	RAPGEF3	98	.	NM_001098531	exon10	c.T899C	p.L300P	GTCACCAGCCCCT	.	PASS	Atlas-SNP
BTBD8	284697	hgsc.bcm.edu	37	1	92568089	92568089	+	Missense_Mutation	SNP	A	A	G	rs17131602	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145.0	66.0	188.0	0.0	0.455172	0	A|0.986;G|0.014	0.014	strong	BTBD8,colon,carcinoma,0,4	BTBD8	32	4	NM_183242	exon3	c.A407G	p.K136R	GGAAAAAGATAAT	.	PASS	Atlas-SNP
PMS2	5395	hgsc.bcm.edu	37	7	6018231	6018231	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	396.0	212.0	325.0	0.0	0.535354	0	.	.	none	.	PMS2	88	.	NM_000535	exon13	c.A2271G	p.E757E	ACCATTTTCATCG	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495709	134495709	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40.0	8.0	70.0	0.0	0.2	0	.	.	none	SGK1_ENST00000367858,NS,lymphoid_neoplasm,-1,2	SGK1	387	2	NM_001143676	exon4	c.G377A	p.R126K	ATCCTCCTCTGCT	.	PASS	Atlas-SNP
BTD	686	hgsc.bcm.edu	37	3	15686611	15686611	+	Silent	SNP	C	C	T	rs372039874		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131.0	64.0	117.0	0.0	0.48855	0	.	.	weak	.	BTD	49	.	NM_000060	exon4	c.C1248T	p.H416H	TCTCCACGTCTGT	.	PASS	Atlas-SNP
SORCS1	114815	hgsc.bcm.edu	37	10	108434858	108434858	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74.0	25.0	66.0	0.0	0.337838	0	.	.	none	.	SORCS1	534	.	NM_001206572	exon14	c.T1889G	p.L630R	ACAAAAAGTGGAA	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907263	12907263	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130.0	30.0	126.0	0.0	0.230769	0	.	.	none	.	HNRNPCL1	68	.	NM_001013631	exon2	c.T880A	p.X294K	GTGCTTAAGAGTC	.	PASS	Atlas-SNP
KRT7	3855	hgsc.bcm.edu	37	12	52636919	52636919	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40.0	8.0	37.0	0.0	0.2	0	.	.	none	.	KRT7	48	.	NM_005556	exon6	c.C982T	p.Q328X	AAGAACCAGGTGG	.	PASS	Atlas-SNP
GATM	2628	hgsc.bcm.edu	37	15	45660421	45660421	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54.0	23.0	98.0	0.0	0.425926	0	.	.	none	.	GATM	34	.	NM_001482	exon4	c.T522C	p.V174V	GCCCACAACTATC	.	PASS	Atlas-SNP
SFTPA1	653509	hgsc.bcm.edu	37	10	81373562	81373562	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	299.0	115.0	306.0	0.0	0.384615	0	.	.	none	.	SFTPA1	23	.	NM_001093770	exon6	c.C485G	p.T162S	CCATCACTTTTGA	.	PASS	Atlas-SNP
MYH10	4628	hgsc.bcm.edu	37	17	8402769	8402769	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154.0	50.0	160.0	0.0	0.324675	0	.	.	none	.	MYH10	148	.	NM_001256012	exon30	c.A3770C	p.K1257T	CCCTGCTTGTTCT	.	PASS	Atlas-SNP
SLC2A9	56606	hgsc.bcm.edu	37	4	9998476	9998476	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	203.0	60.0	216.0	0.0	0.295566	0	.	.	none	.	SLC2A9	158	.	NM_020041	exon3	c.T339C	p.T113T	GGACACAGTCACA	.	PASS	Atlas-SNP
PAPLN	89932	hgsc.bcm.edu	37	14	73718474	73718474	+	Missense_Mutation	SNP	G	G	T	rs141960540	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146.0	76.0	122.0	0.0	0.520548	0	G|0.998;T|0.002	0.002	strong	.	PAPLN	180	.	NM_173462	exon8	c.G692T	p.G231V	AGCGGGGTGCTGA	.	PASS	Atlas-SNP
ROR2	4920	hgsc.bcm.edu	37	9	94495595	94495595	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101.0	8.0	96.0	0.0	0.0792079	0	.	.	none	.	ROR2	167	.	NM_004560	exon6	c.G746A	p.R249H	AGCTCACGCGGCT	.	PASS	Atlas-SNP
ZNF561	93134	hgsc.bcm.edu	37	19	9721218	9721218	+	Silent	SNP	G	G	A	rs138137635	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	33.0	57.0	0.0	0.540984	0	G|0.999;A|0.001	0.001	strong	.	ZNF561	64	.	NM_152289	exon6	c.C1119T	p.A373A	AGTGAAGGCTTTC	.	PASS	Atlas-SNP
PCDH17	27253	hgsc.bcm.edu	37	13	58208047	58208047	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63.0	10.0	47.0	0.0	0.15873	0	.	.	none	PCDH17,colon,carcinoma,-1,1	PCDH17	304	1	NM_001040429	exon1	c.A1367C	p.K456T	CCACCAAGTCGTT	.	PASS	Atlas-SNP
KIAA0232	9778	hgsc.bcm.edu	37	4	6843852	6843852	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34.0	3.0	37.0	0.0	0.0882353	0	.	.	none	KIAA0232,bladder,carcinoma,-1,1	KIAA0232	102	1	NM_014743	exon4	c.A290G	p.K97R	AGAGTAAGAAAAA	.	scavenged	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187629137	187629137	+	Silent	SNP	A	A	G	rs4862726	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41.0	17.0	54.0	0.0	0.414634	0	A|0.975;G|0.025	0.025	strong	.	FAT1	500	.	NM_005245	exon2	c.T1845C	p.F615F	TAAACTAAAGAAA	.	PASS	Atlas-SNP
CD180	4064	hgsc.bcm.edu	37	5	66492387	66492387	+	Missense_Mutation	SNP	C	C	T	rs377501004		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88.0	6.0	64.0	0.0	0.0681818	0	.	.	weak	.	CD180	78	.	NM_005582	exon1	c.G83A	p.C28Y	TCAATGCACATCT	.	PASS	Atlas-SNP
CFHR2	3080	hgsc.bcm.edu	37	1	196918724	196918724	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	219.0	14.0	235.0	0.0	0.0639269	0	.	.	none	.	CFHR2	73	.	NM_005666	exon2	c.T198A	p.F66L	ATCCTTTTGGACT	.	PASS	Atlas-SNP
PCDHA1	56147	hgsc.bcm.edu	37	5	140167033	140167033	+	Silent	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100.0	18.0	116.0	0.0	0.18	0	.	.	none	.	PCDHA1	387	.	NM_031411	exon1	c.T1158G	p.T386T	GGTGACTTGCTCC	.	PASS	Atlas-SNP
ATP13A4	84239	hgsc.bcm.edu	37	3	193272556	193272556	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118.0	12.0	124.0	0.0	0.101695	0	.	.	none	.	ATP13A4	154	.	NM_032279	exon1	c.G33A	p.L11L	ATTGAGCAGAGCG	.	PASS	Atlas-SNP
PRAME	23532	hgsc.bcm.edu	37	22	22893394	22893394	+	Missense_Mutation	SNP	A	A	T	rs41310248	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41.0	25.0	45.0	0.0	0.609756	0	A|0.978;T|0.022	0.022	strong	.	PRAME	78	.	NM_206954	exon4	c.T139A	p.L47M	GCAGCAACTCCAG	.	PASS	Atlas-SNP
CLCN7	1186	hgsc.bcm.edu	37	16	1506130	1506130	+	Silent	SNP	C	C	T	rs41286695	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24.0	14.0	26.0	0.0	0.583333	0	C|0.973;T|0.027	0.027	strong	.	CLCN7	53	.	NM_001287	exon10	c.G900A	p.A300A	TCCAAACGCCGCT	.	PASS	Atlas-SNP
B4GALNT4	338707	hgsc.bcm.edu	37	11	380395	380395	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55.0	4.0	70.0	0.0	0.0727273	0	.	.	none	B4GALNT4,NS,carcinoma,+1,1	B4GALNT4	83	1	NM_178537	exon18	c.C2819T	p.A940V	CCTTCGCGCCCGT	.	PASS	Atlas-SNP
NT5M	56953	hgsc.bcm.edu	37	17	17250197	17250197	+	Missense_Mutation	SNP	G	G	A	rs145194793	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77.0	40.0	63.0	0.0	0.519481	0	G|0.997;A|0.003	0.003	strong	.	NT5M	17	.	NM_020201	exon5	c.G623A	p.R208H	CCCCCCGCCGCAG	.	PASS	Atlas-SNP
PTBP2	58155	hgsc.bcm.edu	37	1	97235290	97235290	+	Silent	SNP	A	A	G	rs139414147	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89.0	33.0	100.0	0.0	0.370787	0	A|0.998;G|0.002	0.002	strong	.	PTBP2	62	.	NM_021190	exon4	c.A147G	p.G49G	TAAAGGAGAAGAT	.	PASS	Atlas-SNP
LIMD2	80774	hgsc.bcm.edu	37	17	61776651	61776651	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96.0	20.0	112.0	0.0	0.208333	0	.	.	none	.	LIMD2	6	.	NM_030576	exon2	c.A8T	p.Q3L	GCAGCCTGGAACA	.	PASS	Atlas-SNP
OMA1	115209	hgsc.bcm.edu	37	1	58999896	58999896	+	Silent	SNP	C	C	A	rs41287650	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	231.0	89.0	281.0	0.0	0.385281	0	C|1.000;A|0.000	0.000	strong	.	OMA1	50	.	NM_145243	exon4	c.G837T	p.G279G	AGAGATCCCTGGA	.	PASS	Atlas-SNP
RSAD1	55316	hgsc.bcm.edu	37	17	48561871	48561871	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43.0	12.0	34.0	0.0	0.27907	0	.	.	none	RSAD1,NS,carcinoma,+2,1	RSAD1	36	1	NM_018346	exon8	c.G1176A	p.E392E	GCAGGAGCTGCTG	.	PASS	Atlas-SNP
OTUD4	54726	hgsc.bcm.edu	37	4	146063471	146063471	+	Missense_Mutation	SNP	C	C	T	rs151020153	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65.0	35.0	50.0	0.0	0.538462	0	C|0.998;T|0.002	0.002	strong	.	OTUD4	120	.	NM_001102653	exon18	c.G1504A	p.V502M	AAGACACATGTTC	.	PASS	Atlas-SNP
BICD1	636	hgsc.bcm.edu	37	12	32481369	32481369	+	Silent	SNP	C	C	T	rs34447944	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93.0	32.0	110.0	0.0	0.344086	0	C|0.940;T|0.060	0.060	strong	BICD1,colon,carcinoma,0,1	BICD1	89	1	NM_001714	exon5	c.C1980T	p.A660A	GCTAGCCCCCATG	.	PASS	Atlas-SNP
MLXIPL	51085	hgsc.bcm.edu	37	7	73010191	73010191	+	Missense_Mutation	SNP	C	C	T	rs149244334	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35.0	16.0	52.0	0.0	0.457143	0	C|0.999;T|0.001	0.001	strong	.	MLXIPL	54	.	NM_032951	exon14	c.G2167A	p.E723K	TGAGCTCCTCAAT	.	PASS	Atlas-SNP
CTAGE5	4253	hgsc.bcm.edu	37	14	39769122	39769122	+	Missense_Mutation	SNP	A	A	C	rs34761053	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60.0	25.0	85.0	0.0	0.416667	0	A|0.995;C|0.005	0.005	strong	.	CTAGE5	75	.	NM_001247989	exon9	c.A742C	p.K248Q	AAACAGAAAGTAA	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46762360	46762360	+	Silent	SNP	G	G	A	rs56325154	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107.0	52.0	95.0	0.0	0.485981	0	G|0.993;A|0.007	0.007	strong	.	CELSR1	242	.	NM_014246	exon30	c.C8223T	p.N2741N	GGTGGTGTTGCAG	.	PASS	Atlas-SNP
PCDHGA9	56107	hgsc.bcm.edu	37	5	140783628	140783628	+	Missense_Mutation	SNP	A	A	G	rs375910829		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139.0	71.0	124.0	0.0	0.510791	0	.	.	weak	.	PCDHGA9	110	.	NM_032089	exon1	c.A1109G	p.N370S	TTTTCAATGCTCA	.	PASS	Atlas-SNP
ENPP5	59084	hgsc.bcm.edu	37	6	46135795	46135795	+	Missense_Mutation	SNP	T	T	C	rs34432940	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81.0	40.0	60.0	0.0	0.493827	0	T|0.993;C|0.007	0.007	strong	.	ENPP5	44	.	NM_021572	exon2	c.A205G	p.I69V	TTGTAATAAAAAC	.	PASS	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54176359	54176359	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74.0	23.0	59.0	0.0	0.310811	0	.	.	none	.	PSME4	247	.	NM_014614	exon2	c.T304C	p.L102L	CATACAATAACTT	.	PASS	Atlas-SNP
ADAMTS18	170692	hgsc.bcm.edu	37	16	77325285	77325285	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129.0	31.0	138.0	0.0	0.24031	0	.	.	none	ADAMTS18,NS,carcinoma,+1,2	ADAMTS18	270	2	NM_199355	exon21	c.C3280T	p.R1094X	ATCTTCGCTCTGG	.	PASS	Atlas-SNP
SETD5	55209	hgsc.bcm.edu	37	3	9483818	9483818	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47.0	17.0	31.0	0.0	0.361702	0	.	.	none	.	SETD5	210	.	NM_001080517	exon10	c.C966G	p.Y322X	ACCATACCCCTTT	.	PASS	Atlas-SNP
APMAP	57136	hgsc.bcm.edu	37	20	24954303	24954303	+	Silent	SNP	G	G	C	rs148400044	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102.0	57.0	98.0	0.0	0.558824	0	G|0.998;C|0.002	0.002	strong	.	APMAP	3	.	NM_020531	exon4	c.C399G	p.A133A	AAACCGGGCAATG	.	PASS	Atlas-SNP
SBF1	6305	hgsc.bcm.edu	37	22	50893668	50893668	+	Silent	SNP	C	C	G	rs374064130		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56.0	35.0	57.0	0.0	0.625	0	.	.	weak	.	SBF1	211	.	NM_002972	exon33	c.G4539C	p.L1513L	GCAGTCCAGGAAC	.	PASS	Atlas-SNP
RET	5979	hgsc.bcm.edu	37	10	43610119	43610119	+	Missense_Mutation	SNP	G	G	A	rs1799939	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46.0	25.0	60.0	0.0	0.543478	0	G|0.839;A|0.161	0.161	strong	RET_ENST00000340058,adrenal_gland,pheochromocytoma,0,2	RET	916	2	NM_020630	exon11	c.G2071A	p.G691S	TCTTCCGGTGCCC	.	PASS	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	96030979	96030979	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91.0	28.0	109.0	0.0	0.307692	0	.	.	none	.	WNK2	277	.	NM_006648	exon18	c.A3984T	p.E1328D	CCCTGAATCTTCG	.	PASS	Atlas-SNP
COL6A6	131873	hgsc.bcm.edu	37	3	130311551	130311551	+	Silent	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108.0	28.0	131.0	0.0	0.259259	0	.	.	none	COL6A6_ENST00000358511,bladder,carcinoma,+1,2	COL6A6	497	2	NM_001102608	exon14	c.A4356T	p.G1452G	CAGAGGACTAAAT	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224227	248224227	+	Missense_Mutation	SNP	T	T	C	rs146249174	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223.0	107.0	234.0	0.0	0.479821	0	T|0.992;C|0.008	0.008	strong	.	OR2L3	97	.	NM_001004687	exon1	c.T244C	p.S82P	ATGGCATCTGATT	.	PASS	Atlas-SNP
PPP4R4	57718	hgsc.bcm.edu	37	14	94722815	94722815	+	Silent	SNP	G	G	A	rs114970142	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35.0	13.0	41.0	0.0	0.371429	0	G|0.989;A|0.011	0.011	strong	.	PPP4R4	107	.	NM_058237	exon17	c.G1884A	p.L628L	CTACCTGTTGCCC	.	PASS	Atlas-SNP
CHST8	64377	hgsc.bcm.edu	37	19	34262922	34262922	+	Missense_Mutation	SNP	C	C	T	rs149660944	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103.0	51.0	112.0	0.0	0.495146	0	C|0.995;T|0.005	0.005	strong	.	CHST8	70	.	NM_001127895	exon5	c.C229T	p.R77W	GTCACTCGGGACT	.	PASS	Atlas-SNP
ROR2	4920	hgsc.bcm.edu	37	9	94499797	94499797	+	Silent	SNP	A	A	G	rs16907720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30.0	14.0	36.0	0.0	0.466667	0	A|0.902;G|0.098	0.098	strong	.	ROR2	167	.	NM_004560	exon5	c.T498C	p.D166D	GTAATCATCCCTG	.	PASS	Atlas-SNP
PRRC2C	23215	hgsc.bcm.edu	37	1	171509275	171509275	+	Silent	SNP	T	T	C	rs75723046	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100.0	44.0	112.0	0.0	0.44	0	T|0.997;C|0.003	0.003	strong	.	.	.	.	NM_015172	exon16	c.T2664C	p.D888D	TACTGATGCAAAT	.	PASS	Atlas-SNP
DCDC2	51473	hgsc.bcm.edu	37	6	24302049	24302049	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131.0	10.0	131.0	0.0	0.0763359	0	.	.	none	.	DCDC2	53	.	NM_001195610	exon5	c.A451C	p.N151H	CTGGGTTTATGAG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1272793	1272793	+	Missense_Mutation	SNP	C	C	T	rs56159668	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90.0	43.0	86.0	0.0	0.477778	0	C|0.992;T|0.008	0.008	strong	.	MUC5B	473	.	NM_002458	exon31	c.C14683T	p.P4895S	ACGGTTCCCAGCT	.	PASS	Atlas-SNP
ZBTB16	7704	hgsc.bcm.edu	37	11	114118019	114118019	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131.0	25.0	110.0	0.0	0.19084	0	.	.	none	.	ZBTB16	101	.	NM_006006	exon6	c.A1724G	p.E575G	CCTACGAGTGCAA	.	PASS	Atlas-SNP
LRIG2	9860	hgsc.bcm.edu	37	1	113637308	113637308	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	209.0	94.0	239.0	0.0	0.449761	0	.	.	none	.	LRIG2	67	.	NM_014813	exon6	c.A734G	p.K245R	CTTTGAAAATGCA	.	PASS	Atlas-SNP
BRWD1	54014	hgsc.bcm.edu	37	21	40582823	40582823	+	Silent	SNP	C	C	T	rs75046572	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116.0	74.0	74.0	0.0	0.637931	0	C|0.970;T|0.030	0.030	strong	.	BRWD1	325	.	NM_018963	exon35	c.G3933A	p.T1311T	ATAGTTCGTAGCT	.	PASS	Atlas-SNP
CTSE	1510	hgsc.bcm.edu	37	1	206319201	206319201	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88.0	13.0	102.0	0.0	0.147727	0	.	.	none	.	CTSE	72	.	NM_001910	exon3	c.G326A	p.C109Y	TGTACTGCACTAG	.	PASS	Atlas-SNP
HIST1H3J	8356	hgsc.bcm.edu	37	6	27858310	27858310	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81.0	8.0	93.0	0.0	0.0987654	0	.	.	none	.	HIST1H3J	16	.	NM_003535	exon1	c.C261T	p.S87S	CGCCGAGCTCTGG	.	PASS	Atlas-SNP
ENPP7	339221	hgsc.bcm.edu	37	17	77709383	77709383	+	Missense_Mutation	SNP	C	C	T	rs148221256	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	23.0	85.0	0.0	0.315068	0	C|0.998;T|0.002	0.002	strong	.	ENPP7	63	.	NM_178543	exon3	c.C941T	p.A314V	AGGAGGCGTTCCC	.	PASS	Atlas-SNP
SCML4	256380	hgsc.bcm.edu	37	6	108067907	108067907	+	Missense_Mutation	SNP	C	C	T	rs142985964	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63.0	35.0	85.0	0.0	0.555556	0	C|0.999;T|0.001	0.001	strong	.	SCML4	65	.	NM_198081	exon4	c.G473A	p.G158D	ATCTCACCACCAT	.	PASS	Atlas-SNP
OSGIN1	29948	hgsc.bcm.edu	37	16	83992895	83992895	+	Missense_Mutation	SNP	A	A	G	rs150635654	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79.0	37.0	80.0	0.0	0.468354	0	A|0.999;G|0.001	0.001	strong	.	OSGIN1	33	.	NM_182981	exon3	c.A98G	p.Y33C	TGTCCTACCTGCT	.	PASS	Atlas-SNP
ATAD2	29028	hgsc.bcm.edu	37	8	124360487	124360487	+	Silent	SNP	G	G	A	rs77106954	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	26.0	124.0	0.0	0.356164	0	G|0.979;A|0.021	0.021	strong	.	ATAD2	160	.	NM_014109	exon15	c.C1833T	p.H611H	CCTGGTGTGAATC	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	117029826	117029826	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	4.0	53.0	0.0	0.0655738	0	.	.	none	.	COL27A1	200	.	NM_032888	exon34	c.G3490A	p.A1164T	GGGGAAGCCGGGA	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	12088	12088	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17.0	6.0	6.0	0.0	0.352941	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.C1329T	p.P443P	ATCCCCCATTCTC	.	PASS	Atlas-SNP
SGK196	0	hgsc.bcm.edu	37	8	42977591	42977591	+	Silent	SNP	G	G	C	rs34040483	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85.0	38.0	90.0	0.0	0.447059	0	G|0.992;C|0.008	0.008	strong	.	.	.	.	NM_032237	exon5	c.G624C	p.L208L	CGACCTGCCGAAG	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124330421	124330421	+	Missense_Mutation	SNP	C	C	G	rs75209396	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	192.0	94.0	161.0	0.0	0.489583	0	C|0.950;G|0.050	0.050	strong	.	DMBT1	677	.	NM_007329	exon4	c.C155G	p.S52W	TTCCCTCGGAGTC	.	PASS	Atlas-SNP
AIPL1	23746	hgsc.bcm.edu	37	17	6337404	6337404	+	Silent	SNP	G	G	A	rs11650007	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89.0	38.0	100.0	0.0	0.426966	0	G|0.983;A|0.017	0.017	strong	.	AIPL1	34	.	NM_014336	exon2	c.C111T	p.F37F	GGTGCGGAAATGA	.	PASS	Atlas-SNP
SH3RF3	344558	hgsc.bcm.edu	37	2	110065896	110065896	+	Missense_Mutation	SNP	C	C	T	rs192679474	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97.0	42.0	114.0	0.0	0.43299	0	C|0.998;T|0.002	0.002	strong	.	SH3RF3	62	.	NM_001099289	exon8	c.C2099T	p.S700F	CCACATCCAGCCC	.	PASS	Atlas-SNP
NAALADL2	254827	hgsc.bcm.edu	37	3	174974265	174974265	+	Silent	SNP	C	C	T	rs192980349	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102.0	48.0	118.0	0.0	0.470588	0	C|0.999;T|0.001	0.001	strong	.	NAALADL2	86	.	NM_207015	exon4	c.C885T	p.N295N	AAAAAACGTAACA	.	PASS	Atlas-SNP
ATG2B	55102	hgsc.bcm.edu	37	14	96800027	96800027	+	Missense_Mutation	SNP	C	C	T	rs183527316	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98.0	50.0	81.0	0.0	0.510204	0	C|0.998;T|0.002	0.002	strong	.	ATG2B	169	.	NM_018036	exon8	c.G1205A	p.R402H	TTACCACGGCTAG	.	PASS	Atlas-SNP
PPFIBP2	8495	hgsc.bcm.edu	37	11	7662851	7662851	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92.0	24.0	94.0	0.0	0.26087	0	.	.	none	.	PPFIBP2	87	.	NM_003621	exon16	c.A1517C	p.K506T	GGGGAAAGTAAGT	.	PASS	Atlas-SNP
HIST2H3D	653604	hgsc.bcm.edu	37	1	149784843	149784843	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	238.0	15.0	239.0	0.0	0.0630252	0	.	.	none	.	HIST2H3D	15	.	NM_001123375	exon1	c.C394T	p.R132C	CCCCGCGGATGCG	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128367451	128367451	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116.0	13.0	177.0	0.0	0.112069	0	.	.	none	.	MYO7B	359	.	NM_001080527	exon24	c.C3052T	p.L1018L	GTCATCCTGAGGT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495218	134495218	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70.0	21.0	62.0	0.0	0.3	0	.	.	none	SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,4	SGK1	387	4	NM_001143676	exon5	c.C438T	p.H146H	TTCAGGGCTGCAG	.	PASS	Atlas-SNP
TTC12	54970	hgsc.bcm.edu	37	11	113234603	113234603	+	Silent	SNP	G	G	A	rs34940277	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94.0	74.0	89.0	0.0	0.787234	0	G|0.999;A|0.001	0.001	strong	.	TTC12	66	.	NM_017868	exon20	c.G1770A	p.T590T	CTGCACGAATAGT	.	PASS	Atlas-SNP
MTUS1	57509	hgsc.bcm.edu	37	8	17532715	17532715	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128.0	27.0	92.0	0.0	0.210938	0	.	.	none	.	MTUS1	144	.	NM_001001924	exon8	c.T2885G	p.V962G	AGGTTAACAAGTT	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144947062	144947062	+	Silent	SNP	C	C	T	rs7819087	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113.0	70.0	123.0	0.0	0.619469	0	C|0.955;T|0.045	0.045	strong	.	EPPK1	199	.	NM_031308	exon1	c.G360A	p.T120T	ATAGCCCGTAGTG	.	PASS	Atlas-SNP
ZFP2	80108	hgsc.bcm.edu	37	5	178359075	178359075	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44.0	17.0	27.0	0.0	0.386364	0	.	.	none	.	ZFP2	70	.	NM_030613	exon5	c.G761C	p.S254T	GTCAAAGCATGCA	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144941940	144941940	+	Silent	SNP	G	G	A	rs73715514	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117.0	58.0	112.0	0.0	0.495726	0	G|0.951;A|0.049	0.049	strong	.	EPPK1	199	.	NM_031308	exon1	c.C5482T	p.L1828L	TTTCCAGCAATTT	.	PASS	Atlas-SNP
FAM5C	339479	hgsc.bcm.edu	37	1	190067970	190067970	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135.0	35.0	96.0	0.0	0.259259	0	.	.	none	FAM5C,colon,carcinoma,-2,1	FAM5C	343	1	NM_199051	exon8	c.A1479C	p.Q493H	GAGATCTTGCAGG	.	PASS	Atlas-SNP
ASIP	434	hgsc.bcm.edu	37	20	32856838	32856838	+	Silent	SNP	C	C	A	rs36093428	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53.0	35.0	62.0	0.0	0.660377	0	C|0.994;A|0.006	0.006	strong	.	ASIP	6	.	NM_001672	exon3	c.C264A	p.P88P	GACCCCCCTATCT	.	PASS	Atlas-SNP
CCR2	729230	hgsc.bcm.edu	37	3	46399581	46399581	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143.0	51.0	168.0	0.0	0.356643	0	.	.	none	.	CCR2	103	.	NM_001123041	exon2	c.A563C	p.Y188S	CTGTTTATGTCTG	.	PASS	Atlas-SNP
SOX5	6660	hgsc.bcm.edu	37	12	23757393	23757393	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124.0	9.0	137.0	0.0	0.0725806	0	.	.	none	.	SOX5	134	.	NM_006940	exon9	c.C1092A	p.N364K	ACCAAGGTTGCCT	.	PASS	Atlas-SNP
GCH1	2643	hgsc.bcm.edu	37	14	55369053	55369053	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41.0	15.0	40.0	0.0	0.365854	0	.	.	none	.	GCH1	16	.	NM_000161	exon1	c.A329G	p.Q110R	GTCTCCTGGTAGC	.	PASS	Atlas-SNP
DNAJA2	10294	hgsc.bcm.edu	37	16	47007480	47007480	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40.0	11.0	39.0	0.0	0.275	0	.	.	none	.	DNAJA2	28	.	NM_005880	exon1	c.G4A	p.A2T	CGTTAGCCATGGC	.	PASS	Atlas-SNP
OR1L3	26735	hgsc.bcm.edu	37	9	125437664	125437664	+	Missense_Mutation	SNP	T	T	G	rs56304399	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132.0	72.0	124.0	0.0	0.545455	0	T|0.993;G|0.007	0.007	strong	.	OR1L3	51	.	NM_001005234	exon1	c.T256G	p.L86V	AACTTCTTATCAG	.	PASS	Atlas-SNP
HRC	3270	hgsc.bcm.edu	37	19	49658345	49658345	+	Silent	SNP	G	G	A	rs117942355	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	27.0	67.0	0.0	0.442623	0	G|1.000;A|0.000	0.000	strong	.	HRC	85	.	NM_002152	exon1	c.C150T	p.S50S	CTCCTCGGAGAGC	.	PASS	Atlas-SNP
KIF5B	3799	hgsc.bcm.edu	37	10	32320002	32320002	+	Missense_Mutation	SNP	G	G	A	rs35441986	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79.0	44.0	83.0	0.0	0.556962	0	G|0.998;A|0.002	0.002	strong	.	KIF5B	81	.	NM_004521	exon14	c.C1580T	p.S527L	CCTACCGATTTCT	.	PASS	Atlas-SNP
COL12A1	1303	hgsc.bcm.edu	37	6	75827165	75827165	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67.0	22.0	98.0	0.0	0.328358	0	.	.	none	COL12A1,NS,carcinoma,0,1	COL12A1	385	1	NM_004370	exon47	c.C7452T	p.D2484D	AAAGTCGTCCACA	.	PASS	Atlas-SNP
ALDH9A1	223	hgsc.bcm.edu	37	1	165638577	165638577	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	201.0	69.0	200.0	0.0	0.343284	0	.	.	none	.	ALDH9A1	75	.	NM_000696	exon7	c.A1041C	p.E347D	TGTATCTTCCAGA	.	PASS	Atlas-SNP
MYO6	4646	hgsc.bcm.edu	37	6	76572352	76572352	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124.0	6.0	133.0	0.0	0.0483871	0	.	.	none	.	MYO6	124	.	NM_004999	exon16	c.T1586G	p.L529W	ATATTTTGGATGA	.	PASS	Atlas-SNP
P2RY8	286530	hgsc.bcm.edu	37	X	1585084	1585084	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87.0	15.0	120.0	0.0	0.172414	0	.	.	none	.	P2RY8	53	.	NM_178129	exon2	c.T368G	p.L123R	ACCCCCAGGAAGC	.	PASS	Atlas-SNP
FAM135B	51059	hgsc.bcm.edu	37	8	139160926	139160926	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49.0	13.0	41.0	0.0	0.265306	0	.	.	none	.	FAM135B	423	.	NM_015912	exon14	c.T3285C	p.F1095F	CTGATAAAAACTG	.	PASS	Atlas-SNP
RTN4RL1	146760	hgsc.bcm.edu	37	17	1840732	1840732	+	Silent	SNP	G	G	A	rs372962204		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76.0	38.0	66.0	0.0	0.5	0	.	.	weak	.	RTN4RL1	21	.	NM_178568	exon2	c.C384T	p.H128H	GAGGGCGTGAAGC	.	PASS	Atlas-SNP
MAP1B	4131	hgsc.bcm.edu	37	5	71491950	71491950	+	Missense_Mutation	SNP	T	T	C	rs143194383	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83.0	49.0	74.0	0.0	0.590361	0	T|1.000;C|0.000	0.000	strong	.	MAP1B	243	.	NM_005909	exon5	c.T2768C	p.I923T	ACGACATTGAAAA	.	PASS	Atlas-SNP
KCNJ2	3759	hgsc.bcm.edu	37	17	68171425	68171425	+	Missense_Mutation	SNP	G	G	A	rs199473653		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	306.0	85.0	285.0	0.0	0.277778	0	.	.	weak	.	KCNJ2	74	.	NM_000891	exon2	c.G245A	p.R82Q	GCTGGCGGTGGAT	.	PASS	Atlas-SNP
ENTPD1	953	hgsc.bcm.edu	37	10	97471746	97471746	+	Silent	SNP	G	G	A	rs200247284	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76.0	33.0	64.0	0.0	0.434211	0	G|0.994;A|0.006	0.006	strong	.	ENTPD1	44	.	NM_001098175	exon1	c.G33A	p.Q11Q	CCAGCAGAAGGGT	.	PASS	Atlas-SNP
NBR1	4077	hgsc.bcm.edu	37	17	41342737	41342737	+	Silent	SNP	G	G	A	rs200554551	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107.0	48.0	124.0	0.0	0.448598	0	G|0.997;A|0.003	0.003	strong	.	NBR1	55	.	NM_031862	exon9	c.G807A	p.P269P	TGAACCGTTCTGT	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	29543736	29543736	+	Missense_Mutation	SNP	A	A	G	rs35093491	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97.0	48.0	80.0	0.0	0.494845	0	A|0.973;G|0.027	0.027	strong	.	ALK	533	.	NM_004304	exon7	c.T1427C	p.V476A	AAACCCACAGGCA	.	PASS	Atlas-SNP
ACOT4	122970	hgsc.bcm.edu	37	14	74061757	74061757	+	Missense_Mutation	SNP	A	A	G	rs141714008		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122.0	59.0	153.0	0.0	0.483607	0	A|1.000;G|0.000	0.000	weak	.	ACOT4	25	.	NM_152331	exon3	c.A665G	p.K222R	AGGTAAAAGGCCC	.	PASS	Atlas-SNP
NELL1	4745	hgsc.bcm.edu	37	11	20939776	20939776	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96.0	20.0	90.0	0.0	0.208333	0	.	.	none	.	NELL1	179	.	NM_006157	exon6	c.A652T	p.T218S	TATATAACACAGT	.	PASS	Atlas-SNP
CACFD1	11094	hgsc.bcm.edu	37	9	136333487	136333487	+	Missense_Mutation	SNP	G	G	A	rs3094381	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	6.0	5.0	5.0	0.0	0.833333	0	G|0.912;A|0.088	0.088	strong	.	CACFD1	1	.	NM_001242369	exon5	c.G454A	p.A152T	TCCTTCGCAGCCC	.	PASS	Atlas-SNP
NOP9	161424	hgsc.bcm.edu	37	14	24772965	24772965	+	Silent	SNP	C	C	A	rs116960868	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111.0	56.0	112.0	0.0	0.504505	0	C|0.990;A|0.010	0.010	strong	C14orf21,colon,carcinoma,-2,1	.	.	1	NM_174913	exon7	c.C1312A	p.R438R	TCATCCCGGCAAG	.	PASS	Atlas-SNP
RSPH6A	81492	hgsc.bcm.edu	37	19	46313918	46313918	+	Silent	SNP	C	C	G	rs141102105	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64.0	33.0	93.0	0.0	0.515625	0	C|0.997;G|0.003	0.003	strong	RSPH6A,NS,carcinoma,-2,1	RSPH6A	70	1	NM_030785	exon2	c.G831C	p.A277A	GAACAGCGCCTTC	.	PASS	Atlas-SNP
LMX1A	4009	hgsc.bcm.edu	37	1	165322487	165322487	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38.0	11.0	36.0	0.0	0.289474	0	.	.	none	.	LMX1A	87	.	NM_001174069	exon3	c.G89T	p.S30I	TTGGGGCTCACCG	.	PASS	Atlas-SNP
TFEC	22797	hgsc.bcm.edu	37	7	115580893	115580893	+	Silent	SNP	G	G	A	rs34298819	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147.0	70.0	153.0	0.0	0.47619	0	G|0.988;A|0.012	0.012	strong	.	TFEC	51	.	NM_012252	exon8	c.C756T	p.S252S	AGGATGGCTCTGC	.	PASS	Atlas-SNP
PEG3	5178	hgsc.bcm.edu	37	19	57335959	57335959	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135.0	35.0	140.0	0.0	0.259259	0	.	.	none	.	PEG3	414	.	NM_001146184	exon3	c.A65G	p.E22G	TCTAGCTCATACA	.	PASS	Atlas-SNP
HIST2H2AC	8338	hgsc.bcm.edu	37	1	149858806	149858806	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	209.0	11.0	211.0	0.0	0.0526316	0	.	.	none	HIST2H2AC,NS,carcinoma,0,3	HIST2H2AC	75	3	NM_003517	exon1	c.G282A	p.L94L	GGAACTGAACAAG	.	PASS	Atlas-SNP
C10orf137	26098	hgsc.bcm.edu	37	10	127412393	127412393	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102.0	17.0	113.0	0.0	0.166667	0	.	.	none	.	C10orf137	153	.	NM_015608	exon4	c.T398C	p.L133P	AAAAACTCCTGAA	.	PASS	Atlas-SNP
NT5C1B	93034	hgsc.bcm.edu	37	2	18767638	18767638	+	Missense_Mutation	SNP	A	A	G	rs147855918	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130.0	59.0	113.0	0.0	0.453846	0	A|0.997;G|0.003	0.003	strong	.	NT5C1B	72	.	NM_001199087	exon4	c.T371C	p.L124P	TTCCGCAGTGATG	.	PASS	Atlas-SNP
ZEB2	9839	hgsc.bcm.edu	37	2	145274844	145274844	+	Splice_Site	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50.0	27.0	56.0	0.0	0.54	0	.	.	none	ZEB2,NS,NS,0,1	ZEB2	218	1	NM_001171653	exon3	c.73+1G>A	.	TTCTTACCGTTTT	.	PASS	Atlas-SNP
PCDH9	5101	hgsc.bcm.edu	37	13	67802190	67802190	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154.0	54.0	103.0	0.0	0.350649	0	.	.	none	.	PCDH9	252	.	NM_203487	exon2	c.T383A	p.I128K	ATTTTTATTTTGA	.	PASS	Atlas-SNP
NUP62	23636	hgsc.bcm.edu	37	19	50412396	50412396	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85.0	39.0	66.0	0.0	0.458824	0	.	.	none	NUP62,NS,carcinoma,0,2	NUP62	50	2	NM_153719	exon3	c.G669A	p.A223A	TATTGACGCAAAG	.	PASS	Atlas-SNP
GRIN2A	2903	hgsc.bcm.edu	37	16	9857231	9857231	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86.0	32.0	99.0	0.0	0.372093	0	.	.	none	GRIN2A,colon,carcinoma,0,1	GRIN2A	366	1	NM_001134408	exon14	c.G3827A	p.R1276H	TGGCAACGAGTGT	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151165641	151165641	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	201.0	11.0	197.0	0.0	0.0547264	0	.	.	none	.	IGSF10	279	.	NM_178822	exon4	c.A2128C	p.K710Q	TGTGTTTTCCAAC	.	PASS	Atlas-SNP
KRTAP19-5	337972	hgsc.bcm.edu	37	21	31874241	31874241	+	Silent	SNP	G	G	T	rs150340950	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66.0	23.0	57.0	0.0	0.348485	0	G|0.975;T|0.025	0.025	strong	KRTAP19-5,NS,carcinoma,-2,1	KRTAP19-5	32	1	NM_181611	exon1	c.C168A	p.R56R	GCAGCTGCGGTAT	.	PASS	Atlas-SNP
POM121L2	94026	hgsc.bcm.edu	37	6	27278340	27278340	+	Missense_Mutation	SNP	A	A	G	rs147268352	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110.0	24.0	79.0	0.0	0.218182	0	A|0.999;G|0.001	0.001	strong	.	POM121L2	61	.	NM_033482	exon1	c.T1610C	p.I537T	CCCAAAATCGGTT	.	PASS	Atlas-SNP
CCDC15	80071	hgsc.bcm.edu	37	11	124857192	124857192	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137.0	20.0	138.0	0.0	0.145985	0	.	.	none	.	CCDC15	134	.	NM_025004	exon8	c.A1070C	p.K357T	GTGTTAAGCCAGA	.	PASS	Atlas-SNP
FAIM3	9214	hgsc.bcm.edu	37	1	207078467	207078467	+	Missense_Mutation	SNP	G	G	A	rs41304091	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64.0	23.0	65.0	0.0	0.359375	0	G|0.992;A|0.008	0.008	strong	.	FAIM3	36	.	NM_005449	exon8	c.C1070T	p.A357V	GATGGGGCATGGA	.	PASS	Atlas-SNP
SLC22A11	55867	hgsc.bcm.edu	37	11	64337280	64337280	+	Silent	SNP	G	G	A	rs34836439	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44.0	20.0	38.0	0.0	0.454545	0	G|0.996;A|0.004	0.004	strong	.	SLC22A11	54	.	NM_018484	exon9	c.G1539A	p.P513P	CCTCCCGGAGACC	.	PASS	Atlas-SNP
COL4A2	1284	hgsc.bcm.edu	37	13	111102770	111102770	+	Silent	SNP	C	C	T	rs78615289	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18.0	8.0	28.0	0.0	0.444444	0	C|0.984;T|0.016	0.016	strong	.	COL4A2	178	.	NM_001846	exon20	c.C1308T	p.P436P	AGGACCCCCCGGG	.	PASS	Atlas-SNP
MRPS12	6183	hgsc.bcm.edu	37	19	39421979	39421979	+	Silent	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94.0	27.0	84.0	0.0	0.287234	0	.	.	none	.	MRPS12	11	.	NM_033362	exon2	c.T45G	p.T15T	CCTAACTTGTGGT	.	PASS	Atlas-SNP
WBSCR17	64409	hgsc.bcm.edu	37	7	71177023	71177023	+	Silent	SNP	G	G	A	rs75947590	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58.0	28.0	57.0	0.0	0.482759	0	G|0.998;A|0.002	0.002	strong	.	WBSCR17	208	.	NM_022479	exon11	c.G1689A	p.K563K	GAACAAGGGCACG	.	PASS	Atlas-SNP
PRSS36	146547	hgsc.bcm.edu	37	16	31152818	31152818	+	Missense_Mutation	SNP	C	C	T	rs117442264	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32.0	12.0	25.0	0.0	0.375	0	C|0.990;T|0.010	0.010	strong	.	PRSS36	50	.	NM_001258291	exon12	c.G1873A	p.V625I	CCAGGACCCAGCC	.	PASS	Atlas-SNP
OGFR	11054	hgsc.bcm.edu	37	20	61444660	61444660	+	Missense_Mutation	SNP	C	C	A	rs61743079	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	8.0	3.0	4.0	0.0	0.375	0	C|0.981;A|0.019	0.019	weak	OGFR,NS,neuroblastoma,0,1	OGFR	63	1	NM_007346	exon7	c.C1693A	p.R565S	GGCCCCCGCCCGG	.	scavenged	Atlas-SNP
RAB21	23011	hgsc.bcm.edu	37	12	72148943	72148943	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	11.0	9.0	0.0	0.0	0.818182	.	.	.	none	.	RAB21	17	.	NM_014999	exon1	c.G34A	p.A12T	GGGGCGGCGGCGG	.	PASS	Atlas-SNP
JAKMIP1	152789	hgsc.bcm.edu	37	4	6062160	6062160	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83.0	29.0	92.0	0.0	0.349398	0	.	.	none	.	JAKMIP1	250	.	NM_001099433	exon11	c.G1635A	p.E545E	TCCCTTCTCAACC	.	PASS	Atlas-SNP
KCNH7	90134	hgsc.bcm.edu	37	2	163228507	163228507	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77.0	33.0	117.0	0.0	0.428571	0	.	.	none	KCNH7,NS,carcinoma,0,1	KCNH7	378	1	NM_033272	exon16	c.T3423G	p.T1141T	AAGTGAAGTCAAG	.	PASS	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62194238	62194238	+	Silent	SNP	C	C	T	rs34996572	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70.0	33.0	67.0	0.0	0.471429	0	C|0.984;T|0.016	0.016	strong	.	.	.	.	NM_001037335	exon9	c.G5937A	p.P1979P	CCCCTGCGGCGTC	.	PASS	Atlas-SNP
SMYD1	150572	hgsc.bcm.edu	37	2	88387508	88387508	+	Silent	SNP	C	C	A	rs113636517	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191.0	132.0	239.0	1.0	0.691099	0.0041841	C|0.995;A|0.005	0.005	strong	.	SMYD1	95	.	NM_198274	exon3	c.C442A	p.R148R	GACCTGCGGGTGG	.	PASS	Atlas-SNP
RBM44	375316	hgsc.bcm.edu	37	2	238725962	238725962	+	Missense_Mutation	SNP	G	G	A	rs182474506	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99.0	44.0	103.0	0.0	0.444444	0	G|0.999;A|0.001	0.001	strong	.	RBM44	167	.	NM_001080504	exon3	c.G403A	p.D135N	GAATTAGATCCTG	.	PASS	Atlas-SNP
DDX51	317781	hgsc.bcm.edu	37	12	132625027	132625027	+	Silent	SNP	G	G	A	rs61942919	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84.0	32.0	87.0	0.0	0.380952	0	G|0.995;A|0.005	0.005	strong	DDX51,NS,carcinoma,-1,1	DDX51	33	1	NM_175066	exon11	c.C1614T	p.R538R	CCCGTAGCGCGAG	.	PASS	Atlas-SNP
ZNF131	7690	hgsc.bcm.edu	37	5	43173541	43173541	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85.0	38.0	87.0	0.0	0.447059	0	.	.	none	.	ZNF131	51	.	NM_003432	exon7	c.C1074T	p.Y358Y	GCTCTACGAATGC	.	PASS	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101804366	101804366	+	Missense_Mutation	SNP	T	T	C	rs35901514	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67.0	37.0	54.0	0.0	0.552239	0	T|0.993;C|0.007	0.007	strong	.	COL15A1	211	.	NM_001855	exon24	c.T2551C	p.F851L	CCTGGCTTTCCAG	.	PASS	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	37	7	2983886	2983886	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	199.0	88.0	174.0	0.0	0.442211	0	.	.	none	CARD11,colon,carcinoma,-1,6	CARD11	339	6	NM_032415	exon5	c.A644T	p.K215M	ATGTTCTTCTCCT	.	PASS	Atlas-SNP
USP13	8975	hgsc.bcm.edu	37	3	179424788	179424788	+	Missense_Mutation	SNP	T	T	C	rs141550831	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150.0	89.0	157.0	0.0	0.593333	0	T|0.999;C|0.001	0.001	strong	USP13,NS,carcinoma,-1,1	USP13	117	1	NM_003940	exon5	c.T544C	p.W182R	GACACGTGGGAAA	.	PASS	Atlas-SNP
SEL1L2	80343	hgsc.bcm.edu	37	20	13912308	13912308	+	Missense_Mutation	SNP	C	C	T	rs143129534	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108.0	40.0	98.0	1.0	0.37037	0.0102041	C|0.988;T|0.012	0.012	strong	SEL1L2,colon,carcinoma,-1,1	SEL1L2	103	1	NM_001271539	exon3	c.G224A	p.R75H	ATTTTACGTTGAT	.	scavenged	Atlas-SNP
ARHGAP18	93663	hgsc.bcm.edu	37	6	129929191	129929191	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38.0	9.0	25.0	0.0	0.236842	0	.	.	none	.	ARHGAP18	52	.	NM_033515	exon9	c.T1129G	p.C377G	CTTGGCAAAGATT	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45120282	45120282	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115.0	74.0	131.0	0.0	0.643478	0	.	.	none	.	NACAD	44	.	NM_001146334	exon7	c.G4631A	p.R1544Q	AGAGCCCGCACGG	.	PASS	Atlas-SNP
PARP11	57097	hgsc.bcm.edu	37	12	3931308	3931308	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93.0	12.0	87.0	0.0	0.129032	0	.	.	none	.	PARP11	39	.	NM_020367	exon5	c.C360T	p.N120N	GGCCTCGTTTTCA	.	PASS	Atlas-SNP
ENPP2	5168	hgsc.bcm.edu	37	8	120569823	120569823	+	Missense_Mutation	SNP	G	G	A	rs61738778	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106.0	51.0	120.0	0.0	0.481132	0	G|0.996;A|0.004	0.004	strong	.	ENPP2	254	.	NM_006209	exon26	c.C2686T	p.R896C	AGCTGCGGCTGGT	.	PASS	Atlas-SNP
ETFB	2109	hgsc.bcm.edu	37	19	51857774	51857774	+	Missense_Mutation	SNP	T	T	G	rs143144671	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71.0	42.0	67.0	0.0	0.591549	0	T|0.998;G|0.002	0.002	strong	.	ETFB	46	.	NM_001014763	exon1	c.A119C	p.E40A	AGCCATTCCTGGG	.	PASS	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	96030957	96030957	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95.0	27.0	116.0	0.0	0.284211	0	.	.	none	.	WNK2	277	.	NM_006648	exon18	c.A3962G	p.H1321R	CTGAGCACCCCGC	.	PASS	Atlas-SNP
OTC	5009	hgsc.bcm.edu	37	X	38262964	38262964	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59.0	18.0	47.0	0.0	0.305085	0	.	.	none	.	OTC	60	.	NM_000531	exon6	c.G634A	p.G212R	AAATTCGGAATGC	.	PASS	Atlas-SNP
LTB	4050	hgsc.bcm.edu	37	6	31549604	31549604	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80.0	27.0	69.0	0.0	0.3375	0	.	.	none	.	LTB	19	.	NM_002341	exon2	c.C195T	p.A65A	TTGCTGGGCCTGT	.	PASS	Atlas-SNP
CHST1	8534	hgsc.bcm.edu	37	11	45671241	45671241	+	Silent	SNP	C	C	G	rs7115779	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25.0	11.0	27.0	0.0	0.44	0	C|0.989;G|0.011	0.011	strong	CHST1,colon,adenoma,0,1	CHST1	81	1	NM_003654	exon4	c.G1233C	p.S411S	GGGTCACGAGAAG	.	PASS	Atlas-SNP
MRPL38	64978	hgsc.bcm.edu	37	17	73895744	73895744	+	Missense_Mutation	SNP	G	G	A	rs1128878	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57.0	21.0	54.0	0.0	0.368421	0	G|0.999;A|0.001	0.001	strong	.	MRPL38	26	.	NM_032478	exon7	c.C722T	p.P241L	TTACCCGGGATGT	.	PASS	Atlas-SNP
LEPR	3953	hgsc.bcm.edu	37	1	66102617	66102617	+	Silent	SNP	A	A	G	rs61781316	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44.0	17.0	71.0	0.0	0.386364	0	A|0.997;G|0.003	0.003	strong	.	LEPR	284	.	NM_002303	exon20	c.A3417G	p.A1139A	TTTTGCATCTTAC	.	PASS	Atlas-SNP
OR8G2	26492	hgsc.bcm.edu	37	11	124096271	124096271	+	Missense_Mutation	SNP	A	A	G	rs201854907	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	201.0	16.0	175.0	0.0	0.079602	0	A|0.996;G|0.005	0.005	strong	.	.	.	.	NM_001007249	exon1	c.A874G	p.T292A	TTTTATACTATTG	.	PASS	Atlas-SNP
ACTN1	87	hgsc.bcm.edu	37	14	69341653	69341653	+	Missense_Mutation	SNP	T	T	A	rs11557769	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46.0	25.0	66.0	0.0	0.543478	0	T|0.988;A|0.012	0.012	strong	ACTN1,NS,carcinoma,+2,1	ACTN1	77	1	NM_001130004	exon22	c.A2668T	p.T890S	GGCCGGTGTAGGG	.	PASS	Atlas-SNP
CD83	9308	hgsc.bcm.edu	37	6	14118297	14118297	+	Splice_Site	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32.0	10.0	29.0	0.0	0.3125	0	.	.	none	.	CD83	23	.	NM_001040280	exon2	c.153+1G>A	.	GTCAAGGTAGGTG	.	PASS	Atlas-SNP
NOP9	161424	hgsc.bcm.edu	37	14	24771172	24771172	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58.0	11.0	75.0	0.0	0.189655	0	.	.	none	.	.	.	.	NM_174913	exon4	c.G810A	p.V270V	CACAGTGTTTATC	.	PASS	Atlas-SNP
DUSP2	1844	hgsc.bcm.edu	37	2	96810556	96810556	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76.0	9.0	92.0	0.0	0.118421	0	.	.	none	DUSP2,NS,carcinoma,+2,1	DUSP2	20	1	NM_004418	exon2	c.C454T	p.P152S	TTGGCGGCAGCGC	.	PASS	Atlas-SNP
CYP3A4	1576	hgsc.bcm.edu	37	7	99358595	99358595	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	261.0	110.0	287.0	1.0	0.421456	0.00348432	.	.	none	.	CYP3A4	56	.	NM_017460	exon12	c.G1263A	p.K421K	GTTCTTCTTGCTG	.	PASS	Atlas-SNP
WDTC1	23038	hgsc.bcm.edu	37	1	27631526	27631526	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58.0	33.0	42.0	0.0	0.568965	0	.	.	none	.	WDTC1	69	.	NM_001276252	exon15	c.G1678A	p.G560S	GACGATGGCTCCT	.	PASS	Atlas-SNP
SLFN11	91607	hgsc.bcm.edu	37	17	33680127	33680127	+	Missense_Mutation	SNP	T	T	C	rs143643982	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47.0	26.0	43.0	0.0	0.553191	0	T|0.999;C|0.001	0.001	strong	.	SLFN11	112	.	NM_152270	exon5	c.A1954G	p.K652E	AAGTTTTCCGGGT	.	PASS	Atlas-SNP
FAF2	23197	hgsc.bcm.edu	37	5	175926010	175926010	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55.0	22.0	43.0	0.0	0.4	0	.	.	none	.	FAF2	38	.	NM_014613	exon9	c.G935A	p.R312Q	AGAAACGGGAGGA	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	3253868	3253868	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97.0	28.0	61.0	0.0	0.28866	0	.	.	none	.	CSMD1	1469	.	NM_033225	exon17	c.T2441A	p.V814D	TCTCTGACCTCCA	.	PASS	Atlas-SNP
PRSS58	136541	hgsc.bcm.edu	37	7	141955390	141955390	+	Silent	SNP	C	C	T	rs145731516	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109.0	47.0	101.0	0.0	0.431193	0	C|0.994;T|0.006	0.006	strong	.	PRSS58	41	.	NM_001001317	exon3	c.G144A	p.P48P	CCAAAGCGGGTGG	.	PASS	Atlas-SNP
LYRM7	90624	hgsc.bcm.edu	37	5	130515811	130515811	+	Silent	SNP	G	G	A	rs113642581	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48.0	23.0	54.0	0.0	0.479167	0	A|0.027;C|0.000;G|0.973	0.027	strong	.	LYRM7	7	.	NM_181705	exon2	c.G42A	p.L14L	AACACTGCACAGG	.	PASS	Atlas-SNP
OR7A10	390892	hgsc.bcm.edu	37	19	14952301	14952301	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100.0	49.0	88.0	0.0	0.49	0	.	.	none	.	OR7A10	33	.	NM_001005190	exon1	c.T389G	p.L130R	TAGTGCAGAGGGT	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44065109	44065109	+	Missense_Mutation	SNP	C	C	T	rs373848470		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60.0	30.0	58.0	0.0	0.5	0	.	.	weak	.	LOXHD1	367	.	NM_144612	exon38	c.G5869A	p.E1957K	CGATCTCGTAGGC	.	PASS	Atlas-SNP
SERBP1	26135	hgsc.bcm.edu	37	1	67895779	67895779	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110.0	39.0	127.0	0.0	0.354545	0	.	.	none	.	SERBP1	31	.	NM_001018067	exon1	c.C205T	p.Q69X	GCAGCTGTTTGCC	.	PASS	Atlas-SNP
COL9A3	1299	hgsc.bcm.edu	37	20	61452556	61452556	+	Silent	SNP	G	G	A	rs149690829	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51.0	27.0	61.0	0.0	0.529412	0	G|1.000;A|0.000	0.000	strong	.	COL9A3	70	.	NM_001853	exon6	c.G333A	p.P111P	GGGGCCGCCCGGG	.	PASS	Atlas-SNP
ADAMTS12	81792	hgsc.bcm.edu	37	5	33614391	33614391	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104.0	10.0	111.0	0.0	0.0961538	0	.	.	none	.	ADAMTS12	464	.	NM_030955	exon16	c.T2479A	p.F827I	GCCAGAAGTACAT	.	PASS	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2224449	2224449	+	Missense_Mutation	SNP	G	G	A	rs34534613	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34.0	17.0	34.0	0.0	0.5	0	G|0.997;A|0.003	0.003	strong	.	CACNA1C	1023	.	NM_001129831	exon2	c.G109A	p.G37R	GCAGCGGGGCTGG	.	PASS	Atlas-SNP
SLC22A15	55356	hgsc.bcm.edu	37	1	116577849	116577849	+	Missense_Mutation	SNP	C	C	T	rs201564754	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	247.0	64.0	245.0	0.0	0.259109	0	C|1.000;T|0.000	0.000	strong	.	SLC22A15	65	.	NM_018420	exon7	c.C986T	p.A329V	TGAGTGCGGGTGA	.	PASS	Atlas-SNP
DIP2A	23181	hgsc.bcm.edu	37	21	47971585	47971585	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95.0	32.0	66.0	0.0	0.336842	0	.	.	none	.	DIP2A	332	.	NM_015151	exon24	c.G2878T	p.A960S	CTGGTTGCTGGGA	.	PASS	Atlas-SNP
KIF1A	547	hgsc.bcm.edu	37	2	241710437	241710437	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63.0	15.0	45.0	0.0	0.238095	0	.	.	none	.	KIF1A	152	.	NM_001244008	exon15	c.A1292G	p.E431G	ATGCGCTCGTGGA	.	PASS	Atlas-SNP
SPATC1	375686	hgsc.bcm.edu	37	8	145095768	145095768	+	Missense_Mutation	SNP	C	C	T	rs150277218	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64.0	30.0	58.0	0.0	0.46875	0	C|0.999;T|0.001	0.001	strong	.	SPATC1	77	.	NM_001134374	exon3	c.C1066T	p.H356Y	ACCACCCACATCG	.	PASS	Atlas-SNP
CXorf58	254158	hgsc.bcm.edu	37	X	23933912	23933912	+	Splice_Site	SNP	G	G	A	rs62584865	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110.0	40.0	77.0	0.0	0.363636	0	G|0.991;A|0.009	0.009	strong	.	CXorf58	53	.	NM_001169574	exon4	c.311+1G>A	.	ATTCAGGTAATGT	.	PASS	Atlas-SNP
RANBP17	64901	hgsc.bcm.edu	37	5	170338066	170338066	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171.0	41.0	143.0	0.0	0.239766	0	.	.	none	.	RANBP17	108	.	NM_022897	exon7	c.T688G	p.F230V	TTTGACTTCATTG	.	PASS	Atlas-SNP
PRRC2A	7916	hgsc.bcm.edu	37	6	31603046	31603046	+	Silent	SNP	C	C	T	rs139053368	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105.0	19.0	114.0	0.0	0.180952	0	C|0.999;T|0.001	0.001	strong	.	PRRC2A	152	.	NM_004638	exon22	c.C5298T	p.D1766D	TAGTGACAAGGTC	.	PASS	Atlas-SNP
COL8A1	1295	hgsc.bcm.edu	37	3	99513830	99513830	+	Missense_Mutation	SNP	G	G	A	rs139380413	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39.0	20.0	50.0	0.0	0.512821	0	G|0.999;A|0.001	0.001	strong	.	COL8A1	68	.	NM_001850	exon5	c.G1085A	p.R362Q	GTGACCGGGGCAT	.	PASS	Atlas-SNP
TNFRSF13B	23495	hgsc.bcm.edu	37	17	16843666	16843666	+	Missense_Mutation	SNP	C	C	T	rs104894649	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	32.0	46.0	0.0	0.52459	0	C|0.999;T|0.001	0.001	strong	.	TNFRSF13B	34	.	NM_012452	exon4	c.G605A	p.R202H	CTTTGACGGGGCC	.	PASS	Atlas-SNP
CUTA	51596	hgsc.bcm.edu	37	6	33384473	33384473	+	Missense_Mutation	SNP	C	C	T	rs41267649	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173.0	142.0	183.0	0.0	0.820809	0	C|0.986;T|0.014	0.014	strong	.	CUTA	5	.	NM_001014433	exon6	c.G551A	p.R184H	ACCTGGCGCACCC	.	PASS	Atlas-SNP
RIN2	54453	hgsc.bcm.edu	37	20	19937289	19937289	+	Silent	SNP	C	C	T	rs368413043		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66.0	33.0	55.0	0.0	0.5	0	.	.	weak	.	RIN2	126	.	NM_001242581	exon4	c.C336T	p.S112S	CTATTCCGAGGAA	.	PASS	Atlas-SNP
KCNU1	157855	hgsc.bcm.edu	37	8	36664917	36664917	+	Missense_Mutation	SNP	G	G	A	rs180964986	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	18.0	100.0	0.0	0.246575	0	G|1.000;A|0.000	0.000	strong	KCNU1,NS,carcinoma,0,1	KCNU1	359	1	NM_001031836	exon6	c.G605A	p.R202H	CCTTGCGCCTGCT	.	PASS	Atlas-SNP
UBR2	23304	hgsc.bcm.edu	37	6	42613298	42613298	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47.0	20.0	45.0	0.0	0.425532	0	.	.	none	.	UBR2	134	.	NM_015255	exon21	c.T2379C	p.H793H	GGCTCATAGTGAA	.	PASS	Atlas-SNP
ATAD2	29028	hgsc.bcm.edu	37	8	124357253	124357253	+	Silent	SNP	G	G	A	rs16898247	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91.0	40.0	69.0	0.0	0.43956	0	G|0.843;A|0.157	0.157	strong	ATAD2,NS,carcinoma,-2,1	ATAD2	160	1	NM_014109	exon19	c.C2589T	p.H863H	CCACACGTGGATA	.	PASS	Atlas-SNP
ZBTB24	9841	hgsc.bcm.edu	37	6	109796673	109796673	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74.0	4.0	82.0	0.0	0.0540541	0	.	.	none	.	ZBTB24	64	.	NM_014797	exon5	c.C1217T	p.P406L	CATTCCGGTAATG	.	PASS	Atlas-SNP
DNAH7	56171	hgsc.bcm.edu	37	2	196825256	196825256	+	Silent	SNP	G	G	C	rs115124743	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128.0	80.0	106.0	0.0	0.625	0	G|0.969;C|0.031	0.031	strong	.	DNAH7	512	.	NM_018897	exon18	c.C2619G	p.V873V	AGAGGAGACTGTG	.	PASS	Atlas-SNP
VIL1	7429	hgsc.bcm.edu	37	2	219313993	219313993	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101.0	48.0	119.0	0.0	0.475248	0	.	.	none	.	VIL1	65	.	NM_007127	exon20	c.A2418C	p.P806P	GACTCCAGCTGCC	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144943223	144943223	+	Missense_Mutation	SNP	T	T	C	rs139952490	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50.0	20.0	36.0	0.0	0.4	0	T|0.995;C|0.005	0.005	strong	.	EPPK1	199	.	NM_031308	exon1	c.A4199G	p.N1400S	AACTTGTTGTCCT	.	PASS	Atlas-SNP
ACVR1C	130399	hgsc.bcm.edu	37	2	158412701	158412701	+	Missense_Mutation	SNP	T	T	G	rs55920843	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134.0	33.0	146.0	0.0	0.246269	0	T|0.993;G|0.007	0.007	strong	.	ACVR1C	85	.	NM_145259	exon3	c.A448C	p.N150H	CCACATTTGGTCT	.	PASS	Atlas-SNP
SNX5	27131	hgsc.bcm.edu	37	20	17933265	17933265	+	Missense_Mutation	SNP	C	C	T	rs145056868	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55.0	30.0	77.0	0.0	0.545455	0	C|1.000;T|0.000	0.000	strong	.	SNX5	38	.	NM_014426	exon5	c.G479A	p.R160H	AAGTTGCGATCTT	.	PASS	Atlas-SNP
SLC4A5	57835	hgsc.bcm.edu	37	2	74450058	74450058	+	Missense_Mutation	SNP	C	C	T	rs36081793	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82.0	47.0	104.0	0.0	0.573171	0	C|0.977;T|0.023	0.023	strong	.	SLC4A5	215	.	NM_021196	exon25	c.G3316A	p.V1106I	TTATAACCGAGGG	.	PASS	Atlas-SNP
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651150	1651150	+	Missense_Mutation	SNP	G	G	A	rs201376522	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55.0	38.0	56.0	0.0	0.690909	0	.	.	weak	KRTAP5-5,right_upper_lobe,carcinoma,-1,2	KRTAP5-5	86	2	NM_001001480	exon1	c.G80A	p.G27D	GCTCCGGCTGTGG	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46761565	46761565	+	Silent	SNP	G	G	C	rs34184256	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87.0	29.0	103.0	0.0	0.333333	0	G|0.992;C|0.008	0.008	strong	.	CELSR1	242	.	NM_014246	exon31	c.C8322G	p.L2774L	CACGCCGAGCTTC	.	PASS	Atlas-SNP
EPHB6	2051	hgsc.bcm.edu	37	7	142561786	142561786	+	Silent	SNP	T	T	C	rs56300555	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143.0	73.0	171.0	0.0	0.51049	0	T|0.990;C|0.010	0.010	strong	.	EPHB6	168	.	NM_004445	exon7	c.T228C	p.H76H	ATGTCATGTGGCA	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38883000	38883000	+	Silent	SNP	C	C	T	rs150857304	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103.0	79.0	89.0	0.0	0.76699	0	C|0.998;T|0.002	0.002	strong	.	DNAH8	1239	.	NM_001206927	exon68	c.C9987T	p.S3329S	AGTAAGCGCTCAG	.	PASS	Atlas-SNP
BIVM-ERCC5	0	hgsc.bcm.edu	37	13	103460019	103460019	+	Silent	SNP	G	G	A	rs111947510	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66.0	21.0	89.0	0.0	0.318182	0	G|0.991;A|0.009	0.009	strong	.	.	.	.	NM_001204425	exon1	c.G402A	p.L134L	CAGCCTGGGCAAG	.	PASS	Atlas-SNP
SERBP1	26135	hgsc.bcm.edu	37	1	67895758	67895758	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149.0	50.0	169.0	0.0	0.33557	0	.	.	none	.	SERBP1	31	.	NM_001018067	exon1	c.A226C	p.K76Q	GGTCTTTCTGGGA	.	PASS	Atlas-SNP
CARHSP1	23589	hgsc.bcm.edu	37	16	8953030	8953030	+	Silent	SNP	C	C	T	rs2231706	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141.0	63.0	124.0	0.0	0.446809	0	C|0.989;T|0.011	0.011	strong	.	CARHSP1	12	.	NM_001042476	exon2	c.G156A	p.S52S	TCACGCCGAGAAG	.	PASS	Atlas-SNP
GATA2	2624	hgsc.bcm.edu	37	3	128204641	128204641	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102.0	31.0	94.0	0.0	0.303922	0	.	.	none	.	GATA2	122	.	NM_001145662	exon3	c.C800A	p.P267H	CCTCCGGGGTGGA	.	PASS	Atlas-SNP
SLC44A3	126969	hgsc.bcm.edu	37	1	95330440	95330440	+	Silent	SNP	C	C	T	rs142406496	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99.0	51.0	83.0	0.0	0.515152	0	C|0.996;T|0.004	0.004	strong	.	SLC44A3	109	.	NM_001114106	exon11	c.C1380T	p.N460N	GCAAAACGCACTG	.	PASS	Atlas-SNP
PROC	5624	hgsc.bcm.edu	37	2	128178900	128178900	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127.0	47.0	202.0	0.0	0.370079	0	.	.	none	PROC,colon,carcinoma,-1,1	PROC	31	1	NM_000312	exon3	c.C112T	p.R38W	GTGCTGCGGATCC	.	PASS	Atlas-SNP
ELP3	55140	hgsc.bcm.edu	37	8	27957438	27957438	+	Silent	SNP	C	C	T	rs200001470	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65.0	27.0	60.0	0.0	0.415385	0	C|1.000;T|0.000	0.000	strong	.	ELP3	36	.	NM_018091	exon3	c.C213T	p.V71V	CAAGGTCTTGATG	.	PASS	Atlas-SNP
PARVB	29780	hgsc.bcm.edu	37	22	44495953	44495953	+	Missense_Mutation	SNP	A	A	G	rs56194750	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66.0	35.0	79.0	0.0	0.530303	0	A|0.997;G|0.003	0.003	strong	.	PARVB	44	.	NM_001003828	exon4	c.A322G	p.M108V	CGCACGATGATTG	.	PASS	Atlas-SNP
NKTR	4820	hgsc.bcm.edu	37	3	42662976	42662976	+	Silent	SNP	A	A	C	rs35419602	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78.0	29.0	67.0	0.0	0.371795	0	A|0.988;C|0.012	0.012	strong	.	NKTR	116	.	NM_005385	exon6	c.A342C	p.R114R	AAATCGAGGGAAA	.	PASS	Atlas-SNP
COL24A1	255631	hgsc.bcm.edu	37	1	86488270	86488270	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	166.0	16.0	148.0	0.0	0.0963855	0	.	.	none	.	COL24A1	202	.	NM_152890	exon17	c.A2153C	p.E718A	CCTTGTTCACCCT	.	PASS	Atlas-SNP
B3GNT5	84002	hgsc.bcm.edu	37	3	182987591	182987591	+	Missense_Mutation	SNP	G	G	A	rs115825683	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63.0	26.0	69.0	0.0	0.412698	0	G|0.994;A|0.006	0.006	strong	.	B3GNT5	26	.	NM_032047	exon2	c.G5A	p.R2K	ATATGAGAATGTT	.	PASS	Atlas-SNP
GPD2	2820	hgsc.bcm.edu	37	2	157367399	157367399	+	Silent	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144.0	107.0	199.0	1.0	0.743056	0.00502513	.	.	none	.	GPD2	59	.	NM_001083112	exon4	c.G366T	p.L122L	ATATCTGCAGAAG	.	PASS	Atlas-SNP
CASZ1	54897	hgsc.bcm.edu	37	1	10705018	10705018	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81.0	40.0	103.0	0.0	0.493827	0	.	.	none	.	CASZ1	150	.	NM_001079843	exon18	c.A3824G	p.N1275S	AAGCCATTGGCTG	.	PASS	Atlas-SNP
VCX3B	425054	hgsc.bcm.edu	37	X	8434346	8434346	+	Silent	SNP	G	G	A	rs808146	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	450.0	135.0	326.0	0.0	0.3	0	.	.	weak	.	VCX3B	34	.	NM_001001888	exon3	c.G663A	p.E221E	GGTGGAGGAACCA	.	PASS	Atlas-SNP
YBX1	4904	hgsc.bcm.edu	37	1	43149084	43149084	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104.0	28.0	104.0	0.0	0.269231	0	.	.	none	.	YBX1	49	.	NM_004559	exon2	c.T177C	p.V59V	GAAGGTTTTGGGA	.	PASS	Atlas-SNP
AKAP3	10566	hgsc.bcm.edu	37	12	4735922	4735922	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112.0	30.0	98.0	0.0	0.267857	0	.	.	none	.	AKAP3	212	.	NM_006422	exon4	c.G2146C	p.E716Q	AGCACTCATATAA	.	PASS	Atlas-SNP
DEFB110	245913	hgsc.bcm.edu	37	6	49986738	49986738	+	Silent	SNP	C	C	T	rs115648436	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132.0	65.0	159.0	0.0	0.492424	0	C|0.991;T|0.009	0.009	strong	.	DEFB110	5	.	NM_001037497	exon2	c.G156A	p.R52R	AGCAATCCTAATT	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11009679	11009679	+	Splice_Site	SNP	G	G	A	rs1281013	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51.0	29.0	56.0	0.0	0.568627	0	G|0.907;A|0.093	0.093	strong	.	C1orf127	134	.	NM_001170754	exon12	c.1290+2C>T	.	AGACGTGCTTTGG	.	PASS	Atlas-SNP
LIG4	3981	hgsc.bcm.edu	37	13	108861048	108861048	+	Missense_Mutation	SNP	C	C	T	rs2232642	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79.0	21.0	107.0	0.0	0.265823	0	C|0.958;T|0.042	0.042	strong	.	LIG4	91	.	NM_206937	exon3	c.G2569A	p.A857T	CCTCAGCTAAACA	.	PASS	Atlas-SNP
ATF4	468	hgsc.bcm.edu	37	22	39917561	39917561	+	Silent	SNP	C	C	T	rs375843215		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100.0	45.0	112.0	0.0	0.45	0	.	.	weak	.	ATF4	27	.	NM_001675	exon1	c.C111T	p.Y37Y	TGATTACCTGGAG	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11008102	11008102	+	Missense_Mutation	SNP	G	G	A	rs1281018	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71.0	37.0	64.0	0.0	0.521127	0	G|0.914;A|0.086	0.086	strong	.	C1orf127	134	.	NM_001170754	exon12	c.C2090T	p.A697V	AGGGGCGCTGCCA	.	PASS	Atlas-SNP
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465038	39465038	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118.0	35.0	125.0	0.0	0.29661	0	.	.	none	.	KRTAP16-1	12	.	NM_001146182	exon1	c.T468C	p.P156P	AATAGCAGGCTCA	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73676965	73676965	+	Missense_Mutation	SNP	G	G	A	rs201074268	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	42.0	64.0	0.0	0.688525	0	G|0.998;A|0.002	0.002	strong	.	ALMS1	384	.	NM_015120	exon8	c.G3308A	p.G1103D	AGCCTGGTATTTT	.	PASS	Atlas-SNP
SLC22A18AS	5003	hgsc.bcm.edu	37	11	2909507	2909507	+	Missense_Mutation	SNP	G	G	A	rs146094810	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60.0	33.0	49.0	0.0	0.55	0	G|0.998;A|0.002	0.002	strong	.	SLC22A18AS	7	.	NM_007105	exon4	c.C665T	p.P222L	GGGTTGGGGGGGC	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495169	134495169	+	Missense_Mutation	SNP	G	G	A	rs141028225	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72.0	21.0	80.0	0.0	0.291667	0	G|1.000;C|0.000	.	alt	.	SGK1	387	.	NM_001143676	exon5	c.C487T	p.L163F	TCATAAGCTCAGG	.	PASS	Atlas-SNP
NCAPD2	9918	hgsc.bcm.edu	37	12	6630996	6630996	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66.0	21.0	70.0	0.0	0.318182	0	.	.	none	NCAPD2,NS,carcinoma,0,1	NCAPD2	99	1	NM_014865	exon15	c.C1747T	p.R583W	AATCCCCGGGAGT	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48312084	48312084	+	Missense_Mutation	SNP	G	G	C	rs78575608	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120.0	26.0	164.0	0.0	0.216667	0	G|0.974;C|0.026	0.026	strong	.	ABCA13	1192	.	NM_152701	exon17	c.G2821C	p.V941L	CAAGAAGTTGATA	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495154	134495154	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60.0	12.0	75.0	0.0	0.2	0	.	.	none	SGK1_ENST00000367858,NS,carcinoma,0,5	SGK1	387	5	NM_001143676	exon5	c.C502T	p.P168S	GAGAAGGGTTGGC	.	PASS	Atlas-SNP
CHD1	1105	hgsc.bcm.edu	37	5	98216991	98216991	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183.0	40.0	197.0	0.0	0.218579	0	.	.	none	.	CHD1	137	.	NM_001270	exon20	c.G2956T	p.E986X	GGGGCTCTTGTTC	.	PASS	Atlas-SNP
TMEM219	124446	hgsc.bcm.edu	37	16	29979376	29979376	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95.0	7.0	99.0	0.0	0.0736842	0	.	.	none	.	TMEM219	10	.	NM_001083613	exon4	c.C386T	p.T129I	TTATCACAGCCAG	.	PASS	Atlas-SNP
MLH1	4292	hgsc.bcm.edu	37	3	37053568	37053568	+	Missense_Mutation	SNP	A	A	G	rs1799977	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	38.0	81.0	0.0	0.520548	0	A|0.799;G|0.201	0.201	strong	MLH1,NS,carcinoma,0,1	MLH1	226	1	NM_000249	exon8	c.A655G	p.I219V	CGCTCCATCTTTG	.	PASS	Atlas-SNP
CHMP5	51510	hgsc.bcm.edu	37	9	33266075	33266075	+	Missense_Mutation	SNP	A	A	C	rs146626883	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	29.0	72.0	0.0	0.39726	0	A|0.999;C|0.001	0.001	strong	CHMP5,rectum,carcinoma,-1,1	CHMP5	15	1	NM_016410	exon2	c.A137C	p.K46T	AGTATAAGGATCA	.	PASS	Atlas-SNP
MMP24	10893	hgsc.bcm.edu	37	20	33842284	33842284	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57.0	15.0	72.0	0.0	0.263158	0	.	.	none	.	MMP24	35	.	NM_006690	exon4	c.C544A	p.L182I	GGTGAGCTAGACA	.	PASS	Atlas-SNP
GALNTL6	442117	hgsc.bcm.edu	37	4	173269737	173269737	+	Silent	SNP	T	T	C	rs114177519	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148.0	78.0	111.0	0.0	0.527027	0	T|0.994;C|0.006	0.006	strong	.	GALNTL6	102	.	NM_001034845	exon5	c.T450C	p.N150N	TCATAATGAAGGT	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11008594	11008594	+	Missense_Mutation	SNP	A	A	T	rs1281016	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	159.0	83.0	126.0	0.0	0.522013	0	A|0.922;T|0.078	0.078	strong	.	C1orf127	134	.	NM_001170754	exon12	c.T1598A	p.V533D	CCTGAGACCAGAA	.	PASS	Atlas-SNP
ABCG8	64241	hgsc.bcm.edu	37	2	44073405	44073405	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109.0	26.0	115.0	0.0	0.238532	0	.	.	none	.	ABCG8	98	.	NM_022437	exon3	c.T277C	p.F93L	CTAAGCTTCAAAG	.	PASS	Atlas-SNP
AKAP8L	26993	hgsc.bcm.edu	37	19	15491357	15491357	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93.0	48.0	98.0	0.0	0.516129	0	.	.	none	.	AKAP8L	64	.	NM_014371	exon13	c.A1603G	p.I535V	TGCTGATGAGCTT	.	PASS	Atlas-SNP
C17orf74	201243	hgsc.bcm.edu	37	17	7330307	7330307	+	Missense_Mutation	SNP	C	C	T	rs146528431	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	41.0	77.0	0.0	0.672131	0	C|0.995;T|0.005	0.005	strong	.	C17orf74	56	.	NM_175734	exon3	c.C997T	p.R333W	AACGCCCGGCCTG	.	PASS	Atlas-SNP
PTPN3	5774	hgsc.bcm.edu	37	9	112145817	112145817	+	Silent	SNP	C	C	T	rs146869100	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79.0	41.0	82.0	0.0	0.518987	0	C|0.998;T|0.002	0.002	strong	.	PTPN3	106	.	NM_002829	exon23	c.G2268A	p.Q756Q	CCAGTACTGGTGA	.	PASS	Atlas-SNP
ZP3	7784	hgsc.bcm.edu	37	7	76062798	76062798	+	Missense_Mutation	SNP	G	G	A	rs74676082	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21.0	13.0	39.0	0.0	0.619048	0	G|0.996;A|0.004	0.004	strong	.	ZP3	32	.	NM_001110354	exon4	c.G547A	p.A183T	TGGAACGCTGAGA	.	PASS	Atlas-SNP
PUS3	83480	hgsc.bcm.edu	37	11	125764156	125764156	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62.0	8.0	33.0	0.0	0.129032	0	.	.	none	.	PUS3	33	.	NM_031307	exon4	c.T970G	p.L324V	CATATAAGACTAG	.	PASS	Atlas-SNP
TENM1	10178	hgsc.bcm.edu	37	X	123539063	123539063	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60.0	25.0	39.0	0.0	0.416667	0	.	.	none	.	.	.	.	NM_001163278	exon27	c.T5209G	p.F1737V	TGGCAAAAGTGAC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152275921	152275921	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156.0	57.0	161.0	0.0	0.365385	0	.	.	none	FLG,NS,carcinoma,0,1	FLG	900	1	NM_002016	exon3	c.G11441A	p.R3814H	TCATTACGTGTTT	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	11044	11044	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	6.0	6.0	10.0	0.0	1	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.C285T	p.Y95Y	ACTCTACCTCTCT	.	PASS	Atlas-SNP
SSC5D	284297	hgsc.bcm.edu	37	19	56011279	56011279	+	Missense_Mutation	SNP	C	C	T	rs35651406	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48.0	26.0	40.0	0.0	0.541667	0	C|0.997;T|0.003	0.003	strong	.	SSC5D	65	.	NM_001195267	exon10	c.C1802T	p.A601V	AGCTGGCCACCAA	.	PASS	Atlas-SNP
DTNB	1838	hgsc.bcm.edu	37	2	25611102	25611102	+	Silent	SNP	G	G	A	rs200383554	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36.0	22.0	45.0	0.0	0.611111	0	G|1.000;A|0.000	0.000	strong	.	DTNB	43	.	NM_021907	exon17	c.C1704T	p.V568V	TCCCCCGACTCCG	.	PASS	Atlas-SNP
LIG4	3981	hgsc.bcm.edu	37	13	108862810	108862810	+	Silent	SNP	G	G	A	rs2232638	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72.0	14.0	103.0	0.0	0.194444	0	G|0.956;A|0.044	0.044	strong	.	LIG4	91	.	NM_206937	exon3	c.C807T	p.Y269Y	TTCTATGTAGAAA	.	PASS	Atlas-SNP
ZP3	7784	hgsc.bcm.edu	37	7	76062913	76062913	+	Missense_Mutation	SNP	C	C	G	rs139729790	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59.0	26.0	74.0	0.0	0.440678	0	C|0.991;G|0.009	0.009	strong	ZP3_ENST00000394857,NS,lymphoid_neoplasm,0,2	ZP3	32	2	NM_001110354	exon4	c.C662G	p.P221R	CCACACCGACACC	.	PASS	Atlas-SNP
JAK1	3716	hgsc.bcm.edu	37	1	65312343	65312343	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	20.0	94.0	0.0	0.273973	0	.	.	none	JAK1,NS,malignant_melanoma,0,1	JAK1	209	1	NM_002227	exon14	c.G1976A	p.R659H	ACGTCGCGGACAC	.	PASS	Atlas-SNP
PTPN12	5782	hgsc.bcm.edu	37	7	77267956	77267956	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101.0	47.0	128.0	0.0	0.465347	0	.	.	none	.	PTPN12	83	.	NM_002835	exon17	c.G2189A	p.G730D	CGGGAGGTATTCA	.	PASS	Atlas-SNP
CYP3A4	1576	hgsc.bcm.edu	37	7	99358604	99358604	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	240.0	102.0	270.0	1.0	0.425	0.0037037	.	.	none	.	CYP3A4	56	.	NM_017460	exon12	c.A1254G	p.R418R	GCTGAATCTGGTT	.	PASS	Atlas-SNP
ABCA2	20	hgsc.bcm.edu	37	9	139904722	139904722	+	Silent	SNP	C	C	T	rs34125425	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63.0	30.0	60.0	0.0	0.47619	0	C|0.984;T|0.016	0.016	strong	.	ABCA2	113	.	NM_212533	exon41	c.G6366A	p.A2122A	CTTGCCCGCACCG	.	PASS	Atlas-SNP
P4HA2	8974	hgsc.bcm.edu	37	5	131539462	131539462	+	Silent	SNP	T	T	C	rs144253110	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136.0	64.0	118.0	0.0	0.470588	0	T|0.999;C|0.001	0.001	strong	.	P4HA2	72	.	NM_001017974	exon10	c.A1230G	p.V410V	AGTCTTTACTGTT	.	PASS	Atlas-SNP
LTBP1	4052	hgsc.bcm.edu	37	2	33172827	33172827	+	Missense_Mutation	SNP	G	G	A	rs147166401	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67.0	39.0	84.0	0.0	0.58209	0	G|0.992;A|0.008	0.008	strong	.	LTBP1	317	.	NM_206943	exon1	c.G436A	p.E146K	CCGCAGGAGACCC	.	PASS	Atlas-SNP
GLRA4	441509	hgsc.bcm.edu	37	X	102974119	102974119	+	Silent	SNP	G	G	A	rs41300882	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196.0	141.0	128.0	0.0	0.719388	0	G|0.995;A|0.005	0.005	strong	.	GLRA4	86	.	NM_001024452	exon7	c.C799T	p.L267L	TGAGTAGGCTGGG	.	PASS	Atlas-SNP
TUB	7275	hgsc.bcm.edu	37	11	8119298	8119298	+	Missense_Mutation	SNP	A	A	G	rs55892969	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106.0	59.0	112.0	0.0	0.556604	0	A|0.983;G|0.017	0.017	strong	.	TUB	71	.	NM_003320	exon9	c.A1088G	p.K363R	AGAGTAAAACTTC	.	PASS	Atlas-SNP
UNC13B	10497	hgsc.bcm.edu	37	9	35399243	35399243	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	186.0	8.0	223.0	0.0	0.0430108	0	.	.	none	.	UNC13B	153	.	NM_006377	exon33	c.G3913A	p.E1305K	ACAATGGAGAGGA	.	PASS	Atlas-SNP
TXN2	25828	hgsc.bcm.edu	37	22	36872873	36872873	+	Silent	SNP	C	C	T	rs150502647	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138.0	67.0	120.0	0.0	0.485507	0	C|0.993;T|0.007	0.007	strong	.	TXN2	15	.	NM_012473	exon3	c.G294A	p.P98P	TAACCTCGGCCCC	.	PASS	Atlas-SNP
OR10G9	219870	hgsc.bcm.edu	37	11	123893757	123893757	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	239.0	25.0	199.0	0.0	0.104603	0	.	.	none	OR10G9,NS,carcinoma,0,2	OR10G9	80	2	NM_001001953	exon1	c.C38T	p.T13M	TCCTCACGGGCCT	.	scavenged	Atlas-SNP
TAS2R43	259289	hgsc.bcm.edu	37	12	11244199	11244199	+	Missense_Mutation	SNP	C	C	G	rs201245949	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103.0	12.0	26.0	0.0	0.116505	0	C|0.994;G|0.006	0.006	strong	.	TAS2R43	19	.	NM_176884	exon1	c.G630C	p.Q210H	ATGGAGCTGCATC	.	PASS	Atlas-SNP
KIF13B	23303	hgsc.bcm.edu	37	8	29033628	29033628	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	3.0	81.0	0.0	0.0491803	0	.	.	none	KIF13B_ENST00000524189,colon,carcinoma,+1,2	KIF13B	192	2	NM_015254	exon10	c.A902C	p.K301T	ACAAATTTATTCT	.	scavenged	Atlas-SNP
DIS3	22894	hgsc.bcm.edu	37	13	73340177	73340177	+	Missense_Mutation	SNP	G	G	A	rs35017269	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25.0	15.0	23.0	0.0	0.6	0	G|0.989;A|0.011	0.011	strong	.	DIS3	103	.	NM_014953	exon15	c.C1903T	p.P635S	CTTCAGGAGAGGA	.	PASS	Atlas-SNP
ABCC4	10257	hgsc.bcm.edu	37	13	95696540	95696540	+	Silent	SNP	C	C	T	rs11568695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126.0	72.0	95.0	0.0	0.571429	0	C|0.950;T|0.050	0.050	strong	ABCC4_ENST00000376887,colon,carcinoma,-1,2	ABCC4	248	2	NM_005845	exon28	c.G3609A	p.A1203A	TGCCGTCGCTTCA	.	PASS	Atlas-SNP
SUV39H1	6839	hgsc.bcm.edu	37	X	48558888	48558888	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94.0	52.0	86.0	0.0	0.553191	0	.	.	none	.	SUV39H1	36	.	NM_003173	exon3	c.C572T	p.T191I	CACCCACTGGAGG	.	PASS	Atlas-SNP
CSDE1	7812	hgsc.bcm.edu	37	1	115272916	115272916	+	Missense_Mutation	SNP	T	T	C	rs149300730	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108.0	39.0	100.0	0.0	0.361111	0	T|1.000;C|0.000	0.000	weak	.	CSDE1	145	.	NM_001242891	exon13	c.A1457G	p.N486S	TTAGGATTGGAAA	.	PASS	Atlas-SNP
NAA15	80155	hgsc.bcm.edu	37	4	140264020	140264020	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128.0	40.0	137.0	0.0	0.3125	0	.	.	none	.	NAA15	88	.	NM_057175	exon5	c.G443A	p.R148K	CGCAGAGAGCATC	.	PASS	Atlas-SNP
PSG11	5680	hgsc.bcm.edu	37	19	43519324	43519324	+	Missense_Mutation	SNP	G	G	A	rs139355393	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102.0	49.0	120.0	0.0	0.480392	0	G|1.000;A|0.000	0.000	weak	.	PSG11	57	.	NM_002785	exon4	c.C908T	p.A303V	TTACGAGCAGAGC	.	PASS	Atlas-SNP
UHRF2	115426	hgsc.bcm.edu	37	9	6413515	6413515	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77.0	14.0	87.0	0.0	0.181818	0	.	.	none	UHRF2,NS,carcinoma,-1,1	UHRF2	50	1	NM_152896	exon1	c.G25C	p.D9H	ACCATTGATGGCT	.	PASS	Atlas-SNP
FAM83H	286077	hgsc.bcm.edu	37	8	144808953	144808953	+	Missense_Mutation	SNP	G	G	T	rs200179667	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47.0	22.0	62.0	0.0	0.468085	0	G|0.999;T|0.001	0.001	strong	.	FAM83H	68	.	NM_198488	exon5	c.C2678A	p.P893Q	GTAGTTGGACTTC	.	PASS	Atlas-SNP
ART5	116969	hgsc.bcm.edu	37	11	3660238	3660238	+	Missense_Mutation	SNP	G	G	A	rs142998376	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	33.0	83.0	0.0	0.452055	0	G|0.998;A|0.002	0.002	strong	.	ART5	38	.	NM_053017	exon3	c.C815T	p.A272V	CCTGGCGCAGACA	.	PASS	Atlas-SNP
DHX34	9704	hgsc.bcm.edu	37	19	47858526	47858526	+	Silent	SNP	C	C	T	rs138629177		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105.0	53.0	122.0	0.0	0.504762	0	C|1.000;T|0.000	0.000	weak	.	DHX34	98	.	NM_014681	exon3	c.C936T	p.A312A	GTCGGCCACCATC	.	PASS	Atlas-SNP
BCL9	607	hgsc.bcm.edu	37	1	147090956	147090956	+	Missense_Mutation	SNP	C	C	T	rs61751616	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46.0	23.0	25.0	0.0	0.5	0	C|0.990;T|0.010	0.010	strong	.	BCL9	150	.	NM_004326	exon8	c.C995T	p.P332L	CCCCTCCGCCTCC	.	PASS	Atlas-SNP
KRTAP27-1	643812	hgsc.bcm.edu	37	21	31709723	31709723	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	230.0	45.0	157.0	0.0	0.195652	0	.	.	none	.	KRTAP27-1	53	.	NM_001077711	exon1	c.T264G	p.T88T	GGAGTAAGTAGTT	.	PASS	Atlas-SNP
KIAA0146	23514	hgsc.bcm.edu	37	8	48612997	48612997	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103.0	10.0	119.0	0.0	0.0970874	0	.	.	none	.	KIAA0146	64	.	NM_001080394	exon12	c.T1718A	p.L573Q	ACACCCTGTGGCC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6578788	6578788	+	Missense_Mutation	SNP	C	C	T	rs111982303	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62.0	38.0	71.0	0.0	0.612903	0	C|0.988;T|0.012	0.012	strong	.	DNHD1	198	.	NM_144666	exon25	c.C8263T	p.P2755S	ATAGGACCAGTAA	.	PASS	Atlas-SNP
C17orf70	80233	hgsc.bcm.edu	37	17	79517729	79517729	+	Missense_Mutation	SNP	G	G	A	rs62076033	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79.0	36.0	83.0	0.0	0.455696	0	G|0.997;A|0.003	0.003	strong	.	C17orf70	79	.	NM_025161	exon3	c.C791T	p.A264V	CCAGGGGCTGACC	.	PASS	Atlas-SNP
PPP2R1B	5519	hgsc.bcm.edu	37	11	111637053	111637053	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35.0	17.0	25.0	0.0	0.485714	0	.	.	none	.	PPP2R1B	44	.	NM_001177562	exon1	c.A33G	p.P11P	TGCTCCTGGGCCG	.	PASS	Atlas-SNP
MYO9A	4649	hgsc.bcm.edu	37	15	72189925	72189925	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	192.0	52.0	229.0	0.0	0.270833	0	.	.	none	.	MYO9A	203	.	NM_006901	exon25	c.G4919A	p.R1640H	GAAATGCGATTAT	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101779435	101779435	+	Silent	SNP	T	T	C	rs149160478		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95.0	49.0	97.0	0.0	0.515789	0	T|1.000;C|0.000	0.000	weak	.	UTP20	222	.	NM_014503	exon61	c.T8131C	p.L2711L	TTCTCATTAGCCT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495674	134495674	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45.0	7.0	71.0	0.0	0.155556	0	.	.	none	.	SGK1	387	.	NM_001143676	exon4	c.G412A	p.A138T	TATTGGCAATCTT	.	PASS	Atlas-SNP
TREML2	79865	hgsc.bcm.edu	37	6	41166063	41166063	+	Missense_Mutation	SNP	C	C	A	rs147506354	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72.0	59.0	75.0	0.0	0.819444	0	C|0.998;A|0.002	0.002	strong	.	TREML2	41	.	NM_024807	exon2	c.G160T	p.V54F	ACCAAACCTTGCC	.	PASS	Atlas-SNP
RXFP2	122042	hgsc.bcm.edu	37	13	32367033	32367033	+	Missense_Mutation	SNP	C	C	G	rs138951290	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138.0	67.0	114.0	0.0	0.485507	0	C|0.999;G|0.001	0.001	strong	RXFP2,NS,carcinoma,0,1	RXFP2	95	1	NM_130806	exon16	c.C1594G	p.R532G	AACATTCGACCTG	.	PASS	Atlas-SNP
NOP58	51602	hgsc.bcm.edu	37	2	203157538	203157538	+	Silent	SNP	A	A	G	rs16839032	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132.0	66.0	116.0	0.0	0.5	0	A|0.989;G|0.011	0.011	strong	NOP58,NS,carcinoma,0,1	NOP58	41	1	NM_015934	exon9	c.A819G	p.E273E	CTATGAATATCTA	.	PASS	Atlas-SNP
RABGGTB	5876	hgsc.bcm.edu	37	1	76260248	76260248	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78.0	20.0	72.0	0.0	0.25641	0	.	.	none	.	RABGGTB	37	.	NM_004582	exon9	c.A909C	p.E303D	GGGAGAAGAACAG	.	PASS	Atlas-SNP
TNF	7124	hgsc.bcm.edu	37	6	31543607	31543607	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43.0	7.0	71.0	0.0	0.162791	0	.	.	none	.	TNF	15	.	NM_000594	exon1	c.G89A	p.C30Y	GGCGGTGCTTGTT	.	PASS	Atlas-SNP
HBE1	3046	hgsc.bcm.edu	37	11	5289816	5289816	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54.0	6.0	49.0	0.0	0.111111	0	.	.	none	.	HBE1	42	.	NM_005330	exon3	c.C327T	p.N109N	CATCACGTTACCC	.	PASS	Atlas-SNP
BTG2	7832	hgsc.bcm.edu	37	1	203274836	203274836	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110.0	30.0	125.0	0.0	0.272727	0	.	.	none	.	BTG2	16	.	NM_006763	exon1	c.G102A	p.R34R	GCAGAGGCTTAAG	.	PASS	Atlas-SNP
NUDC	10726	hgsc.bcm.edu	37	1	27268110	27268110	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105.0	6.0	84.0	0.0	0.0571429	0	.	.	none	.	NUDC	15	.	NM_006600	exon3	c.A322C	p.T108P	GAGCTAACTGATG	.	PASS	Atlas-SNP
EFCAB7	84455	hgsc.bcm.edu	37	1	64011657	64011657	+	Missense_Mutation	SNP	A	A	G	rs41313264	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170.0	75.0	164.0	0.0	0.441176	0	A|0.993;G|0.007	0.007	strong	.	EFCAB7	45	.	NM_032437	exon7	c.A875G	p.Y292C	ATCAGTACAGGAT	.	PASS	Atlas-SNP
HPSE2	60495	hgsc.bcm.edu	37	10	100481475	100481475	+	Missense_Mutation	SNP	C	C	T	rs142102360	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52.0	21.0	61.0	0.0	0.403846	0	C|0.997;T|0.003	0.003	strong	.	HPSE2	203	.	NM_001166246	exon5	c.G895A	p.A299T	AGCTGGCTCTGGA	.	PASS	Atlas-SNP
NPAS2	4862	hgsc.bcm.edu	37	2	101606810	101606810	+	Silent	SNP	G	G	A	rs1053091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108.0	43.0	105.0	0.0	0.398148	0	G|0.989;A|0.011	0.011	strong	.	NPAS2	88	.	NM_002518	exon18	c.G1920A	p.A640A	AGCTGCGCTCCCG	.	PASS	Atlas-SNP
COX3	5742	hgsc.bcm.edu	37	MT	9932	9932	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	8.0	8.0	4.0	0.0	1	0	.	.	none	.	.	.	.	ENST00000362079	exon1	c.G726A	p.W242W	ATACTGGCATTTT	.	PASS	Atlas-SNP
CERS6	253782	hgsc.bcm.edu	37	2	169312974	169312974	+	Missense_Mutation	SNP	G	G	A	rs4496303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72.0	36.0	75.0	0.0	0.5	0	A|0.008;G|0.990;T|0.002	0.008	strong	.	.	.	.	NM_001256126	exon1	c.G16A	p.A6T	ATCTTAGCCTGGT	.	PASS	Atlas-SNP
MASTL	84930	hgsc.bcm.edu	37	10	27462061	27462061	+	Silent	SNP	G	G	A	rs41282228	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66.0	31.0	52.0	0.0	0.469697	0	G|0.989;A|0.011	0.011	strong	.	MASTL	81	.	NM_001172303	exon9	c.G2139A	p.Q713Q	AAATCAGATCAAG	.	PASS	Atlas-SNP
TUBGCP3	10426	hgsc.bcm.edu	37	13	113140350	113140350	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150.0	101.0	154.0	0.0	0.673333	0	.	.	none	.	TUBGCP3	74	.	NM_006322	exon22	c.G2681A	p.R894H	GACACACGGAGCC	.	PASS	Atlas-SNP
GDF9	2661	hgsc.bcm.edu	37	5	132200000	132200000	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100.0	13.0	95.0	0.0	0.13	0	.	.	none	.	GDF9	50	.	NM_005260	exon1	c.T226G	p.S76A	TAGGTGACCCACC	.	PASS	Atlas-SNP
DNAJA4	55466	hgsc.bcm.edu	37	15	78565495	78565495	+	Silent	SNP	G	G	A	rs74978019	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	255.0	113.0	234.0	1.0	0.443137	0.0042735	G|0.997;A|0.003	0.003	strong	DNAJA4_ENST00000446172,NS,carcinoma,+1,2	DNAJA4	63	2	NM_018602	exon4	c.G459A	p.T153T	AGTCACGAAGAAA	.	PASS	Atlas-SNP
SNX5	27131	hgsc.bcm.edu	37	20	17949050	17949050	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63.0	16.0	114.0	2.0	0.253968	0.0175439	.	.	none	SNX5,NS,lymphoid_neoplasm,+2,1	SNX5	38	1	NM_014426	exon1	c.T19C	p.L7L	GCAGCAACTCGGG	.	scavenged	Atlas-SNP
BAI3	577	hgsc.bcm.edu	37	6	69348966	69348966	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43.0	9.0	36.0	0.0	0.209302	0	.	.	none	BAI3,NS,carcinoma,+1,1	BAI3	451	1	NM_001704	exon3	c.A399C	p.V133V	TCGAGTATTTCCA	.	scavenged	Atlas-SNP
OR10J1	26476	hgsc.bcm.edu	37	1	159410258	159410258	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	226.0	69.0	229.0	0.0	0.30531	0	.	.	none	OR10J1,NS,carcinoma,0,1	OR10J1	118	1	NM_012351	exon1	c.A710C	p.K237T	TCCTCAAGATTGC	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494655	134494655	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85.0	16.0	81.0	0.0	0.188235	0	.	.	none	.	SGK1	387	.	NM_001143676	exon6	c.C563T	p.A188V	GGTTTAGCATGAG	.	PASS	Atlas-SNP
LRRC16B	90668	hgsc.bcm.edu	37	14	24534916	24534916	+	Missense_Mutation	SNP	G	G	T	rs79328356	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64.0	33.0	68.0	0.0	0.515625	0	G|0.958;T|0.042	0.042	strong	LRRC16B,NS,carcinoma,+1,1	LRRC16B	120	1	NM_138360	exon34	c.G3482T	p.G1161V	TTCCCGGGTTGGA	.	PASS	Atlas-SNP
CSNK1A1	1452	hgsc.bcm.edu	37	5	148904609	148904609	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	261.0	18.0	212.0	0.0	0.0689655	0	.	.	none	.	CSNK1A1	63	.	NM_001025105	exon3	c.A356T	p.Q119L	CATACCTGGTCAG	.	PASS	Atlas-SNP
STRN3	29966	hgsc.bcm.edu	37	14	31404490	31404490	+	Silent	SNP	A	A	C	rs149753992		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80.0	37.0	77.0	0.0	0.4625	0	A|1.000;C|0.000	0.000	weak	.	STRN3	117	.	NM_001083893	exon7	c.T867G	p.A289A	GTCAGCAGCTAAA	.	PASS	Atlas-SNP
FAM53B	9679	hgsc.bcm.edu	37	10	126370517	126370517	+	Missense_Mutation	SNP	G	G	C	rs147832040	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71.0	40.0	76.0	0.0	0.56338	0	G|0.998;C|0.002	0.002	strong	.	FAM53B	22	.	NM_014661	exon4	c.C565G	p.R189G	CAAATCGGTGGTG	.	PASS	Atlas-SNP
CCDC135	84229	hgsc.bcm.edu	37	16	57760115	57760115	+	Missense_Mutation	SNP	C	C	A	rs143054335	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154.0	64.0	157.0	0.0	0.415584	0	C|1.000;A|0.000	0.000	strong	CCDC135,NS,carcinoma,0,1	CCDC135	97	1	NM_032269	exon13	c.C1894A	p.R632S	TCCAAGCGCGAGT	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186121996	186121996	+	Missense_Mutation	SNP	C	C	T	rs114629728	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168.0	72.0	156.0	0.0	0.428571	0	C|0.996;T|0.004	0.004	strong	.	HMCN1	797	.	NM_031935	exon96	c.C15011T	p.T5004I	AAGTCACTGTAAA	.	PASS	Atlas-SNP
CDH15	1013	hgsc.bcm.edu	37	16	89260195	89260195	+	Silent	SNP	G	G	A	rs62068507	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13.0	7.0	20.0	0.0	0.538462	0	G|0.995;A|0.005	0.005	strong	.	CDH15	54	.	NM_004933	exon13	c.G2025A	p.P675P	TCACCCGACAGCG	.	PASS	Atlas-SNP
CRIP1	1396	hgsc.bcm.edu	37	14	105954687	105954687	+	Missense_Mutation	SNP	G	G	T	rs7824	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110.0	57.0	123.0	0.0	0.518182	0	C|0.064;G|0.923;T|0.013	0.013	strong	.	CRIP1	1	.	NM_001311	exon4	c.G155T	p.C52F	CCTACTGCAACCA	.	PASS	Atlas-SNP
CLUL1	27098	hgsc.bcm.edu	37	18	618015	618015	+	Silent	SNP	C	C	G	rs116985056	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91.0	30.0	109.0	0.0	0.32967	0	C|0.999;G|0.001	0.001	strong	.	CLUL1	57	.	NM_199167	exon2	c.C15G	p.L5L	GCCACTCTTGGTG	.	PASS	Atlas-SNP
F2	2147	hgsc.bcm.edu	37	11	46751059	46751059	+	Silent	SNP	G	G	A	rs5900	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48.0	27.0	37.0	0.0	0.5625	0	A|0.014;C|0.000;G|0.986	0.014	strong	.	F2	75	.	NM_000506	exon12	c.G1602A	p.P534P	GCGGCCGGTCTGC	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46008011	46008011	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135.0	71.0	147.0	0.0	0.525926	0	.	.	none	.	FYCO1	115	.	NM_024513	exon8	c.G2815C	p.A939P	AGGCTGCCTCTTT	.	PASS	Atlas-SNP
BAZ2B	29994	hgsc.bcm.edu	37	2	160182374	160182374	+	Missense_Mutation	SNP	T	T	C	rs148382881	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103.0	20.0	132.0	0.0	0.194175	0	T|0.987;C|0.013	0.013	strong	.	BAZ2B	196	.	NM_013450	exon35	c.A5999G	p.N2000S	GACTCATTAGTCT	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144942794	144942794	+	Missense_Mutation	SNP	G	G	A	rs373737061		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82.0	44.0	66.0	0.0	0.536585	0	.	.	weak	EPPK1,NS,carcinoma,0,1	EPPK1	199	1	NM_031308	exon1	c.C4628T	p.T1543M	TCCAGCGTCTTCC	.	PASS	Atlas-SNP
GALNT8	26290	hgsc.bcm.edu	37	12	4854722	4854722	+	Missense_Mutation	SNP	G	G	A	rs201387598	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94.0	43.0	111.0	0.0	0.457447	0	G|0.999;A|0.001	0.001	weak	.	GALNT8	89	.	NM_017417	exon5	c.G988A	p.E330K	AACTGGGAACTCT	.	PASS	Atlas-SNP
PDCD11	22984	hgsc.bcm.edu	37	10	105160184	105160184	+	Missense_Mutation	SNP	A	A	G	rs150893869	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17.0	10.0	23.0	0.0	0.588235	0	A|0.995;G|0.005	0.005	strong	.	PDCD11	160	.	NM_014976	exon3	c.A133G	p.K45E	AAAAGAAAAAAGA	.	PASS	Atlas-SNP
TLN2	83660	hgsc.bcm.edu	37	15	63131091	63131091	+	Missense_Mutation	SNP	C	C	T	rs140301741	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58.0	31.0	62.0	0.0	0.534483	0	C|0.998;T|0.002	0.002	strong	.	TLN2	253	.	NM_015059	exon55	c.C7411T	p.L2471F	GACAATCTTGTCC	.	PASS	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33517507	33517507	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23.0	2.0	15.0	0.0	0.0869565	0	.	.	none	RHPN2,face,carcinoma,0,2	RHPN2	107	2	NM_033103	exon3	c.G217A	p.V73M	GCCGCACTTGCTC	.	scavenged	Atlas-SNP
LEMD3	23592	hgsc.bcm.edu	37	12	65563416	65563416	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63.0	9.0	66.0	0.0	0.142857	0	.	.	none	.	LEMD3	68	.	NM_001167614	exon1	c.G40A	p.D14N	CTCTCGGATGAGG	.	PASS	Atlas-SNP
USH1C	10083	hgsc.bcm.edu	37	11	17527386	17527386	+	Silent	SNP	A	A	G	rs369021714		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80.0	41.0	74.0	0.0	0.5125	0	.	.	weak	.	USH1C	157	.	NM_153676	exon19	c.T2124C	p.S708S	AACTTCAGATTTC	.	PASS	Atlas-SNP
FRMD1	79981	hgsc.bcm.edu	37	6	168458002	168458002	+	Silent	SNP	G	G	A	rs55991596	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72.0	37.0	77.0	0.0	0.513889	0	G|0.958;A|0.042	0.042	strong	.	FRMD1	52	.	NM_024919	exon11	c.C1425T	p.A475A	GACCCCGGCTGTC	.	PASS	Atlas-SNP
CD109	135228	hgsc.bcm.edu	37	6	74481186	74481186	+	Missense_Mutation	SNP	C	C	T	rs41266745	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43.0	23.0	57.0	0.0	0.534884	0	C|0.998;T|0.002	0.002	strong	.	CD109	170	.	NM_133493	exon15	c.C1709T	p.P570L	CTGAACCATCTGA	.	PASS	Atlas-SNP
LARS	51520	hgsc.bcm.edu	37	5	145522992	145522992	+	Silent	SNP	C	C	T	rs146906828	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88.0	45.0	79.0	0.0	0.511364	0	C|0.997;T|0.003	0.003	strong	.	LARS	100	.	NM_020117	exon19	c.G1860A	p.E620E	CGGAGACTCTGCC	.	PASS	Atlas-SNP
CARD14	79092	hgsc.bcm.edu	37	17	78157961	78157961	+	Missense_Mutation	SNP	G	G	A	rs114688446	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	34.0	68.0	0.0	0.465753	0	A|0.001;G|0.994;T|0.005	0.001	strong	.	CARD14	98	.	NM_024110	exon4	c.G599A	p.S200N	TGCTCAGCCTCTC	.	PASS	Atlas-SNP
RGS1	5996	hgsc.bcm.edu	37	1	192545417	192545417	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178.0	43.0	182.0	0.0	0.241573	0	.	.	none	.	RGS1	75	.	NM_002922	exon2	c.G140A	p.G47E	GTAGTGGAATGGA	.	PASS	Atlas-SNP
TULP4	56995	hgsc.bcm.edu	37	6	158923378	158923378	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82.0	4.0	87.0	0.0	0.0487805	0	.	.	none	.	TULP4	137	.	NM_020245	exon13	c.G2683A	p.G895S	AGCAGTGGCAACG	.	PASS	Atlas-SNP
CCDC80	151887	hgsc.bcm.edu	37	3	112356977	112356977	+	Silent	SNP	T	T	C	rs35149092	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	233.0	116.0	239.0	0.0	0.497854	0	T|0.996;C|0.004	0.004	strong	.	CCDC80	100	.	NM_199511	exon2	c.A1776G	p.E592E	ATCCTGTTCTGTT	.	PASS	Atlas-SNP
DPCR1	135656	hgsc.bcm.edu	37	6	30919798	30919798	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45.0	16.0	25.0	0.0	0.355556	0	.	.	none	.	DPCR1	99	.	NM_080870	exon2	c.A3557C	p.K1186T	CAGAAAAGCCTAC	.	PASS	Atlas-SNP
KTN1	3895	hgsc.bcm.edu	37	14	56119783	56119783	+	Missense_Mutation	SNP	G	G	A	rs139730003	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163.0	75.0	154.0	0.0	0.460123	0	G|1.000;A|0.000	0.000	weak	.	KTN1	147	.	NM_004986	exon27	c.G2743A	p.A915T	GAAGTAGCACAAC	.	PASS	Atlas-SNP
AGGF1	55109	hgsc.bcm.edu	37	5	76331449	76331449	+	Missense_Mutation	SNP	G	G	A	rs34203073	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	244.0	105.0	208.0	2.0	0.430328	0.00961538	G|0.986;A|0.014	0.014	strong	AGGF1,colon,carcinoma,0,1	AGGF1	71	1	NM_018046	exon3	c.G397A	p.E133K	GCTATCGAAACTT	.	scavenged	Atlas-SNP
EPG5	57724	hgsc.bcm.edu	37	18	43514856	43514856	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140.0	60.0	120.0	0.0	0.428571	0	.	.	none	.	EPG5	199	.	NM_020964	exon11	c.C2176T	p.L726F	GCATGAGGTAGAA	.	PASS	Atlas-SNP
MCCC1	56922	hgsc.bcm.edu	37	3	182804555	182804555	+	Missense_Mutation	SNP	C	C	T	rs375244642		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60.0	28.0	80.0	0.0	0.466667	0	.	.	weak	.	MCCC1	87	.	NM_020166	exon4	c.G295A	p.G99S	CGGGGCCGATGGA	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140580963	140580963	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150.0	59.0	203.0	0.0	0.393333	0	.	.	none	.	PCDHB11	162	.	NM_018931	exon1	c.C1616T	p.P539L	GCTCCCCGGCTTT	.	PASS	Atlas-SNP
OR2T1	26696	hgsc.bcm.edu	37	1	248570057	248570057	+	Silent	SNP	T	T	C	rs138375160	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157.0	73.0	181.0	0.0	0.464968	0	T|0.994;C|0.006	0.006	strong	.	OR2T1	89	.	NM_030904	exon1	c.T762C	p.V254V	CTGTGTTTTGATG	.	PASS	Atlas-SNP
ALB	213	hgsc.bcm.edu	37	4	74280774	74280774	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125.0	30.0	98.0	0.0	0.24	0	.	.	none	.	ALB	132	.	NM_000477	exon9	c.A1081C	p.R361R	GCAAGAAGGCATC	.	PASS	Atlas-SNP
SF3B1	23451	hgsc.bcm.edu	37	2	198270136	198270136	+	Missense_Mutation	SNP	T	T	C	rs367701030	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156.0	44.0	177.0	0.0	0.282051	0	.	.	alt	.	SF3B1	1038	.	NM_012433	exon10	c.A1300G	p.T434A	TTGGAGTAGCTGT	.	PASS	Atlas-SNP
SLC22A18AS	5003	hgsc.bcm.edu	37	11	2909573	2909573	+	Missense_Mutation	SNP	G	G	A	rs139893801	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64.0	33.0	60.0	0.0	0.515625	0	G|0.999;A|0.001	0.001	strong	.	SLC22A18AS	7	.	NM_007105	exon4	c.C599T	p.T200I	CGTCCTGTCATTC	.	PASS	Atlas-SNP
APLF	200558	hgsc.bcm.edu	37	2	68765205	68765205	+	Missense_Mutation	SNP	C	C	T	rs13404469	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123.0	91.0	173.0	0.0	0.739837	0	C|0.910;T|0.090	0.090	strong	.	APLF	69	.	NM_173545	exon7	c.C1006T	p.L336F	GACTCACTTCAGG	.	PASS	Atlas-SNP
OR12D3	81797	hgsc.bcm.edu	37	6	29342271	29342271	+	Missense_Mutation	SNP	G	G	A	rs369042428		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106.0	29.0	124.0	0.0	0.273585	0	.	.	weak	.	OR12D3	55	.	NM_030959	exon1	c.C794T	p.T265I	ATGGAGGTGGCTG	.	PASS	Atlas-SNP
EEF1D	1936	hgsc.bcm.edu	37	8	144671955	144671955	+	Silent	SNP	C	C	T	rs61757370	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55.0	29.0	53.0	0.0	0.527273	0	C|0.987;T|0.013	0.013	strong	.	EEF1D	48	.	NM_001130053	exon3	c.G297A	p.A99A	CAGGTCCGCGGGG	.	PASS	Atlas-SNP
ATP2A1	487	hgsc.bcm.edu	37	16	28898778	28898778	+	Silent	SNP	C	C	G	rs113803159	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69.0	39.0	65.0	0.0	0.565217	0	C|0.995;G|0.005	0.005	strong	.	ATP2A1	116	.	NM_004320	exon8	c.C663G	p.G221G	CTTGGGCATCGTG	.	PASS	Atlas-SNP
DACT2	168002	hgsc.bcm.edu	37	6	168708678	168708678	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41.0	8.0	59.0	0.0	0.195122	0	.	.	none	.	DACT2	46	.	NM_214462	exon4	c.G1759C	p.A587P	CTTGGGCTGAGGT	.	PASS	Atlas-SNP
SPNS1	83985	hgsc.bcm.edu	37	16	28995211	28995211	+	Silent	SNP	C	C	T	rs113165798	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44.0	24.0	44.0	0.0	0.545455	0	C|0.995;T|0.005	0.005	strong	.	SPNS1	47	.	NM_001142448	exon12	c.C1425T	p.G475G	GGGCGGCGCAGCC	.	PASS	Atlas-SNP
TREX2	11219	hgsc.bcm.edu	37	X	152710522	152710522	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20.0	7.0	21.0	0.0	0.35	0	.	.	none	.	TREX2	36	.	NM_080701	exon2	c.G367T	p.D123Y	GGAAATCATAATC	.	PASS	Atlas-SNP
VWA3A	146177	hgsc.bcm.edu	37	16	22143031	22143031	+	Missense_Mutation	SNP	G	G	A	rs199942653		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	220.0	92.0	262.0	1.0	0.418182	0.00381679	G|0.999;A|0.001	0.001	weak	.	VWA3A	115	.	NM_173615	exon19	c.G1853A	p.G618D	CTGGGGGCATCCC	.	PASS	Atlas-SNP
USP11	8237	hgsc.bcm.edu	37	X	47092423	47092423	+	Missense_Mutation	SNP	G	G	A	rs149757747	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81.0	21.0	70.0	0.0	0.259259	0	G|1.000;A|0.000	0.000	strong	.	USP11	93	.	NM_004651	exon1	c.G110A	p.C37Y	TTGGCTGTAGAAG	.	PASS	Atlas-SNP
LCMT2	9836	hgsc.bcm.edu	37	15	43621483	43621483	+	Missense_Mutation	SNP	C	C	T	rs144228208	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63.0	45.0	93.0	0.0	0.714286	0	C|1.000;T|0.000	0.000	weak	LCMT2,NS,carcinoma,-1,1	LCMT2	48	1	NM_014793	exon1	c.G1205A	p.G402D	TGGCTGCCTTTCC	.	PASS	Atlas-SNP
DDX23	9416	hgsc.bcm.edu	37	12	49229991	49229991	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135.0	34.0	158.0	0.0	0.251852	0	.	.	none	.	DDX23	82	.	NM_004818	exon11	c.T1295C	p.I432T	ACACCAATGATGT	.	PASS	Atlas-SNP
ARHGAP32	9743	hgsc.bcm.edu	37	11	128842603	128842603	+	Silent	SNP	G	G	A	rs376118787		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137.0	40.0	128.0	0.0	0.291971	0	.	.	weak	.	ARHGAP32	307	.	NM_001142685	exon21	c.C3756T	p.P1252P	CTCTTCGGGGGAC	.	PASS	Atlas-SNP
ABLIM3	22885	hgsc.bcm.edu	37	5	148618836	148618836	+	Missense_Mutation	SNP	C	C	T	rs201076202	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179.0	85.0	189.0	0.0	0.47486	0	.	.	weak	.	ABLIM3	91	.	NM_014945	exon12	c.C1070T	p.S357F	CCTACTCCCAGGT	.	PASS	Atlas-SNP
BEST2	54831	hgsc.bcm.edu	37	19	12866544	12866544	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147.0	21.0	123.0	0.0	0.142857	0	.	.	none	.	BEST2	35	.	NM_017682	exon6	c.C830T	p.T277I	TCTTCACCCTCTT	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44159672	44159672	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154.0	74.0	136.0	0.0	0.480519	0	.	.	none	.	LOXHD1	367	.	NM_144612	exon13	c.T1730G	p.L577R	CCAAAAAGGCAGA	.	PASS	Atlas-SNP
DSG2	1829	hgsc.bcm.edu	37	18	29126108	29126108	+	Missense_Mutation	SNP	T	T	G	rs142841727	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107.0	53.0	116.0	0.0	0.495327	0	T|0.995;G|0.005	0.005	strong	DSG2,NS,lymphoid_neoplasm,0,1	DSG2	115	1	NM_001943	exon15	c.T2759G	p.V920G	AAAAGGTAGCTAC	.	PASS	Atlas-SNP
MRC2	9902	hgsc.bcm.edu	37	17	60766283	60766283	+	Missense_Mutation	SNP	C	C	T	rs201851897	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118.0	35.0	135.0	0.0	0.29661	0	C|1.000;T|0.000	0.000	strong	MRC2,NS,carcinoma,0,1	MRC2	126	1	NM_006039	exon23	c.C3296T	p.T1099M	GCTGCACGGAGGA	.	PASS	Atlas-SNP
FOXO1	2308	hgsc.bcm.edu	37	13	41239736	41239736	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	207.0	46.0	106.0	0.0	0.222222	0	.	.	none	.	FOXO1	110	.	NM_002015	exon1	c.G614A	p.S205N	GCCGAGCTGTTGC	.	PASS	Atlas-SNP
PYGL	5836	hgsc.bcm.edu	37	14	51378517	51378517	+	Missense_Mutation	SNP	C	C	G	rs35026927	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164.0	81.0	160.0	0.0	0.493902	0	C|0.996;G|0.004	0.004	strong	PYGL,colon,carcinoma,+2,1	PYGL	77	1	NM_002863	exon16	c.G1900C	p.D634H	TAGGGTCATTGTT	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109647006	109647006	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115.0	51.0	109.0	0.0	0.443478	0	.	.	none	ACACB,caecum,adenoma,-1,1	ACACB	330	1	NM_001093	exon20	c.C3097T	p.R1033W	ACCCTCCGGCACC	.	PASS	Atlas-SNP
EGFLAM	133584	hgsc.bcm.edu	37	5	38438505	38438505	+	Missense_Mutation	SNP	G	G	C	rs35767836	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123.0	54.0	107.0	0.0	0.439024	0	G|0.987;C|0.013	0.013	strong	.	EGFLAM	302	.	NM_001205301	exon17	c.G2412C	p.E804D	GAAGGAGGGCTAT	.	PASS	Atlas-SNP
NLRP8	126205	hgsc.bcm.edu	37	19	56473502	56473502	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150.0	8.0	159.0	0.0	0.0533333	0	.	.	none	.	NLRP8	225	.	NM_176811	exon4	c.G2112C	p.K704N	TGATAAGCTGGAA	.	PASS	Atlas-SNP
TIGD1	200765	hgsc.bcm.edu	37	2	233413648	233413648	+	Silent	SNP	G	G	A	rs72991949	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	4.0	4.0	4.0	0.0	1	0	G|0.858;A|0.142	0.142	strong	.	TIGD1	17	.	NM_145702	exon1	c.C945T	p.Y315Y	CTCCTCGTATATC	.	PASS	Atlas-SNP
SLITRK2	84631	hgsc.bcm.edu	37	X	144906370	144906370	+	Silent	SNP	A	A	G	rs45540333	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	174.0	122.0	130.0	0.0	0.701149	0	A|0.986;G|0.014	0.014	strong	.	SLITRK2	221	.	NM_001144005	exon5	c.A2427G	p.K809K	CAGGAAATGCTTT	.	PASS	Atlas-SNP
MYBL1	4603	hgsc.bcm.edu	37	8	67478431	67478431	+	Missense_Mutation	SNP	T	T	G	rs61729530	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123.0	70.0	102.0	0.0	0.569106	0	T|0.991;G|0.009	0.009	strong	.	MYBL1	73	.	NM_001080416	exon15	c.A1998C	p.E666D	ATGTATTTCCAAT	.	PASS	Atlas-SNP
FGD5	152273	hgsc.bcm.edu	37	3	14862049	14862049	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84.0	32.0	84.0	0.0	0.380952	0	.	.	none	FGD5_ENST00000285046,NS,carcinoma,0,2	FGD5	248	2	NM_152536	exon1	c.G1471A	p.G491S	GTGGCCGGCTATG	.	PASS	Atlas-SNP
LYST	1130	hgsc.bcm.edu	37	1	235887393	235887393	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128.0	14.0	150.0	0.0	0.109375	0	.	.	none	.	LYST	370	.	NM_000081	exon39	c.G9250A	p.D3084N	CATTATCTCTCAA	.	PASS	Atlas-SNP
HCAR1	27198	hgsc.bcm.edu	37	12	123214166	123214166	+	Missense_Mutation	SNP	G	G	A	rs140482291	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70.0	36.0	48.0	0.0	0.514286	0	G|0.998;A|0.002	0.002	strong	.	HCAR1	21	.	NM_032554	exon1	c.C721T	p.L241F	AATAGAGTCTAGC	.	PASS	Atlas-SNP
OR5K3	403277	hgsc.bcm.edu	37	3	98110414	98110414	+	Missense_Mutation	SNP	T	T	A	rs199575537	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27.0	2.0	23.0	0.0	0.0740741	0	.	.	weak	OR5K3,NS,carcinoma,0,2	OR5K3	60	2	NM_001005516	exon1	c.T905A	p.I302N	AAAAAATTATGAA	.	scavenged	Atlas-SNP
EGFR	1956	hgsc.bcm.edu	37	7	55229255	55229255	+	Missense_Mutation	SNP	G	G	A	rs2227983	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44.0	25.0	52.0	0.0	0.568182	0	A|0.243;C|0.000;G|0.757;T|0.000	0.243	strong	.	EGFR	20426	.	NM_005228	exon13	c.G1562A	p.R521K	AGCCCAGGGACTG	.	PASS	Atlas-SNP
PCDH10	57575	hgsc.bcm.edu	37	4	134072208	134072208	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43.0	10.0	58.0	0.0	0.232558	0	.	.	none	PCDH10,NS,carcinoma,-2,2	PCDH10	290	2	NM_032961	exon1	c.C913G	p.P305A	CTCTCGCCGCGCA	.	PASS	Atlas-SNP
RAB11FIP3	9727	hgsc.bcm.edu	37	16	570737	570737	+	Silent	SNP	G	G	A	rs142673366	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93.0	37.0	91.0	0.0	0.397849	0	G|0.999;A|0.001	0.001	strong	.	RAB11FIP3	31	.	NM_014700	exon14	c.G2169A	p.A723A	GGAGGCGATTCAG	.	PASS	Atlas-SNP
MBOAT1	154141	hgsc.bcm.edu	37	6	20124710	20124710	+	Missense_Mutation	SNP	G	G	A	rs146228602	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85.0	14.0	92.0	0.0	0.164706	0	G|0.999;A|0.001	0.001	strong	MBOAT1,NS,carcinoma,+1,1	MBOAT1	48	1	NM_001080480	exon8	c.C836T	p.P279L	CGAGCCGGAAAGC	.	PASS	Atlas-SNP
HLTF	6596	hgsc.bcm.edu	37	3	148756993	148756993	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	22.0	69.0	0.0	0.30137	0	.	.	none	.	HLTF	87	.	NM_139048	exon23	c.G2639A	p.R880H	TCCAAACGAGTAA	.	PASS	Atlas-SNP
OFD1	8481	hgsc.bcm.edu	37	X	13786875	13786875	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	211.0	48.0	157.0	0.0	0.227488	0	.	.	none	.	OFD1	109	.	NM_003611	exon22	c.C2967T	p.D989D	AGTGGACACGCTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507998	195507998	+	Missense_Mutation	SNP	G	G	C	rs199622660		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86.0	21.0	93.0	0.0	0.244186	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.C10453G	p.H3485D	TGGTGTGACCTGT	.	PASS	Atlas-SNP
INO80D	54891	hgsc.bcm.edu	37	2	206872126	206872126	+	Silent	SNP	C	C	T	rs116331438	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	241.0	118.0	202.0	0.0	0.489627	0	C|0.999;T|0.001	0.001	strong	INO80D_ENST00000403263,NS,carcinoma,0,2	INO80D	134	2	NM_017759	exon10	c.G1800A	p.P600P	GTCATCCGGCAAC	.	PASS	Atlas-SNP
PCDHGA5	56110	hgsc.bcm.edu	37	5	140745959	140745959	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101.0	48.0	128.0	0.0	0.475248	0	.	.	none	.	PCDHGA5	215	.	NM_032054	exon1	c.G2062A	p.D688N	GATCTGGACCTCA	.	PASS	Atlas-SNP
LYST	1130	hgsc.bcm.edu	37	1	235918870	235918870	+	Silent	SNP	T	T	G	rs61738992	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88.0	41.0	96.0	0.0	0.465909	0	T|0.976;G|0.024	0.024	strong	.	LYST	370	.	NM_000081	exon25	c.A7137C	p.L2379L	GTTGGCTAGCAAG	.	PASS	Atlas-SNP
ARHGAP12	94134	hgsc.bcm.edu	37	10	32097650	32097650	+	Missense_Mutation	SNP	C	C	T	rs34750454	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102.0	31.0	102.0	0.0	0.303922	0	C|0.987;T|0.013	0.013	weak	.	ARHGAP12	79	.	NM_018287	exon19	c.G2293A	p.V765I	CCTTAACAGCAGC	.	PASS	Atlas-SNP
SEC61A1	29927	hgsc.bcm.edu	37	3	127774411	127774411	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158.0	64.0	155.0	0.0	0.405063	0	.	.	none	.	SEC61A1	39	.	NM_013336	exon3	c.T128C	p.L43S	TCTTCTTAGTGTG	.	PASS	Atlas-SNP
AFAP1L1	134265	hgsc.bcm.edu	37	5	148695859	148695859	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124.0	13.0	91.0	0.0	0.104839	0	.	.	none	.	AFAP1L1	86	.	NM_001146337	exon11	c.C1260T	p.P420P	GGTTCCCTGCTGT	.	PASS	Atlas-SNP
CXorf30	645090	hgsc.bcm.edu	37	X	36317108	36317108	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150.0	59.0	120.0	0.0	0.393333	0	.	.	none	.	CXorf30	76	.	NM_001098843	exon7	c.A41C	p.E14A	GCATTGAAATACC	.	PASS	Atlas-SNP
UTP14A	10813	hgsc.bcm.edu	37	X	129045815	129045815	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66.0	17.0	66.0	0.0	0.257576	0	.	.	none	.	UTP14A	74	.	NM_006649	exon6	c.G455A	p.R152Q	AGAACCGGCAGGC	.	PASS	Atlas-SNP
CDC25C	995	hgsc.bcm.edu	37	5	137627769	137627769	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91.0	32.0	97.0	0.0	0.351648	0	.	.	none	.	CDC25C	37	.	NM_001790	exon8	c.C652G	p.P218A	TCTCTGGCATCGA	.	PASS	Atlas-SNP
MAN1C1	57134	hgsc.bcm.edu	37	1	26110236	26110236	+	Missense_Mutation	SNP	G	G	A	rs79507311	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40.0	27.0	31.0	0.0	0.675	0	G|0.990;A|0.010	0.010	strong	.	MAN1C1	48	.	NM_020379	exon12	c.G1849A	p.V617M	CTCCCGGTGAACC	.	PASS	Atlas-SNP
SLC6A13	6540	hgsc.bcm.edu	37	12	333237	333237	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86.0	5.0	96.0	0.0	0.0581395	0	.	.	none	.	SLC6A13	62	.	NM_016615	exon11	c.G1232A	p.R411H	TTCTTGCGGAACA	.	PASS	Atlas-SNP
EPHB4	2050	hgsc.bcm.edu	37	7	100417879	100417879	+	Missense_Mutation	SNP	C	C	T	rs201531252		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46.0	24.0	49.0	0.0	0.521739	0	C|0.999;T|0.001	0.001	weak	.	EPHB4	106	.	NM_004444	exon5	c.G848A	p.G283E	CAGGACCCTTCTC	.	PASS	Atlas-SNP
GTPBP8	29083	hgsc.bcm.edu	37	3	112718352	112718352	+	Missense_Mutation	SNP	G	G	T	rs1054263	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180.0	73.0	247.0	0.0	0.405556	0	G|0.948;T|0.052	0.052	strong	GTPBP8,lymph_node,lymphoid_neoplasm,0,1	GTPBP8	22	1	NM_014170	exon5	c.G726T	p.Q242H	GCTTCAGATCCAG	.	PASS	Atlas-SNP
BMP10	27302	hgsc.bcm.edu	37	2	69093413	69093413	+	Missense_Mutation	SNP	G	G	A	rs34008398	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	209.0	151.0	285.0	0.0	0.722488	0	G|0.991;A|0.009	0.009	strong	.	BMP10	70	.	NM_014482	exon2	c.C625T	p.R209C	GCCAACGTCTGAT	.	PASS	Atlas-SNP
PRKD1	5587	hgsc.bcm.edu	37	14	30066797	30066797	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143.0	29.0	126.0	0.0	0.202797	0	.	.	none	.	PRKD1	316	.	NM_002742	exon16	c.C2334T	p.S778S	TGTGCCGCTTAGG	.	PASS	Atlas-SNP
FASTKD2	22868	hgsc.bcm.edu	37	2	207632128	207632128	+	Silent	SNP	C	C	T	rs150195745		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49.0	25.0	55.0	0.0	0.510204	0	C|1.000;T|0.000	0.000	weak	.	FASTKD2	49	.	NM_001136193	exon2	c.C711T	p.H237H	TCTTCACGCCATA	.	PASS	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	37	3	121208294	121208294	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150.0	38.0	178.0	0.0	0.253333	0	.	.	none	.	POLQ	273	.	NM_199420	exon16	c.G3484A	p.A1162T	CAACAGCTACTCC	.	PASS	Atlas-SNP
HIP1R	9026	hgsc.bcm.edu	37	12	123345296	123345296	+	Missense_Mutation	SNP	G	G	A	rs141813189	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	177.0	82.0	145.0	0.0	0.463277	0	G|0.999;A|0.001	0.001	strong	.	HIP1R	68	.	NM_003959	exon28	c.G2731A	p.A911T	GAGATCGCAGCCA	.	PASS	Atlas-SNP
TDP2	51567	hgsc.bcm.edu	37	6	24653283	24653283	+	Silent	SNP	T	T	C	rs11559067	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86.0	74.0	74.0	0.0	0.860465	0	T|0.977;C|0.023	0.023	strong	.	TDP2	29	.	NM_016614	exon6	c.A735G	p.L245L	TTTCTTTAAAACC	.	PASS	Atlas-SNP
CTAGE5	4253	hgsc.bcm.edu	37	14	39818076	39818076	+	Missense_Mutation	SNP	A	A	G	rs61742363	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129.0	61.0	88.0	0.0	0.472868	0	A|0.988;G|0.012	0.012	strong	.	CTAGE5	75	.	NM_001247989	exon23	c.A2158G	p.R720G	TTGAGAAGAGGAC	.	PASS	Atlas-SNP
S100A7A	338324	hgsc.bcm.edu	37	1	153390649	153390649	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	184.0	47.0	155.0	0.0	0.255435	0	.	.	none	.	S100A7A	24	.	NM_176823	exon2	c.A91G	p.S31G	AAGCCAAGCCTGC	.	PASS	Atlas-SNP
HLX	3142	hgsc.bcm.edu	37	1	221057573	221057573	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136.0	40.0	114.0	1.0	0.294118	0.00877193	.	.	none	HLX,NS,carcinoma,0,1	HLX	67	1	NM_021958	exon4	c.C994T	p.R332W	AAGTGGCGGCACT	.	scavenged	Atlas-SNP
WNK1	65125	hgsc.bcm.edu	37	12	922913	922913	+	Missense_Mutation	SNP	T	T	C	rs200234585		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67.0	31.0	77.0	0.0	0.462687	0	.	.	weak	.	WNK1	403	.	NM_001184985	exon2	c.T865C	p.S289P	TGGGAATCCACAG	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23510038	23510038	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172.0	50.0	215.0	0.0	0.290698	0	.	.	none	.	PRDM9	344	.	NM_020227	exon4	c.C203A	p.A68D	TCAGAGCCACTCG	.	PASS	Atlas-SNP
OR6C76	390326	hgsc.bcm.edu	37	12	55820685	55820685	+	Silent	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154.0	50.0	116.0	0.0	0.324675	0	.	.	none	.	OR6C76	98	.	NM_001005183	exon1	c.T648G	p.T216T	CTATACTTACATC	.	PASS	Atlas-SNP
MCF2L2	23101	hgsc.bcm.edu	37	3	182941927	182941927	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77.0	4.0	96.0	0.0	0.0519481	0	.	.	none	.	MCF2L2	164	.	NM_015078	exon19	c.A2167G	p.R723G	TTGCCCTAGCTCG	.	PASS	Atlas-SNP
NTF3	4908	hgsc.bcm.edu	37	12	5604064	5604064	+	Silent	SNP	T	T	C	rs200399901	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37.0	19.0	28.0	0.0	0.513514	0	T|0.999;C|0.001	0.001	strong	.	NTF3	50	.	NM_001102654	exon2	c.T723C	p.T241T	ACTGACTTCAGAG	.	PASS	Atlas-SNP
UHRF2	115426	hgsc.bcm.edu	37	9	6413640	6413640	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16.0	7.0	24.0	0.0	0.4375	0	.	.	none	.	UHRF2	50	.	NM_152896	exon1	c.G150A	p.K50K	GGGCAAGCAGGTG	.	PASS	Atlas-SNP
SETD4	54093	hgsc.bcm.edu	37	21	37420606	37420606	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71.0	15.0	63.0	0.0	0.211268	0	.	.	none	.	SETD4	37	.	NM_001007259	exon5	c.A296C	p.K99T	ACTTACTTAGTAA	.	PASS	Atlas-SNP
CLDN24	100132463	hgsc.bcm.edu	37	4	184243174	184243174	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147.0	8.0	150.0	0.0	0.0544218	0	.	.	none	.	CLDN24	5	.	NM_001185149	exon1	c.C406A	p.P136T	AGACGGGAACCAG	.	PASS	Atlas-SNP
WBSCR17	64409	hgsc.bcm.edu	37	7	71142240	71142240	+	Silent	SNP	G	G	A	rs77485397	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49.0	25.0	45.0	0.0	0.510204	0	G|0.995;A|0.005	0.005	strong	WBSCR17,NS,carcinoma,+1,2	WBSCR17	208	2	NM_022479	exon9	c.G1449A	p.P483P	GGGGCCGCTGGAG	.	PASS	Atlas-SNP
TLR4	7099	hgsc.bcm.edu	37	9	120476365	120476365	+	Silent	SNP	G	G	A	rs5030721	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	24.0	57.0	0.0	0.393443	0	G|0.993;A|0.007	0.007	strong	.	TLR4	220	.	NM_138554	exon3	c.G1959A	p.K653K	CTATAAGTTCTAT	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101755803	101755803	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76.0	18.0	79.0	0.0	0.236842	0	.	.	none	.	UTP20	222	.	NM_014503	exon44	c.G5755A	p.G1919R	CAGGTCGGAGATT	.	PASS	Atlas-SNP
DDR2	4921	hgsc.bcm.edu	37	1	162729613	162729613	+	Silent	SNP	C	C	T	rs56351141	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82.0	29.0	107.0	0.0	0.353659	0	C|0.991;T|0.009	0.009	strong	DDR2_ENST00000367922,right_upper_lobe,carcinoma,0,2	DDR2	228	2	NM_001014796	exon9	c.C699T	p.T233T	ATTGACCGATGGT	.	PASS	Atlas-SNP
CCDC146	57639	hgsc.bcm.edu	37	7	76866265	76866265	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69.0	30.0	81.0	0.0	0.434783	0	.	.	none	.	CCDC146	87	.	NM_020879	exon3	c.T158C	p.L53S	GCTAGTTACATGC	.	PASS	Atlas-SNP
PCIF1	63935	hgsc.bcm.edu	37	20	44574722	44574722	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83.0	22.0	61.0	0.0	0.26506	0	.	.	none	.	PCIF1	51	.	NM_022104	exon13	c.C1396T	p.P466S	TTCCTGCCCCGGG	.	PASS	Atlas-SNP
NMUR2	56923	hgsc.bcm.edu	37	5	151777633	151777633	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83.0	5.0	64.0	0.0	0.060241	0	.	.	none	NMUR2,NS,carcinoma,0,1	NMUR2	111	1	NM_020167	exon2	c.A799C	p.N267H	TCTTGTTGACTGA	.	PASS	Atlas-SNP
HCN2	610	hgsc.bcm.edu	37	19	605093	605093	+	Silent	SNP	G	G	A	rs55839339	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72.0	34.0	82.0	0.0	0.472222	0	G|0.984;A|0.016	0.016	strong	.	HCN2	36	.	NM_001194	exon3	c.G1089A	p.A363A	CAGCGCGGTGATG	.	PASS	Atlas-SNP
MRGPRE	116534	hgsc.bcm.edu	37	11	3249972	3249972	+	Missense_Mutation	SNP	C	C	A	rs200284450	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43.0	21.0	45.0	0.0	0.488372	0	.	.	weak	.	MRGPRE	35	.	NM_001039165	exon2	c.G58T	p.D20Y	CCACATCCTCCTG	.	PASS	Atlas-SNP
B4GALNT1	2583	hgsc.bcm.edu	37	12	58022555	58022555	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69.0	26.0	91.0	0.0	0.376812	0	.	.	none	.	B4GALNT1	53	.	NM_001478	exon8	c.A943A	p.T315T	GCTTGTCGCTGTC	.	PASS	Atlas-SNP
ARHGEF11	9826	hgsc.bcm.edu	37	1	156928576	156928576	+	Missense_Mutation	SNP	C	C	T	rs142957547	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134.0	58.0	131.0	0.0	0.432836	0	C|0.996;T|0.004	0.004	strong	.	ARHGEF11	168	.	NM_198236	exon17	c.G1460A	p.R487H	ACTTGGCGCTCTC	.	PASS	Atlas-SNP
DPYSL5	56896	hgsc.bcm.edu	37	2	27121394	27121394	+	Silent	SNP	G	G	A	rs79644076	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223.0	110.0	213.0	1.0	0.493274	0.00469484	G|0.995;A|0.005	0.005	strong	.	DPYSL5	69	.	NM_001253724	exon2	c.G27A	p.R9R	CGTGAGGATCCTC	.	PASS	Atlas-SNP
AK8	158067	hgsc.bcm.edu	37	9	135703450	135703450	+	Missense_Mutation	SNP	G	G	T	rs114347984	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49.0	18.0	55.0	0.0	0.367347	0	G|0.997;T|0.003	0.003	strong	.	AK8	45	.	NM_152572	exon7	c.C506A	p.T169K	AGGACCGTGTCTG	.	PASS	Atlas-SNP
ACTG1	71	hgsc.bcm.edu	37	17	79479101	79479101	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37.0	10.0	73.0	0.0	0.27027	0	.	.	none	ACTG1,spleen,lymphoid_neoplasm,0,1	ACTG1	55	1	NM_001614	exon3	c.T191A	p.I64N	GTCAGGATGCCAC	.	PASS	Atlas-SNP
EPB41L4A	64097	hgsc.bcm.edu	37	5	111531387	111531387	+	Silent	SNP	A	A	T	rs149373122	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77.0	37.0	86.0	0.0	0.480519	0	A|0.993;T|0.007	0.007	strong	.	EPB41L4A	130	.	NM_022140	exon16	c.T1395A	p.G465G	ATCTTCACCACTG	.	PASS	Atlas-SNP
OGDHL	55753	hgsc.bcm.edu	37	10	50944528	50944528	+	Missense_Mutation	SNP	C	C	A	rs140281439	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63.0	28.0	58.0	0.0	0.444444	0	C|0.998;A|0.002	0.002	strong	OGDHL,NS,carcinoma,0,1	OGDHL	149	1	NM_018245	exon21	c.G2629T	p.A877S	GTGCTGCGGCCCC	.	PASS	Atlas-SNP
BTG1	694	hgsc.bcm.edu	37	12	92539189	92539189	+	Silent	SNP	G	G	A	rs201780644	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106.0	30.0	109.0	0.0	0.283019	0	G|1.000;A|0.000	0.000	strong	.	BTG1	30	.	NM_001731	exon1	c.C123T	p.S41S	GCTCTGGCTGAAG	.	PASS	Atlas-SNP
TSPEAR	54084	hgsc.bcm.edu	37	21	45949769	45949769	+	Silent	SNP	G	G	A	rs117791519	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57.0	40.0	36.0	0.0	0.701754	0	G|0.996;A|0.004	0.004	strong	.	TSPEAR	110	.	NM_144991	exon5	c.C702T	p.N234N	CGGGGCGTTCCTG	.	PASS	Atlas-SNP
KRAS	3845	hgsc.bcm.edu	37	12	25362777	25362777	+	Silent	SNP	A	A	G	rs1137282	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122.0	63.0	102.0	0.0	0.516393	0	T|0.136;G|0.154;C|0.028;A|0.682	0.154	strong	.	KRAS	30930	.	NM_004985	exon5	c.T519C	p.D173D	TTTACCATCTTTG	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151962183	151962183	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	288.0	20.0	245.0	0.0	0.0694444	0	.	.	none	MLL3_ENST00000355193,right_upper_lobe,carcinoma,0,2	MLL3	1564	2	NM_170606	exon8	c.T1124G	p.V375G	GGAGTAACCGCTA	.	scavenged	Atlas-SNP
C3orf30	152405	hgsc.bcm.edu	37	3	118865647	118865647	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47.0	22.0	68.0	0.0	0.468085	0	.	.	none	C3orf30,NS,carcinoma,0,1	C3orf30	64	1	NM_152539	exon1	c.G611A	p.R204Q	CTGAGCGAAGAAC	.	PASS	Atlas-SNP
GORASP1	64689	hgsc.bcm.edu	37	3	39140352	39140352	+	Missense_Mutation	SNP	C	C	A	rs138864486	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131.0	58.0	107.0	0.0	0.442748	0	C|0.993;A|0.007	0.007	strong	.	GORASP1	42	.	NM_031899	exon8	c.G949T	p.D317Y	TGTTGTCCAAGAG	.	PASS	Atlas-SNP
HNF1A	6927	hgsc.bcm.edu	37	12	121435427	121435427	+	Missense_Mutation	SNP	G	G	A	rs2464196	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127.0	124.0	114.0	0.0	0.976378	0	G|0.725;A|0.275	0.275	strong	.	HNF1A	302	.	NM_000545	exon7	c.G1460A	p.S487N	CCCAGAGCCCCTT	.	PASS	Atlas-SNP
SLC7A1	6541	hgsc.bcm.edu	37	13	30110256	30110256	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71.0	31.0	78.0	0.0	0.43662	0	.	.	none	.	SLC7A1	64	.	NM_003045	exon3	c.G70C	p.E24Q	TCTCCTCCCGGCT	.	PASS	Atlas-SNP
PARVA	55742	hgsc.bcm.edu	37	11	12525965	12525965	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131.0	63.0	160.0	0.0	0.480916	0	.	.	none	.	PARVA	27	.	NM_018222	exon6	c.G766C	p.V256L	CAAGTGGTTGTGG	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2164244	2164244	+	Missense_Mutation	SNP	G	G	A	rs139963923		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63.0	24.0	78.0	0.0	0.380952	0	G|1.000;A|0.000	0.000	weak	.	PKD1	184	.	NM_000296	exon11	c.C2780T	p.T927M	TCCGCCGTCACCC	.	PASS	Atlas-SNP
VANGL1	81839	hgsc.bcm.edu	37	1	116206871	116206871	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46.0	25.0	60.0	0.0	0.543478	0	.	.	none	.	VANGL1	65	.	NM_138959	exon4	c.A794G	p.Y265C	GCTTCTACAGCCT	.	PASS	Atlas-SNP
PIGT	51604	hgsc.bcm.edu	37	20	44048224	44048224	+	Silent	SNP	T	T	C	rs147475258	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88.0	35.0	57.0	0.0	0.397727	0	T|0.999;C|0.001	0.001	strong	.	PIGT	85	.	NM_001184729	exon5	c.T675C	p.V225V	CCCTGTTTGCAGA	.	PASS	Atlas-SNP
CYP2A7	1549	hgsc.bcm.edu	37	19	41382544	41382544	+	Silent	SNP	G	G	A	rs116333747	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	254.0	119.0	202.0	0.0	0.468504	0	G|0.992;A|0.008	0.008	strong	.	CYP2A7	71	.	NM_000764	exon8	c.C1191T	p.S397S	CAGCACGGAGCCC	.	PASS	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140564454	140564454	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152.0	50.0	133.0	0.0	0.328947	0	.	.	none	.	PCDHB16	159	.	NM_020957	exon1	c.T2320G	p.F774V	CCCAACTTCTCTC	.	PASS	Atlas-SNP
MAGI2	9863	hgsc.bcm.edu	37	7	78636484	78636484	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74.0	25.0	100.0	0.0	0.337838	0	.	.	none	MAGI2,caecum,carcinoma,0,1	MAGI2	246	1	NM_012301	exon2	c.T340G	p.L114V	ATCGTAAGTTGAG	.	PASS	Atlas-SNP
MBTPS1	8720	hgsc.bcm.edu	37	16	84125394	84125394	+	Silent	SNP	G	G	A	rs113848224	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90.0	36.0	120.0	0.0	0.4	0	G|0.998;A|0.002	0.002	strong	.	MBTPS1	85	.	NM_003791	exon7	c.C906T	p.D302D	TAACACGTCGATC	.	PASS	Atlas-SNP
FAM83G	644815	hgsc.bcm.edu	37	17	18881605	18881605	+	Missense_Mutation	SNP	C	C	A	rs201344489	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119.0	72.0	119.0	0.0	0.605042	0	C|0.998;A|0.002	0.002	strong	.	FAM83G	51	.	NM_001039999	exon5	c.G1374T	p.Q458H	CTGGTGCTGGGCG	.	PASS	Atlas-SNP
CACNA2D4	93589	hgsc.bcm.edu	37	12	1910786	1910786	+	Missense_Mutation	SNP	C	C	T	rs62621429	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	32.0	49.0	0.0	0.52459	0	C|0.979;T|0.021	0.021	strong	.	CACNA2D4	220	.	NM_172364	exon30	c.G2746A	p.D916N	CACCATCCACCTC	.	PASS	Atlas-SNP
C12orf77	196415	hgsc.bcm.edu	37	12	25148927	25148927	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179.0	42.0	120.0	0.0	0.234637	0	.	.	none	.	C12orf77	18	.	NM_001101339	exon3	c.G221A	p.S74N	CGTATGCTGTCCA	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89402447	89402447	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100.0	47.0	115.0	0.0	0.47	0	.	.	none	.	ACAN	220	.	NM_001135	exon12	c.G6631A	p.V2211I	CTGGGCGTTGTCA	.	PASS	Atlas-SNP
SHC3	53358	hgsc.bcm.edu	37	9	91652977	91652977	+	Silent	SNP	G	G	A	rs56005403	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40.0	20.0	29.0	0.0	0.5	0	G|0.990;A|0.010	0.010	strong	.	SHC3	66	.	NM_016848	exon11	c.C1587T	p.G529G	AAAGGAGCCCGGG	.	PASS	Atlas-SNP
FABP7	2173	hgsc.bcm.edu	37	6	123104889	123104889	+	Missense_Mutation	SNP	G	G	A	rs77153426	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137.0	65.0	120.0	0.0	0.474453	0	.	.	alt	.	FABP7	10	.	NM_001446	exon4	c.G376A	p.V126I	GTTGCTGTTCGCC	.	PASS	Atlas-SNP
ACAA1	30	hgsc.bcm.edu	37	3	38167095	38167095	+	Missense_Mutation	SNP	A	A	G	rs2229528	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100.0	46.0	105.0	0.0	0.46	0	T|0.067;G|0.026	0.026	strong	.	ACAA1	32	.	NM_001607	exon11	c.T1160C	p.V387A	GTGATGACCTGTC	.	PASS	Atlas-SNP
KIAA1586	57691	hgsc.bcm.edu	37	6	56918304	56918304	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83.0	31.0	74.0	0.0	0.373494	0	.	.	none	.	KIAA1586	59	.	NM_020931	exon4	c.G1007A	p.C336Y	TCCAGTGCACAAT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494661	134494661	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81.0	23.0	82.0	0.0	0.283951	0	.	.	none	SGK1_ENST00000367858,lymph_node,lymphoid_neoplasm,0,3	SGK1	387	3	NM_001143676	exon6	c.C557T	p.P186L	GCATGAGGATTGG	.	PASS	Atlas-SNP
MCMDC2	157777	hgsc.bcm.edu	37	8	67813482	67813482	+	Silent	SNP	G	G	A	rs139959817	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171.0	65.0	180.0	0.0	0.380117	0	G|0.979;A|0.021	0.021	strong	.	MCMDC2	84	.	NM_173518	exon13	c.G1668A	p.L556L	CAGCTTGGAAGCA	.	PASS	Atlas-SNP
KIAA0922	23240	hgsc.bcm.edu	37	4	154519764	154519764	+	Missense_Mutation	SNP	A	A	G	rs72729691	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75.0	34.0	77.0	0.0	0.453333	0	A|0.994;G|0.006	0.006	strong	.	KIAA0922	214	.	NM_001131007	exon21	c.A2146G	p.M716V	ATTGACATGATTG	.	PASS	Atlas-SNP
PCDHAC1	56135	hgsc.bcm.edu	37	5	140306924	140306924	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71.0	15.0	95.0	0.0	0.211268	0	.	.	none	.	PCDHAC1	141	.	NM_031882	exon1	c.A447T	p.Q149H	TGCCCAAGATGAC	.	PASS	Atlas-SNP
ZFP90	146198	hgsc.bcm.edu	37	16	68598023	68598023	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70.0	14.0	79.0	0.0	0.2	0	.	.	none	ZFP90,NS,carcinoma,0,1	ZFP90	67	1	NM_133458	exon4	c.A1333G	p.T445A	ACTCTTACCGAAG	.	PASS	Atlas-SNP
KRT33A	3883	hgsc.bcm.edu	37	17	39502917	39502917	+	Missense_Mutation	SNP	C	C	A	rs144588166	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	30.0	92.0	0.0	0.410959	0	C|0.999;A|0.001	0.001	strong	.	KRT33A	53	.	NM_004138	exon6	c.G880T	p.D294Y	GAGAGTCTCGCTG	.	PASS	Atlas-SNP
CYP2B6	1555	hgsc.bcm.edu	37	19	41497346	41497346	+	Missense_Mutation	SNP	A	A	G	rs35303484	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32.0	16.0	28.0	0.0	0.5	0	A|0.997;G|0.003;T|0.000	0.003	strong	.	CYP2B6	79	.	NM_000767	exon1	c.A136G	p.M46V	CTGCAGATGGATA	.	PASS	Atlas-SNP
GMPS	8833	hgsc.bcm.edu	37	3	155633817	155633817	+	Nonsense_Mutation	SNP	G	G	T	rs201869567	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53.0	4.0	70.0	0.0	0.0754717	0	G|0.999;A|0.001	.	alt	.	GMPS	70	.	NM_003875	exon9	c.G1048T	p.E350X	GCCAATGAAGTAA	.	PASS	Atlas-SNP
DUSP2	1844	hgsc.bcm.edu	37	2	96810609	96810609	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60.0	20.0	75.0	0.0	0.333333	0	.	.	none	.	DUSP2	20	.	NM_004418	exon2	c.G401A	p.G134D	TGGAAGCCGTCGA	.	PASS	Atlas-SNP
CREB3L4	148327	hgsc.bcm.edu	37	1	153941842	153941842	+	Missense_Mutation	SNP	T	T	G	rs186432230	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119.0	62.0	125.0	0.0	0.521008	0	T|1.000;G|0.000	0.000	strong	.	CREB3L4	36	.	NM_001255978	exon4	c.T454G	p.S152A	CCTGATTCCTGCA	.	PASS	Atlas-SNP
OR9Q1	219956	hgsc.bcm.edu	37	11	57947163	57947163	+	Missense_Mutation	SNP	G	G	A	rs111629598	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	210.0	105.0	175.0	0.0	0.5	0	G|0.976;A|0.024	0.024	strong	.	OR9Q1	60	.	NM_001005212	exon3	c.G247A	p.A83T	ATGCTGGCAGTGC	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230404	23230404	+	Missense_Mutation	SNP	A	A	C	rs115653109	byfrequency;by1000genomes;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41.0	12.0	141.0	0.0	0.292683	0	A|0.999;G|0.001	.	alt	.	IGLL5	26	.	NM_001256296	exon1	c.A65C	p.E22A	AGTTGGAAGCAGC	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	6950847	6950847	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103.0	27.0	110.0	0.0	0.262136	0	.	.	none	.	LAMA1	458	.	NM_005559	exon58	c.T8331G	p.F2777L	AAGGTCAAACATG	.	PASS	Atlas-SNP
KIAA1804	0	hgsc.bcm.edu	37	1	233511675	233511675	+	Missense_Mutation	SNP	A	A	C	rs35758282	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116.0	53.0	112.0	0.0	0.456897	0	A|0.998;C|0.002	0.002	strong	.	KIAA1804	129	.	NM_032435	exon7	c.A1689C	p.E563D	AGATGAAAGCAAT	.	PASS	Atlas-SNP
TAS2R14	50840	hgsc.bcm.edu	37	12	11091206	11091206	+	Missense_Mutation	SNP	G	G	A	rs35804287	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77.0	42.0	78.0	0.0	0.545455	0	G|0.989;A|0.011	0.011	strong	.	TAS2R14	26	.	NM_023922	exon1	c.C601T	p.L201F	AGATGAGGAGAAG	.	PASS	Atlas-SNP
SPDEF	25803	hgsc.bcm.edu	37	6	34507305	34507305	+	Silent	SNP	C	C	T	rs374584207		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	190.0	34.0	217.0	0.0	0.178947	0	.	.	weak	.	SPDEF	34	.	NM_012391	exon4	c.G669A	p.A223A	GTGAATCGCCCCA	.	PASS	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68705754	68705754	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50.0	6.0	65.0	0.0	0.12	0	.	.	none	IGHMBP2,right_upper_lobe,carcinoma,0,1	IGHMBP2	83	1	NM_002180	exon14	c.G2716A	p.V906I	GCCGGCGTCACAA	.	PASS	Atlas-SNP
KLHL42	57542	hgsc.bcm.edu	37	12	27950775	27950775	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52.0	17.0	60.0	0.0	0.326923	0	.	.	none	.	.	.	.	NM_020782	exon3	c.G1194A	p.G398G	GGGGGGGTGTCTC	.	PASS	Atlas-SNP
APOLD1	81575	hgsc.bcm.edu	37	12	12940402	12940402	+	Missense_Mutation	SNP	C	C	T	rs146348815		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80.0	30.0	87.0	0.0	0.375	0	C|1.000;T|0.000	0.000	weak	.	APOLD1	10	.	NM_001130415	exon2	c.C656T	p.T219I	GGGACACCAAGGT	.	PASS	Atlas-SNP
MDGA1	266727	hgsc.bcm.edu	37	6	37605158	37605158	+	Missense_Mutation	SNP	C	C	T	rs201115181	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101.0	20.0	127.0	0.0	0.19802	0	C|0.999;T|0.001	0.001	strong	MDGA1,NS,carcinoma,+2,1	MDGA1	104	1	NM_153487	exon17	c.G2854A	p.A952T	GCAACGCCAAGAG	.	PASS	Atlas-SNP
HIST1H2BL	8340	hgsc.bcm.edu	37	6	27775367	27775367	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94.0	29.0	115.0	0.0	0.308511	0	.	.	none	.	HIST1H2BL	48	.	NM_003519	exon1	c.G318A	p.E106E	GGCCAGCTCCCCC	.	PASS	Atlas-SNP
ZNF831	128611	hgsc.bcm.edu	37	20	57768655	57768655	+	Missense_Mutation	SNP	G	G	A	rs61743779	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53.0	30.0	61.0	0.0	0.566038	0	G|0.996;A|0.004	0.004	strong	.	ZNF831	287	.	NM_178457	exon1	c.G2581A	p.D861N	GATGCCGATCCCG	.	PASS	Atlas-SNP
TIGD2	166815	hgsc.bcm.edu	37	4	90034450	90034450	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76.0	7.0	63.0	0.0	0.0921053	0	.	.	none	.	TIGD2	36	.	NM_145715	exon1	c.T325C	p.F109L	AAGTTCTTTTTTG	.	PASS	Atlas-SNP
ATM	472	hgsc.bcm.edu	37	11	108124761	108124761	+	Missense_Mutation	SNP	T	T	C	rs4986761	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41.0	32.0	53.0	0.0	0.780488	0	T|0.993;C|0.007	0.007	strong	ATM,NS,carcinoma,0,2	ATM	1657	2	NM_000051	exon13	c.T2119C	p.S707P	TACTCATCTGAGG	.	PASS	Atlas-SNP
VGLL2	245806	hgsc.bcm.edu	37	6	117586990	117586990	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68.0	24.0	53.0	0.0	0.352941	0	.	.	none	.	VGLL2	18	.	NM_182645	exon1	c.T64G	p.Y22D	GCCGCCTACACCC	.	PASS	Atlas-SNP
KRTAP19-5	337972	hgsc.bcm.edu	37	21	31874240	31874240	+	Missense_Mutation	SNP	T	T	C	rs117415039	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65.0	24.0	57.0	0.0	0.369231	0	T|0.975;C|0.025	0.025	strong	.	KRTAP19-5	32	.	NM_181611	exon1	c.A169G	p.S57G	GGCAGCTGCGGTA	.	PASS	Atlas-SNP
ADARB2	105	hgsc.bcm.edu	37	10	1246060	1246060	+	Silent	SNP	C	C	T	rs138375235	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44.0	31.0	47.0	0.0	0.704545	0	C|0.997;T|0.003	0.003	strong	.	ADARB2	95	.	NM_018702	exon8	c.G1710A	p.A570A	CAGGAGCGCGCCC	.	PASS	Atlas-SNP
ASPSCR1	79058	hgsc.bcm.edu	37	17	79941511	79941511	+	Silent	SNP	C	C	T	rs11539917	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47.0	29.0	59.0	0.0	0.617021	0	C|0.988;T|0.012	0.012	strong	ASPSCR1_ENST00000306729,colon,carcinoma,0,1	ASPSCR1	27	1	NM_001251888	exon3	c.C240T	p.P80P	GGTGCCCGCTTCC	.	PASS	Atlas-SNP
DYX1C1	161582	hgsc.bcm.edu	37	15	55789910	55789910	+	Missense_Mutation	SNP	C	C	T	rs17819126	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47.0	29.0	49.0	0.0	0.617021	0	C|0.959;T|0.041	0.041	strong	.	DYX1C1	54	.	NM_001033560	exon3	c.G271A	p.V91I	ACTTACCACCCGT	.	PASS	Atlas-SNP
TAS1R2	80834	hgsc.bcm.edu	37	1	19181279	19181279	+	Missense_Mutation	SNP	G	G	A	rs140330444	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39.0	14.0	53.0	0.0	0.358974	0	G|1.000;A|0.000	0.000	weak	.	TAS1R2	134	.	NM_152232	exon3	c.C685T	p.R229W	CGCGCCGGGCCAC	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60898891	60898891	+	Silent	SNP	C	C	T	rs138911913	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51.0	23.0	78.0	0.0	0.45098	0	C|0.999;T|0.001	0.001	strong	.	LAMA5	268	.	NM_005560	exon44	c.G5790A	p.L1930L	GCCTCGCAGGACA	.	PASS	Atlas-SNP
SSX3	10214	hgsc.bcm.edu	37	X	48213499	48213499	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	278.0	109.0	187.0	0.0	0.392086	0	.	.	none	.	SSX3	64	.	NM_021014	exon4	c.G215A	p.R72H	TTATTACGCATGA	.	PASS	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	37	14	102516487	102516487	+	Silent	SNP	G	G	A	rs35079638	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91.0	52.0	87.0	0.0	0.571429	0	G|0.998;A|0.002	0.002	strong	.	DYNC1H1	395	.	NM_001376	exon77	c.G13764A	p.T4588T	CCTGACGCAGCTG	.	PASS	Atlas-SNP
PALD1	27143	hgsc.bcm.edu	37	10	72298745	72298745	+	Missense_Mutation	SNP	C	C	T	rs117244352	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99.0	49.0	115.0	0.0	0.494949	0	C|0.990;T|0.010	0.010	strong	.	.	.	.	NM_014431	exon13	c.C1550T	p.T517M	ACGGCACGGCCCA	.	PASS	Atlas-SNP
TMEM144	55314	hgsc.bcm.edu	37	4	159161513	159161513	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89.0	46.0	117.0	0.0	0.516854	0	.	.	none	.	TMEM144	34	.	NM_018342	exon10	c.G745A	p.A249T	TTTCTGGCCTACT	.	PASS	Atlas-SNP
DGCR2	9993	hgsc.bcm.edu	37	22	19028744	19028744	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72.0	4.0	72.0	0.0	0.0555556	0	.	.	none	.	DGCR2	45	.	NM_005137	exon9	c.C1223T	p.T408M	AGGCCCGTGCCAA	.	PASS	Atlas-SNP
SF3B14	0	hgsc.bcm.edu	37	2	24291323	24291323	+	Silent	SNP	G	G	A	rs41281479	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100.0	49.0	110.0	0.0	0.49	0	G|0.997;A|0.003	0.003	strong	.	SF3B14	6	.	NM_016047	exon3	c.C156T	p.N52N	AGGTGTGTTCCCC	.	PASS	Atlas-SNP
RGAG1	57529	hgsc.bcm.edu	37	X	109696758	109696758	+	Silent	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71.0	24.0	62.0	0.0	0.338028	0	.	.	none	.	RGAG1	168	.	NM_020769	exon3	c.T2913G	p.A971A	CATGGCTTCTGGA	.	PASS	Atlas-SNP
USP37	57695	hgsc.bcm.edu	37	2	219360656	219360656	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59.0	21.0	77.0	0.0	0.355932	0	.	.	none	.	USP37	76	.	NM_020935	exon14	c.A1299G	p.L433L	CTGACTTAAAAAT	.	PASS	Atlas-SNP
KNDC1	85442	hgsc.bcm.edu	37	10	135027195	135027195	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52.0	10.0	61.0	0.0	0.192308	0	.	.	none	.	KNDC1	155	.	NM_152643	exon25	c.C4490T	p.A1497V	CACGGGCCCTGGG	.	PASS	Atlas-SNP
RECQL5	9400	hgsc.bcm.edu	37	17	73657118	73657118	+	Silent	SNP	C	C	T	rs149970344		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155.0	61.0	152.0	0.0	0.393548	0	C|1.000;T|0.000	0.000	weak	.	RECQL5	77	.	NM_001003715	exon6	c.G903A	p.V301V	GTTCTGCACCAGC	.	PASS	Atlas-SNP
PKN3	29941	hgsc.bcm.edu	37	9	131469190	131469190	+	Missense_Mutation	SNP	C	C	A	rs56251280	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60.0	33.0	49.0	0.0	0.55	0	C|0.996;A|0.004	0.004	strong	.	PKN3	62	.	NM_013355	exon5	c.C539A	p.A180E	TGCTGGCGGAGGA	.	PASS	Atlas-SNP
BCL2A1	597	hgsc.bcm.edu	37	15	80263051	80263051	+	Silent	SNP	G	G	A	rs147879852		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	187.0	94.0	160.0	0.0	0.502674	0	G|1.000;A|0.000	0.000	weak	BCL2A1,colon,carcinoma,0,1	BCL2A1	28	1	NM_001114735	exon1	c.C411T	p.N137N	GCCTCCGTTTTGC	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13788927	13788927	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	199.0	37.0	207.0	0.0	0.18593	0	.	.	none	.	DNAH5	868	.	NM_001369	exon51	c.A8545C	p.S2849R	CCAAACTTACTAA	.	PASS	Atlas-SNP
DHX32	55760	hgsc.bcm.edu	37	10	127548215	127548215	+	Missense_Mutation	SNP	G	G	A	rs201005566	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66.0	34.0	84.0	0.0	0.515152	0	.	.	weak	.	DHX32	67	.	NM_018180	exon3	c.C806T	p.S269L	TCACCCGAGTGGT	.	PASS	Atlas-SNP
CARKD	55739	hgsc.bcm.edu	37	13	111287893	111287893	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55.0	40.0	91.0	0.0	0.727273	0	.	.	none	.	CARKD	36	.	NM_018210	exon8	c.G730C	p.V244L	ACGGTGGTCCAGA	.	PASS	Atlas-SNP
C12orf40	283461	hgsc.bcm.edu	37	12	40041723	40041723	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103.0	56.0	118.0	1.0	0.543689	0.00847458	.	.	none	C12orf40,NS,carcinoma,-1,1	C12orf40	118	1	NM_001031748	exon6	c.T514A	p.S172T	TTCACATCTGGAA	.	scavenged	Atlas-SNP
TRANK1	9881	hgsc.bcm.edu	37	3	36873866	36873866	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	270.0	153.0	273.0	0.0	0.566667	0	.	.	none	.	TRANK1	398	.	NM_014831	exon21	c.A7076T	p.H2359L	CACAGGTGGGTCT	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170063380	170063380	+	Missense_Mutation	SNP	T	T	C	rs35413340	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79.0	36.0	85.0	0.0	0.455696	0	T|0.999;C|0.001	0.001	strong	.	LRP2	751	.	NM_004525	exon39	c.A6850G	p.T2284A	AAACAGTGATGCC	.	PASS	Atlas-SNP
RFX8	731220	hgsc.bcm.edu	37	2	102019129	102019129	+	Silent	SNP	C	C	T	rs201832728	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89.0	42.0	81.0	0.0	0.47191	0	.	.	weak	.	RFX8	16	.	NM_001145664	exon11	c.G1014A	p.E338E	CATGTCCTCCTCC	.	PASS	Atlas-SNP
PAQR7	164091	hgsc.bcm.edu	37	1	26189517	26189517	+	Missense_Mutation	SNP	C	C	T	rs6689014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113.0	57.0	101.0	0.0	0.504425	0	C|0.995;T|0.005	0.005	strong	.	PAQR7	23	.	NM_178422	exon2	c.G814A	p.G272R	CCTGCCCGAAGAC	.	PASS	Atlas-SNP
HIST4H4	121504	hgsc.bcm.edu	37	12	14923887	14923887	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83.0	5.0	71.0	0.0	0.060241	0	.	.	none	.	HIST4H4	13	.	NM_175054	exon1	c.C132T	p.V44V	GCGCTTGACGCCC	.	PASS	Atlas-SNP
TMEM69	51249	hgsc.bcm.edu	37	1	46159157	46159157	+	Silent	SNP	C	C	T	rs61735666	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92.0	38.0	84.0	0.0	0.413043	0	C|0.996;T|0.004	0.004	strong	.	TMEM69	20	.	NM_016486	exon3	c.C324T	p.F108F	CCCCTTCGTTGCT	.	PASS	Atlas-SNP
SYNCRIP	10492	hgsc.bcm.edu	37	6	86332210	86332210	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113.0	6.0	93.0	0.0	0.0530973	0	.	.	none	.	SYNCRIP	80	.	NM_006372	exon8	c.T998G	p.V333G	GCCATAACCTCAG	.	PASS	Atlas-SNP
ZNF318	24149	hgsc.bcm.edu	37	6	43305991	43305991	+	Silent	SNP	A	A	T	rs374528550		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102.0	58.0	96.0	0.0	0.568627	0	.	.	weak	.	ZNF318	175	.	NM_014345	exon10	c.T5745A	p.V1915V	ACTAACAACTGAA	.	PASS	Atlas-SNP
GBP1	2633	hgsc.bcm.edu	37	1	89523844	89523844	+	Silent	SNP	G	G	A	rs141095851	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125.0	62.0	106.0	0.0	0.496	0	G|0.999;A|0.001	0.001	strong	.	GBP1	68	.	NM_002053	exon6	c.C705T	p.C235C	GACAAAGCATTTT	.	PASS	Atlas-SNP
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124610	26124610	+	Silent	SNP	G	G	A	rs139293879	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92.0	24.0	100.0	0.0	0.26087	0	G|1.000;C|0.000	.	alt	.	HIST1H2AC	29	.	NM_003512	exon1	c.G150A	p.V50V	GCCGGTGTACCTG	.	PASS	Atlas-SNP
PNPLA1	285848	hgsc.bcm.edu	37	6	36269675	36269675	+	Silent	SNP	T	T	A	rs201231660	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87.0	61.0	108.0	0.0	0.701149	0	T|1.000;A|0.000	0.000	strong	.	PNPLA1	92	.	NM_001145717	exon6	c.T813A	p.I271I	AGTGATTTTCCCC	.	PASS	Atlas-SNP
TLR3	7098	hgsc.bcm.edu	37	4	187004078	187004078	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86.0	26.0	101.0	0.0	0.302326	0	.	.	none	.	TLR3	83	.	NM_003265	exon4	c.A1238C	p.N413T	TACTCAACCTAAC	.	PASS	Atlas-SNP
POLR1A	25885	hgsc.bcm.edu	37	2	86317012	86317012	+	Missense_Mutation	SNP	C	C	G	rs146078741	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69.0	18.0	152.0	0.0	0.26087	0	C|0.991;G|0.009	0.009	strong	.	POLR1A	137	.	NM_015425	exon4	c.G473C	p.R158P	TCCTCCCGAATTT	.	PASS	Atlas-SNP
PPP2R1B	5519	hgsc.bcm.edu	37	11	111637049	111637049	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35.0	17.0	24.0	0.0	0.485714	0	.	.	none	.	PPP2R1B	44	.	NM_001177562	exon1	c.G37A	p.A13T	CCGCTGCTCCTGG	.	PASS	Atlas-SNP
PVRL1	5818	hgsc.bcm.edu	37	11	119548402	119548402	+	Missense_Mutation	SNP	C	C	T	rs78809001	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	208.0	34.0	192.0	0.0	0.163462	0	C|0.991;T|0.009	0.009	strong	.	PVRL1	133	.	NM_002855	exon3	c.G596A	p.R199Q	GGGTTCCGGATCT	.	PASS	Atlas-SNP
ABCC4	10257	hgsc.bcm.edu	37	13	95715014	95715014	+	Silent	SNP	A	A	G	rs11568655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81.0	43.0	71.0	0.0	0.530864	0	A|0.966;G|0.034	0.034	strong	.	ABCC4	248	.	NM_005845	exon26	c.T3310C	p.L1104L	TTGTCAAGATCTT	.	PASS	Atlas-SNP
ADIPOQ	9370	hgsc.bcm.edu	37	3	186572089	186572089	+	Missense_Mutation	SNP	T	T	C	rs17366743	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173.0	69.0	159.0	0.0	0.398844	0	T|0.981;C|0.019	0.019	strong	.	ADIPOQ	35	.	NM_001177800	exon4	c.T331C	p.Y111H	TATGTATACCGCT	.	PASS	Atlas-SNP
RAET1L	154064	hgsc.bcm.edu	37	6	150342155	150342155	+	Missense_Mutation	SNP	C	C	T	rs148198102	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	297.0	144.0	307.0	1.0	0.484848	0.00325733	C|0.994;T|0.006	0.006	strong	.	RAET1L	21	.	NM_130900	exon3	c.G517A	p.E173K	CATTCTCCCACTT	.	PASS	Atlas-SNP
PPP2R3B	28227	hgsc.bcm.edu	37	X	322294	322294	+	Missense_Mutation	SNP	G	G	A	rs200157354	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	241.0	161.0	310.0	0.0	0.66805	0	.	.	weak	.	PPP2R3B	43	.	NM_013239	exon2	c.C356T	p.P119L	GTGGCCGGGGGCA	.	PASS	Atlas-SNP
PTK2	5747	hgsc.bcm.edu	37	8	141711117	141711117	+	Missense_Mutation	SNP	G	G	C	rs185796736	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140.0	67.0	131.0	0.0	0.478571	0	G|0.999;C|0.001	0.001	strong	.	PTK2	311	.	NM_005607	exon26	c.C2438G	p.S813C	ACTGTAGAGTCCT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149492640	149492640	+	Silent	SNP	G	G	A	rs372238122		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109.0	58.0	115.0	0.0	0.53211	0	.	.	weak	.	.	.	.	NM_198455	exon43	c.G6420A	p.P2140P	AGTGCCGGAGACT	.	PASS	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	37	15	68654003	68654003	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57.0	5.0	37.0	0.0	0.0877193	0	.	.	none	.	ITGA11	110	.	NM_001004439	exon5	c.T397C	p.Y133H	TGTAGTAGGAGCT	.	PASS	Atlas-SNP
BTG2	7832	hgsc.bcm.edu	37	1	203274867	203274867	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81.0	30.0	90.0	0.0	0.37037	0	.	.	none	BTG2,lymph_node,lymphoid_neoplasm,-1,2	BTG2	16	2	NM_006763	exon1	c.G133C	p.A45P	CAGGAGGCACTCA	.	PASS	Atlas-SNP
SH3PXD2B	285590	hgsc.bcm.edu	37	5	171766135	171766135	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113.0	28.0	100.0	0.0	0.247788	0	.	.	none	.	SH3PXD2B	91	.	NM_001017995	exon13	c.A1974C	p.E658D	TTGGTCTTCGCCC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1097794	1097794	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68.0	5.0	74.0	0.0	0.0735294	0	.	.	none	.	MUC2	614	.	NM_002457	exon37	c.A6875T	p.K2292M	CCTCCAAGCCACA	.	PASS	Atlas-SNP
CLN8	2055	hgsc.bcm.edu	37	8	1719450	1719450	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160.0	18.0	140.0	0.0	0.1125	0	.	.	none	.	CLN8	64	.	NM_018941	exon2	c.G230C	p.S77T	TTCAGAGCACAGC	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52375854	52375854	+	Silent	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73.0	18.0	63.0	0.0	0.246575	0	.	.	none	.	ZNF577	63	.	NM_032679	exon7	c.A1389C	p.T463T	TTCATTTGTGAGG	.	PASS	Atlas-SNP
LRP6	4040	hgsc.bcm.edu	37	12	12279735	12279735	+	Missense_Mutation	SNP	C	C	T	rs34815107	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93.0	46.0	110.0	0.0	0.494624	0	C|0.994;T|0.006	0.006	strong	.	LRP6	170	.	NM_002336	exon20	c.G4202A	p.R1401H	TTCATACGTGGAC	.	PASS	Atlas-SNP
NPHP4	261734	hgsc.bcm.edu	37	1	6012866	6012866	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42.0	11.0	42.0	0.0	0.261905	0	.	.	none	.	NPHP4	119	.	NM_015102	exon7	c.A704C	p.K235T	ATGGGCTTCTGGA	.	PASS	Atlas-SNP
IAH1	285148	hgsc.bcm.edu	37	2	9616161	9616161	+	Missense_Mutation	SNP	C	C	G	rs61732203	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179.0	178.0	170.0	0.0	0.994413	0	C|0.982;G|0.018	0.018	strong	.	IAH1	12	.	NM_001039613	exon2	c.C127G	p.L43V	GACAGGCTGGTCA	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	29449819	29449819	+	Silent	SNP	C	C	T	rs2293563	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119.0	60.0	126.0	0.0	0.504202	0	C|0.816;T|0.184	0.184	strong	ALK,NS,carcinoma,0,1	ALK	533	1	NM_004304	exon18	c.G3036A	p.T1012T	CAGCACCGTCCCG	.	PASS	Atlas-SNP
DYNC1I1	1780	hgsc.bcm.edu	37	7	95442624	95442624	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63.0	7.0	62.0	0.0	0.111111	0	.	.	none	.	DYNC1I1	111	.	NM_004411	exon4	c.T340A	p.S114T	CAAGACTCAGGCG	.	PASS	Atlas-SNP
TMEM54	113452	hgsc.bcm.edu	37	1	33361552	33361552	+	Missense_Mutation	SNP	C	C	T	rs139394643	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37.0	15.0	32.0	0.0	0.405405	0	C|0.998;T|0.002	0.002	strong	.	TMEM54	12	.	NM_033504	exon3	c.G229A	p.A77T	TGGCTGCGATGCC	.	PASS	Atlas-SNP
SLCO6A1	133482	hgsc.bcm.edu	37	5	101834386	101834386	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122.0	5.0	103.0	0.0	0.0409836	0	.	.	none	.	SLCO6A1	153	.	NM_173488	exon1	c.C163T	p.P55S	CCTCTGGAAGTAG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100686777	100686777	+	Missense_Mutation	SNP	C	C	T	rs138142210	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	234.0	125.0	220.0	0.0	0.534188	0	C|0.983;T|0.017	0.017	strong	MUC17,NS,carcinoma,0,3	MUC17	804	3	NM_001040105	exon3	c.C12080T	p.T4027M	CATCAACGCTTTC	.	PASS	Atlas-SNP
USP36	57602	hgsc.bcm.edu	37	17	76823425	76823425	+	Silent	SNP	G	G	T	rs143701541	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38.0	22.0	27.0	0.0	0.578947	0	G|0.980;T|0.020	0.020	strong	.	USP36	243	.	NM_025090	exon6	c.C591A	p.I197I	TCGGGCGATCTCT	.	PASS	Atlas-SNP
BPHL	670	hgsc.bcm.edu	37	6	3129402	3129402	+	Missense_Mutation	SNP	G	G	A	rs199698749	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71.0	25.0	55.0	0.0	0.352113	0	G|1.000;A|0.000	0.000	strong	.	BPHL	32	.	NM_004332	exon4	c.G502A	p.V168I	GCCTACGTCACTG	.	PASS	Atlas-SNP
RABEP2	79874	hgsc.bcm.edu	37	16	28925694	28925694	+	Missense_Mutation	SNP	G	G	A	rs200278634		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112.0	57.0	116.0	0.0	0.508929	0	.	.	weak	.	RABEP2	48	.	NM_024816	exon5	c.C757T	p.R253C	CCTGGCGGCTTTG	.	PASS	Atlas-SNP
FBXO39	162517	hgsc.bcm.edu	37	17	6684003	6684003	+	Silent	SNP	C	C	G	rs17731806	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49.0	28.0	42.0	0.0	0.571429	0	C|0.963;G|0.037	0.037	strong	.	FBXO39	50	.	NM_153230	exon2	c.C816G	p.S272S	TATGTCCTGGGCC	.	PASS	Atlas-SNP
PON1	5444	hgsc.bcm.edu	37	7	94953765	94953765	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48.0	14.0	36.0	0.0	0.291667	0	.	.	none	.	PON1	55	.	NM_000446	exon1	c.C23G	p.T8S	AAGAGGGTGAGCG	.	PASS	Atlas-SNP
EEFSEC	60678	hgsc.bcm.edu	37	3	128060346	128060346	+	Missense_Mutation	SNP	C	C	T	rs374389896		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95.0	52.0	122.0	0.0	0.547368	0	.	.	weak	.	EEFSEC	53	.	NM_021937	exon5	c.C1057T	p.P353S	TTCAGTCCTGCTC	.	PASS	Atlas-SNP
PTPRD	5789	hgsc.bcm.edu	37	9	8376067	8376067	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56.0	5.0	75.0	0.0	0.0892857	0	.	.	none	.	PTPRD	1348	.	NM_002839	exon39	c.A4530C	p.E1510D	TCTCACTTCTCTC	.	PASS	Atlas-SNP
SECISBP2	79048	hgsc.bcm.edu	37	9	91954848	91954848	+	Missense_Mutation	SNP	C	C	G	rs45452691	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43.0	19.0	61.0	0.0	0.44186	0	C|0.961;G|0.039	0.039	strong	.	SECISBP2	64	.	NM_024077	exon9	c.C1282G	p.Q428E	AAATTTCAATCTA	.	PASS	Atlas-SNP
PCDHA13	56136	hgsc.bcm.edu	37	5	140263210	140263210	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72.0	6.0	75.0	0.0	0.0833333	0	.	.	none	PCDHA13,NS,carcinoma,-2,1	PCDHA13	213	1	NM_031865	exon1	c.C1357G	p.P453A	AACGCGCCGGCGT	.	PASS	Atlas-SNP
HORMAD2	150280	hgsc.bcm.edu	37	22	30518155	30518155	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107.0	52.0	106.0	0.0	0.485981	0	.	.	none	.	HORMAD2	12	.	NM_152510	exon10	c.C771T	p.I257I	TGAGATCGCCCAT	.	PASS	Atlas-SNP
CIT	11113	hgsc.bcm.edu	37	12	120222830	120222830	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91.0	25.0	107.0	0.0	0.274725	0	.	.	none	.	CIT	535	.	NM_001206999	exon11	c.C1335T	p.S445S	CATGGAGCTAGTC	.	PASS	Atlas-SNP
C7orf72	100130988	hgsc.bcm.edu	37	7	50175760	50175760	+	Missense_Mutation	SNP	T	T	G	rs149326344	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114.0	28.0	177.0	0.0	0.245614	0	T|0.999;G|0.001	0.001	strong	.	C7orf72	26	.	NM_001161834	exon5	c.T934G	p.F312V	ATTAATTTGTAAG	.	PASS	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	37	16	705344	705344	+	Silent	SNP	C	C	A	rs144704309	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26.0	14.0	21.0	0.0	0.538462	0	C|0.999;A|0.001	0.001	strong	.	WDR90	107	.	NM_145294	exon15	c.C1594A	p.R532R	CTCTGGCGGCTGC	.	PASS	Atlas-SNP
ACTG1	71	hgsc.bcm.edu	37	17	79479099	79479099	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37.0	10.0	74.0	0.0	0.27027	0	.	.	none	.	ACTG1	55	.	NM_001614	exon3	c.C193A	p.L65M	GGGTCAGGATGCC	.	PASS	Atlas-SNP
TMEM108	66000	hgsc.bcm.edu	37	3	133098806	133098806	+	Missense_Mutation	SNP	C	C	T	rs34111099	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109.0	55.0	125.0	0.0	0.504587	0	C|0.952;T|0.048	0.048	strong	TMEM108,rectum,carcinoma,0,1	TMEM108	67	1	NM_023943	exon4	c.C251T	p.P84L	CAACACCGACACC	.	PASS	Atlas-SNP
NEFM	4741	hgsc.bcm.edu	37	8	24774646	24774646	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140.0	79.0	148.0	0.0	0.564286	0	.	.	none	.	NEFM	115	.	NM_005382	exon3	c.C1278G	p.H426Q	TACACACCGACCC	.	PASS	Atlas-SNP
DOCK8	81704	hgsc.bcm.edu	37	9	399255	399255	+	Missense_Mutation	SNP	G	G	A	rs34627722	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96.0	40.0	138.0	0.0	0.416667	0	G|0.945;A|0.055	0.055	strong	.	DOCK8	401	.	NM_203447	exon26	c.G3230A	p.S1077N	ATTGCAGCCAGGT	.	PASS	Atlas-SNP
FGF5	2250	hgsc.bcm.edu	37	4	81188221	81188221	+	Missense_Mutation	SNP	G	G	T	rs112475347	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111.0	57.0	121.0	0.0	0.513514	0	G|0.998;T|0.002	0.002	strong	.	FGF5	49	.	NM_004464	exon1	c.G243T	p.W81C	CCAGTGGAGCCCC	.	PASS	Atlas-SNP
FEZ2	9637	hgsc.bcm.edu	37	2	36818109	36818109	+	Silent	SNP	T	T	C	rs117617575	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197.0	92.0	176.0	0.0	0.467005	0	T|0.998;C|0.002	0.002	strong	.	FEZ2	13	.	NM_001042548	exon2	c.A312G	p.V104V	CCAGTCTACAGGC	.	PASS	Atlas-SNP
OR2C1	4993	hgsc.bcm.edu	37	16	3406651	3406651	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81.0	34.0	67.0	0.0	0.419753	0	.	.	none	.	OR2C1	38	.	NM_012368	exon1	c.G711A	p.A237A	AAAGGCGTTCAAT	.	PASS	Atlas-SNP
SPATA16	83893	hgsc.bcm.edu	37	3	172835469	172835469	+	Missense_Mutation	SNP	T	T	C	rs115897458	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	210.0	92.0	231.0	1.0	0.438095	0.004329	T|0.996;C|0.004	0.004	strong	.	SPATA16	111	.	NM_031955	exon2	c.A53G	p.H18R	TGATCATGATAGA	.	PASS	Atlas-SNP
TTC30A	92104	hgsc.bcm.edu	37	2	178482246	178482246	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	246.0	31.0	241.0	0.0	0.126016	0	.	.	none	.	TTC30A	60	.	NM_152275	exon1	c.A1184C	p.K395T	ACTTGCTTGGTGA	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126329944	126329944	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62.0	4.0	78.0	0.0	0.0645161	0	.	.	none	.	FAT4	1752	.	NM_024582	exon4	c.A5915T	p.D1972V	ATGCAGATGATGG	.	PASS	Atlas-SNP
CEL	1056	hgsc.bcm.edu	37	9	135942008	135942008	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52.0	26.0	33.0	0.0	0.5	0	.	.	none	.	CEL	71	.	NM_001807	exon5	c.C639T	p.L213L	CACGCTCTTCGGG	.	PASS	Atlas-SNP
OR4A47	403253	hgsc.bcm.edu	37	11	48511105	48511105	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106.0	8.0	89.0	0.0	0.0754717	0	.	.	none	.	OR4A47	72	.	NM_001005512	exon1	c.T761G	p.F254C	GTATTTTTATGTA	.	PASS	Atlas-SNP
AP1M1	8907	hgsc.bcm.edu	37	19	16318904	16318904	+	Silent	SNP	G	G	C	rs143435975	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112.0	58.0	109.0	0.0	0.517857	0	G|0.996;C|0.004	0.004	strong	.	AP1M1	48	.	NM_001130524	exon4	c.G342C	p.L114L	GCTGCTGGACGAG	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187541971	187541971	+	Silent	SNP	G	G	A	rs372720339	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119.0	62.0	135.0	0.0	0.521008	0	.	.	alt	.	FAT1	500	.	NM_005245	exon10	c.C5769T	p.I1923I	CTCCCCGATGTTG	.	PASS	Atlas-SNP
ESR1	2099	hgsc.bcm.edu	37	6	152201863	152201863	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50.0	4.0	59.0	0.0	0.08	0	.	.	none	.	ESR1	94	.	NM_000125	exon3	c.C717T	p.A239A	CCAGGCCTGCCGG	.	PASS	Atlas-SNP
DHX57	90957	hgsc.bcm.edu	37	2	39090515	39090515	+	Missense_Mutation	SNP	T	T	G	rs199537184	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58.0	30.0	46.0	0.0	0.517241	0	.	.	weak	.	DHX57	127	.	NM_198963	exon3	c.A371C	p.D124A	CCAGCATCAGCAT	.	PASS	Atlas-SNP
KIAA1143	57456	hgsc.bcm.edu	37	3	44794955	44794955	+	Missense_Mutation	SNP	T	T	C	rs138479225	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140.0	72.0	110.0	0.0	0.514286	0	T|0.997;C|0.003	0.003	strong	.	KIAA1143	10	.	NM_020696	exon3	c.A343G	p.S115G	TTGAGCTTGCTGT	.	PASS	Atlas-SNP
GRIK2	2898	hgsc.bcm.edu	37	6	102074485	102074485	+	Missense_Mutation	SNP	G	G	A	rs201893729	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107.0	60.0	96.0	0.0	0.560748	0	G|0.999;A|0.001	0.001	weak	GRIK2_ENST00000421544,NS,carcinoma,0,2	GRIK2	487	2	NM_021956	exon3	c.G514A	p.V172I	AAAACCGTCACGG	.	PASS	Atlas-SNP
ANKRD66	100287718	hgsc.bcm.edu	37	6	46721588	46721588	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109.0	7.0	115.0	0.0	0.0642202	0	.	.	none	.	.	.	.	NM_001162435	exon4	c.C458T	p.A153V	TCCATGCATTGCA	.	PASS	Atlas-SNP
KCNMB3	27094	hgsc.bcm.edu	37	3	178962370	178962370	+	Silent	SNP	C	C	T	rs139532669	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197.0	97.0	177.0	0.0	0.492386	0	C|0.994;T|0.006	0.006	strong	.	KCNMB3	46	.	NM_014407	exon3	c.G372A	p.P124P	AAGACACGGGTAC	.	PASS	Atlas-SNP
RNF123	63891	hgsc.bcm.edu	37	3	49749979	49749979	+	Missense_Mutation	SNP	C	C	T	rs201817210		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110.0	45.0	126.0	0.0	0.409091	0	C|0.999;T|0.001	0.001	weak	.	RNF123	100	.	NM_022064	exon27	c.C2564T	p.T855I	ATCGCACAGGGTC	.	PASS	Atlas-SNP
BRAT1	221927	hgsc.bcm.edu	37	7	2578924	2578924	+	Silent	SNP	G	G	A	rs61746940	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162.0	70.0	122.0	0.0	0.432099	0	G|0.998;A|0.002	0.002	strong	.	BRAT1	57	.	NM_152743	exon13	c.C1659T	p.L553L	CTGGAGGAGCTGC	.	PASS	Atlas-SNP
ACTG1	71	hgsc.bcm.edu	37	17	79479108	79479108	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37.0	9.0	69.0	0.0	0.243243	0	.	.	none	.	ACTG1	55	.	NM_001614	exon3	c.C184T	p.R62C	TGCCACGCTTGCT	.	PASS	Atlas-SNP
BCCIP	56647	hgsc.bcm.edu	37	10	127541743	127541743	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	28.0	79.0	0.0	0.459016	0	.	.	none	.	BCCIP	48	.	NM_016567	exon8	c.A900G	p.L300L	TGGACTAATTCAA	.	PASS	Atlas-SNP
JAK1	3716	hgsc.bcm.edu	37	1	65313232	65313232	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126.0	39.0	135.0	0.0	0.309524	0	.	.	none	.	JAK1	209	.	NM_002227	exon13	c.C1882T	p.H628Y	CCCTGTGGCTGGG	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494280	134494280	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96.0	20.0	96.0	0.0	0.208333	0	.	.	none	.	SGK1	387	.	NM_001143676	exon8	c.A715T	p.M239L	CCGACATAATATG	.	PASS	Atlas-SNP
C5orf20	140947	hgsc.bcm.edu	37	5	134782396	134782396	+	Missense_Mutation	SNP	T	T	A	rs67187482	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79.0	31.0	76.0	0.0	0.392405	0	T|0.905;A|0.095	0.095	strong	.	C5orf20	16	.	NM_130848	exon1	c.A403T	p.S135C	TGAAACTACAAAC	.	PASS	Atlas-SNP
SYNE3	161176	hgsc.bcm.edu	37	14	95884294	95884294	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81.0	7.0	98.0	0.0	0.0864198	0	.	.	none	.	SYNE3	130	.	NM_152592	exon17	c.C2797T	p.L933F	GCAGAAGCAGCTG	.	PASS	Atlas-SNP
ARAP3	64411	hgsc.bcm.edu	37	5	141052986	141052986	+	Missense_Mutation	SNP	C	C	T	rs150744263	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	224.0	104.0	259.0	1.0	0.464286	0.003861	C|0.997;T|0.003	0.003	strong	.	ARAP3	139	.	NM_022481	exon6	c.G954A	p.M318I	AAAGTACATCAGA	.	PASS	Atlas-SNP
KRTAP1-3	81850	hgsc.bcm.edu	37	17	39191027	39191027	+	Missense_Mutation	SNP	G	G	A	rs140428118	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145.0	76.0	166.0	0.0	0.524138	0	G|0.997;A|0.003	0.003	strong	.	KRTAP1-3	18	.	NM_030966	exon1	c.C47T	p.T16I	CCACTGGTGGAGC	.	PASS	Atlas-SNP
ZFYVE20	64145	hgsc.bcm.edu	37	3	15126313	15126313	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123.0	58.0	119.0	0.0	0.471545	0	.	.	none	.	ZFYVE20	61	.	NM_022340	exon8	c.G527A	p.R176H	TGGTGGCGGCGGT	.	PASS	Atlas-SNP
UHRF2	115426	hgsc.bcm.edu	37	9	6413643	6413643	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14.0	5.0	22.0	0.0	0.357143	0	.	.	none	.	UHRF2	50	.	NM_152896	exon1	c.G153A	p.Q51Q	CAAGCAGGTGAGG	.	PASS	Atlas-SNP
TFDP3	51270	hgsc.bcm.edu	37	X	132352230	132352230	+	Missense_Mutation	SNP	C	C	G	rs28455963	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134.0	52.0	66.0	0.0	0.38806	0	C|0.877;G|0.123	0.123	strong	.	TFDP3	92	.	NM_016521	exon1	c.G58C	p.E20Q	GGTTCTCGTCCAT	.	PASS	Atlas-SNP
LDHAL6A	160287	hgsc.bcm.edu	37	11	18485611	18485611	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67.0	25.0	56.0	0.0	0.373134	0	.	.	none	.	LDHAL6A	35	.	NM_144972	exon2	c.T230C	p.I77T	CAAATATTGTCTC	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186121995	186121995	+	Missense_Mutation	SNP	A	A	T	rs114364265	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169.0	72.0	158.0	0.0	0.426035	0	A|0.996;T|0.004	0.004	strong	.	HMCN1	797	.	NM_031935	exon96	c.A15010T	p.T5004S	GAAGTCACTGTAA	.	PASS	Atlas-SNP
HCFC1	3054	hgsc.bcm.edu	37	X	153223257	153223257	+	Silent	SNP	C	C	T	rs3027888	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98.0	22.0	66.0	0.0	0.22449	0	C|0.998;T|0.002	0.002	strong	.	HCFC1	284	.	NM_005334	exon12	c.G2109A	p.T703T	AGGACCCGTGGAC	.	PASS	Atlas-SNP
RORA	6095	hgsc.bcm.edu	37	15	61521304	61521304	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45.0	18.0	49.0	0.0	0.4	0	.	.	none	.	RORA	114	.	NM_134261	exon1	c.G114A	p.K38K	CTCGCTCTTGCGG	.	PASS	Atlas-SNP
TMEM155	132332	hgsc.bcm.edu	37	4	122682720	122682720	+	Missense_Mutation	SNP	C	C	T	rs138330999	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	243.0	125.0	261.0	0.0	0.514403	0	C|0.995;T|0.005	0.005	strong	TMEM155,NS,carcinoma,0,1	TMEM155	17	1	NM_152399	exon5	c.G185A	p.R62H	TGCAAGCGAACCA	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52375907	52375907	+	Silent	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76.0	17.0	83.0	0.0	0.223684	0	.	.	none	ZNF577,colon,carcinoma,+1,1	ZNF577	63	1	NM_032679	exon7	c.A1336C	p.R446R	GATTTCTTGGAAA	.	PASS	Atlas-SNP
HIST1H2AD	3013	hgsc.bcm.edu	37	6	26199193	26199193	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164.0	31.0	182.0	0.0	0.189024	0	.	.	none	HIST1H2AD,NS,lymphoid_neoplasm,0,1	HIST1H2AD	20	1	NM_021065	exon1	c.G279A	p.E93E	GTTTAGCTCCTCG	.	PASS	Atlas-SNP
PLEKHG1	57480	hgsc.bcm.edu	37	6	151152250	151152250	+	Missense_Mutation	SNP	A	A	G	rs148178393	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71.0	35.0	55.0	0.0	0.492958	0	A|0.991;G|0.009	0.009	strong	.	PLEKHG1	97	.	NM_001029884	exon16	c.A2003G	p.D668G	ATGAGGACTTAAA	.	PASS	Atlas-SNP
GPR128	84873	hgsc.bcm.edu	37	3	100328750	100328750	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	254.0	113.0	225.0	0.0	0.444882	0	.	.	none	.	GPR128	126	.	NM_032787	exon1	c.G50A	p.C17Y	TCGTGTGTGGACT	.	PASS	Atlas-SNP
PRKAA1	5562	hgsc.bcm.edu	37	5	40798278	40798278	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117.0	22.0	83.0	0.0	0.188034	0	.	.	none	.	PRKAA1	27	.	NM_006251	exon1	c.G14A	p.S5N	CAGGAACTGAGTC	.	PASS	Atlas-SNP
PLP2	5355	hgsc.bcm.edu	37	X	49029758	49029758	+	Silent	SNP	G	G	A	rs145837656		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60.0	24.0	38.0	0.0	0.4	0	G|1.000;A|0.000	0.000	weak	.	PLP2	25	.	NM_002668	exon3	c.G273A	p.A91A	CATAGCGGCAATC	.	PASS	Atlas-SNP
LY6G5C	80741	hgsc.bcm.edu	37	6	31647044	31647044	+	Silent	SNP	A	A	G	rs143778717	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69.0	18.0	80.0	0.0	0.26087	0	A|0.999;G|0.001	0.001	strong	.	LY6G5C	8	.	NM_025262	exon2	c.T123C	p.G41G	AAACTTACCTAGA	.	PASS	Atlas-SNP
C9orf114	51490	hgsc.bcm.edu	37	9	131585086	131585086	+	Silent	SNP	G	G	C	rs35677895	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119.0	63.0	97.0	0.0	0.529412	0	G|0.990;C|0.010	0.010	strong	.	C9orf114	28	.	NM_016390	exon12	c.C1089G	p.A363A	CTGCAGGGCGGCC	.	PASS	Atlas-SNP
DHX33	56919	hgsc.bcm.edu	37	17	5364393	5364393	+	Missense_Mutation	SNP	A	A	G	rs141223137	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70.0	28.0	61.0	0.0	0.4	0	A|0.996;G|0.004	0.004	strong	DHX33,NS,carcinoma,+2,3	DHX33	41	3	NM_020162	exon4	c.T715C	p.F239L	GAGAGAACAGGTC	.	PASS	Atlas-SNP
SPATA31D1	389763	hgsc.bcm.edu	37	9	84610059	84610059	+	Silent	SNP	T	T	C	rs200816660	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18.0	11.0	29.0	0.0	0.611111	0	T|0.999;C|0.001	0.001	strong	.	.	.	.	NM_001001670	exon4	c.T4674C	p.T1558T	CCTAACTGGACAG	.	PASS	Atlas-SNP
DUSP8	1850	hgsc.bcm.edu	37	11	1580172	1580172	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121.0	34.0	119.0	0.0	0.280992	0	.	.	none	.	DUSP8	22	.	NM_004420	exon4	c.A484T	p.T162S	TGCGGGTCAGGCC	.	PASS	Atlas-SNP
EGFR	1956	hgsc.bcm.edu	37	7	55238874	55238874	+	Silent	SNP	T	T	A	rs2227984	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40.0	14.0	59.0	0.0	0.35	0	T|0.645;A|0.355	0.355	strong	.	EGFR	20426	.	NM_005228	exon16	c.T1887A	p.T629T	ATGCACTGGGCCA	.	PASS	Atlas-SNP
CYP26A1	1592	hgsc.bcm.edu	37	10	94835624	94835624	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94.0	4.0	75.0	0.0	0.0425532	0	.	.	none	.	CYP26A1	59	.	NM_000783	exon5	c.C906T	p.H302H	AGGACACGAAACC	.	PASS	Atlas-SNP
TNK2	10188	hgsc.bcm.edu	37	3	195594931	195594931	+	Silent	SNP	C	C	T	rs200272067	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45.0	21.0	50.0	0.0	0.466667	0	C|0.997;T|0.003	0.003	strong	.	TNK2	246	.	NM_001010938	exon13	c.G2427A	p.P809P	ACCCCCCGGGCTG	.	PASS	Atlas-SNP
TMPRSS15	5651	hgsc.bcm.edu	37	21	19704490	19704490	+	Missense_Mutation	SNP	G	G	A	rs146718638	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84.0	36.0	62.0	0.0	0.428571	0	G|1.000;A|0.000	0.000	weak	.	TMPRSS15	189	.	NM_002772	exon14	c.C1565T	p.T522M	CAGTCCGCTGAAA	.	PASS	Atlas-SNP
CHMP1A	5119	hgsc.bcm.edu	37	16	89715813	89715813	+	Missense_Mutation	SNP	C	C	T	rs201479143	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80.0	44.0	92.0	0.0	0.55	0	C|0.999;T|0.001	0.001	strong	.	CHMP1A	15	.	NM_001083314	exon3	c.G178A	p.V60I	GCGGGACGCCATC	.	PASS	Atlas-SNP
SCAF8	22828	hgsc.bcm.edu	37	6	155114112	155114112	+	Splice_Site	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	26.0	84.0	0.0	0.42623	0	.	.	none	.	SCAF8	122	.	NM_014892	exon5	c.475+2T>A	.	TCCAGGTATGTTG	.	PASS	Atlas-SNP
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383217	39383217	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132.0	42.0	148.0	0.0	0.318182	0	.	.	none	.	KRTAP9-2	24	.	NM_031961	exon1	c.G311A	p.S104N	GGTCCAGCTGTGG	.	PASS	Atlas-SNP
DNMT3L	29947	hgsc.bcm.edu	37	21	45670790	45670790	+	Missense_Mutation	SNP	C	C	T	rs113593938	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	159.0	88.0	110.0	0.0	0.553459	0	C|0.996;T|0.004	0.004	strong	.	DNMT3L	33	.	NM_013369	exon10	c.G812A	p.R271Q	TTGGGCCGTGCGT	.	PASS	Atlas-SNP
MAML2	84441	hgsc.bcm.edu	37	11	95713077	95713077	+	Missense_Mutation	SNP	C	C	T	rs34520053	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191.0	37.0	149.0	0.0	0.193717	0	C|0.986;T|0.014	0.014	strong	.	MAML2	94	.	NM_032427	exon5	c.G2506A	p.V836I	TTGAAACTGGGTT	.	PASS	Atlas-SNP
SERPINA10	51156	hgsc.bcm.edu	37	14	94750408	94750408	+	Missense_Mutation	SNP	A	A	C	rs117152910	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86.0	42.0	60.0	0.0	0.488372	0	A|0.993;C|0.007	0.007	strong	SERPINA10,caecum,carcinoma,+1,1	SERPINA10	83	1	NM_001100607	exon5	c.T1229G	p.M410R	GGAGGCATGGAAT	.	PASS	Atlas-SNP
GPR20	2843	hgsc.bcm.edu	37	8	142367087	142367087	+	Missense_Mutation	SNP	C	C	T	rs34591516	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80.0	36.0	103.0	0.0	0.45	0	C|0.934;T|0.066	0.066	strong	.	GPR20	43	.	NM_005293	exon2	c.G937A	p.G313S	GCTGGCCGAAGAG	.	PASS	Atlas-SNP
DMRT3	58524	hgsc.bcm.edu	37	9	990235	990235	+	Missense_Mutation	SNP	C	C	T	rs61737966	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29.0	16.0	35.0	0.0	0.551724	0	C|0.995;T|0.005	0.005	strong	.	DMRT3	83	.	NM_021240	exon2	c.C649T	p.R217C	GAGAGCCGCCCTG	.	PASS	Atlas-SNP
NBEAL2	23218	hgsc.bcm.edu	37	3	47046485	47046485	+	Silent	SNP	C	C	T	rs141569354	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86.0	39.0	84.0	0.0	0.453488	0	C|0.995;T|0.005	0.005	strong	.	NBEAL2	267	.	NM_015175	exon39	c.C6318T	p.Y2106Y	GGACTACGTGTCC	.	PASS	Atlas-SNP
FEM1A	55527	hgsc.bcm.edu	37	19	4793128	4793128	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52.0	20.0	43.0	0.0	0.384615	0	.	.	none	.	FEM1A	41	.	NM_018708	exon1	c.A1262C	p.Q421P	TGCAACAGAGCAA	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88782777	88782777	+	Silent	SNP	G	G	A	rs34352064	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56.0	24.0	45.0	0.0	0.428571	0	G|0.995;A|0.005	0.005	strong	.	PIEZO1	79	.	NM_001142864	exon48	c.C7041T	p.D2347D	AGACTGGTCCGAG	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78789900	78789900	+	Splice_Site	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153.0	10.0	164.0	0.0	0.0653595	0	.	.	none	PCSK5_ENST00000545128,NS,carcinoma,0,3	PCSK5	329	3	NM_001190482	exon14	c.1757-2A>C	.	TTCTCAAGGTAAA	.	PASS	Atlas-SNP
UBAP2	55833	hgsc.bcm.edu	37	9	33998847	33998847	+	Missense_Mutation	SNP	T	T	C	rs149441020	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16.0	11.0	25.0	0.0	0.6875	0	T|0.999;C|0.001	0.001	strong	.	UBAP2	82	.	NM_018449	exon3	c.A115G	p.M39V	GACGCATCTGTTC	.	PASS	Atlas-SNP
OR7G3	390883	hgsc.bcm.edu	37	19	9237554	9237554	+	Missense_Mutation	SNP	G	G	A	rs138008445	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132.0	62.0	113.0	0.0	0.469697	0	G|0.995;A|0.005	0.005	strong	.	OR7G3	41	.	NM_001001958	exon1	c.C73T	p.P25S	GGATGGGCTGCAG	.	PASS	Atlas-SNP
FOXO1	2308	hgsc.bcm.edu	37	13	41240299	41240299	+	Silent	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	11.0	5.0	3.0	0.0	0.454545	0	.	.	none	.	FOXO1	110	.	NM_002015	exon1	c.G51T	p.L17L	CCGGGGCAGCGGC	.	PASS	Atlas-SNP
ALG14	199857	hgsc.bcm.edu	37	1	95538342	95538342	+	Missense_Mutation	SNP	C	C	A	rs139521179	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61.0	29.0	58.0	0.0	0.47541	0	C|0.997;A|0.003	0.003	strong	.	ALG14	13	.	NM_144988	exon1	c.G113T	p.S38I	AAGATACTGAGAG	.	PASS	Atlas-SNP
ME2	4200	hgsc.bcm.edu	37	18	48447462	48447462	+	Missense_Mutation	SNP	A	A	C	rs59409558	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108.0	47.0	82.0	0.0	0.435185	0	A|0.991;C|0.009	0.009	strong	.	ME2	49	.	NM_001168335	exon10	c.A961C	p.N321H	ATTGCAAATCTTA	.	PASS	Atlas-SNP
COL24A1	255631	hgsc.bcm.edu	37	1	86591014	86591014	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183.0	12.0	207.0	0.0	0.0655738	0	.	.	none	.	COL24A1	202	.	NM_152890	exon3	c.A1005G	p.K335K	CATTTCTTTGGCC	.	PASS	Atlas-SNP
HGSNAT	138050	hgsc.bcm.edu	37	8	43053062	43053062	+	Missense_Mutation	SNP	G	G	C	rs148632988	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	236.0	123.0	209.0	0.0	0.521186	0	G|0.995;C|0.005	0.005	strong	.	HGSNAT	85	.	NM_152419	exon17	c.G1693C	p.G565R	GTGAAGGGGCTGT	.	PASS	Atlas-SNP
ARSI	340075	hgsc.bcm.edu	37	5	149677635	149677635	+	Silent	SNP	G	G	A	rs139203947	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47.0	23.0	44.0	0.0	0.489362	0	G|0.999;A|0.001	0.001	strong	.	ARSI	65	.	NM_001012301	exon2	c.C852T	p.Y284Y	GAAACCGTAGCGC	.	PASS	Atlas-SNP
WASF3	10810	hgsc.bcm.edu	37	13	27250805	27250805	+	Missense_Mutation	SNP	G	G	T	rs139779405	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69.0	34.0	72.0	0.0	0.492754	0	A|0.000;G|0.999;T|0.001	0.001	strong	.	WASF3	68	.	NM_006646	exon7	c.G660T	p.L220F	CAGGTTGTCTCAG	.	PASS	Atlas-SNP
C12orf77	196415	hgsc.bcm.edu	37	12	25148824	25148824	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	209.0	58.0	178.0	0.0	0.277512	0	.	.	none	.	C12orf77	18	.	NM_001101339	exon3	c.C324A	p.N108K	TTCCGTGTTCATA	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495683	134495683	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46.0	16.0	70.0	0.0	0.347826	0	.	.	none	SGK1_ENST00000367858,NS,lymphoid_neoplasm,0,2	SGK1	387	2	NM_001143676	exon4	c.C403G	p.Q135E	TCTTCTGAATAAA	.	PASS	Atlas-SNP
CLCC1	23155	hgsc.bcm.edu	37	1	109477406	109477406	+	Silent	SNP	C	C	T	rs150029224	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	203.0	102.0	228.0	1.0	0.502463	0.00438596	C|1.000;T|0.000	0.000	strong	.	CLCC1	55	.	NM_001048210	exon11	c.G1542A	p.K514K	CTGGGCCTTTTCC	.	PASS	Atlas-SNP
LAMA4	3910	hgsc.bcm.edu	37	6	112493894	112493894	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100.0	41.0	109.0	0.0	0.41	0	.	.	none	.	LAMA4	227	.	NM_001105206	exon12	c.A1470T	p.E490D	AAGTGCTTCCTGG	.	PASS	Atlas-SNP
MBOAT7	79143	hgsc.bcm.edu	37	19	54687453	54687453	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121.0	40.0	121.0	0.0	0.330579	0	.	.	none	.	MBOAT7	37	.	NM_001146082	exon5	c.C444T	p.S148S	CATCAGGGAGGGC	.	PASS	Atlas-SNP
GRM6	2916	hgsc.bcm.edu	37	5	178415983	178415983	+	Missense_Mutation	SNP	G	G	A	rs5019554	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122.0	49.0	163.0	0.0	0.401639	0	A|0.008;G|0.992	0.008	strong	.	GRM6	149	.	NM_000843	exon6	c.C1307T	p.T436I	CCATCAGTGGGTT	.	PASS	Atlas-SNP
SYNGAP1	8831	hgsc.bcm.edu	37	6	33409006	33409006	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118.0	11.0	70.0	0.0	0.0932203	0	.	.	none	.	SYNGAP1	202	.	NM_006772	exon12	c.G1970A	p.W657X	TGGAATGGGGTTC	.	PASS	Atlas-SNP
TMEM135	65084	hgsc.bcm.edu	37	11	87020670	87020670	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70.0	20.0	65.0	0.0	0.285714	0	.	.	none	.	TMEM135	40	.	NM_022918	exon10	c.T892G	p.F298V	GAAAACTTCCAGC	.	PASS	Atlas-SNP
WDR49	151790	hgsc.bcm.edu	37	3	167240215	167240215	+	Missense_Mutation	SNP	C	C	T	rs202225646	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72.0	39.0	47.0	0.0	0.541667	0	.	.	weak	.	WDR49	188	.	NM_178824	exon12	c.G1606A	p.V536M	TTTCCACTAAATT	.	PASS	Atlas-SNP
SASH1	23328	hgsc.bcm.edu	37	6	148840980	148840980	+	Missense_Mutation	SNP	C	C	T	rs116958992	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16.0	6.0	21.0	0.0	0.375	0	C|0.994;T|0.006	0.006	strong	.	SASH1	123	.	NM_015278	exon10	c.C1160T	p.S387F	CCCGCTCCCTCAC	.	PASS	Atlas-SNP
WNT7B	7477	hgsc.bcm.edu	37	22	46319203	46319203	+	Missense_Mutation	SNP	G	G	A	rs147287645		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66.0	18.0	63.0	0.0	0.272727	0	G|1.000;A|0.000	0.000	weak	.	WNT7B	45	.	NM_058238	exon4	c.C583T	p.R195W	GCATCCGGTCCTC	.	PASS	Atlas-SNP
BAZ1B	9031	hgsc.bcm.edu	37	7	72883898	72883898	+	Missense_Mutation	SNP	G	G	A	rs145043036	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117.0	59.0	136.0	0.0	0.504274	0	G|0.999;A|0.001	0.001	strong	.	BAZ1B	147	.	NM_032408	exon9	c.C2815T	p.H939Y	AGTGATGGTTGAA	.	PASS	Atlas-SNP
IZUMO1	284359	hgsc.bcm.edu	37	19	49245518	49245518	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129.0	31.0	134.0	0.0	0.24031	0	.	.	none	.	IZUMO1	30	.	NM_182575	exon7	c.A548C	p.E183A	TTTAACTCACAGT	.	PASS	Atlas-SNP
