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
SGK1	6446	hgsc.bcm.edu	37	6	134494703	134494703	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	68.0	13.0	56.0	0.0	0.191176	0	.	.	none	SGK1_ENST00000528577,NS,lymphoid_neoplasm,-2,6	SGK1	387	6	NM_001143676	exon6	c.516delA	p.P172fs	.	.	PASS	Atlas-Indel
TOP2B	7155	hgsc.bcm.edu	37	3	25674218	25674218	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	261.0	42.0	204.0	0.0	0.161	.	.	.	none	.	TOP2B	98	.	NM_001068	exon9	c.1080delG	p.K360fs	.	.	PASS	Pindel,Atlas-Indel
ITPKB	3707	hgsc.bcm.edu	37	1	226836447	226836447	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	169.0	32.0	171.0	0.0	0.189	.	.	.	none	.	ITPKB	158	.	NM_002221	exon3	c.1959delC	p.N653fs	.	.	PASS	Pindel,Atlas-Indel
BNC2	54796	hgsc.bcm.edu	37	9	16436374	16436375	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	96.0	17.0	99.0	0.0	0.177	.	.	.	none	.	BNC2	166	.	NM_017637	exon6	c.1818_1819insC	p.P606fs	.	.	PASS	Pindel,Atlas-Indel
TET2	54790	hgsc.bcm.edu	37	4	106196908	106196908	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	110.0	18.0	91.0	0.0	0.163636	0	.	.	none	.	TET2	1762	.	NM_001127208	exon11	c.5240delC	p.P1747fs	.	.	PASS	Atlas-Indel
NF1	4763	hgsc.bcm.edu	37	17	29661926	29661927	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	145.0	24.0	125.0	0.0	0.166	.	.	.	none	.	NF1	1586	.	NM_001042492	exon40	c.5883_5884insC	p.K1961fs	.	.	PASS	Pindel,Atlas-Indel
ABCB1	5243	hgsc.bcm.edu	37	7	87195445	87195445	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	198.0	33.0	144.0	0.0	0.167	.	.	.	none	.	ABCB1	263	.	NM_000927	exon8	c.644delC	p.T215fs	.	.	PASS	Pindel,Atlas-Indel
GLI2	2736	hgsc.bcm.edu	37	2	121708820	121708820	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	221.0	36.0	241.0	0.0	0.163	.	.	.	none	.	GLI2	187	.	NM_005270	exon3	c.255delG	p.G85fs	.	.	PASS	Pindel,Atlas-Indel
EGFL6	25975	hgsc.bcm.edu	37	X	13636081	13636082	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	79.0	22.0	74.0	0.0	0.278	.	.	.	none	.	EGFL6	111	.	NM_001167890	exon8	c.1011_1012insA	p.E337fs	.	.	PASS	Pindel,Atlas-Indel
REST	5978	hgsc.bcm.edu	37	4	57777675	57777676	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	89.0	14.0	97.0	0.0	0.157	.	.	.	none	.	REST	104	.	NM_001193508	exon2	c.871_872insA	p.Y291_V292delinsX	.	.	PASS	Pindel,Atlas-Indel
GRIA2	2891	hgsc.bcm.edu	37	4	158254497	158254497	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	68.0	11.0	49.0	0.0	0.161765	0	.	.	none	.	GRIA2	358	.	NM_001083619	exon8	c.1146delG	p.G382fs	.	.	PASS	Atlas-Indel
C22orf43	51233	hgsc.bcm.edu	37	22	23956338	23956340	+	In_Frame_Del	DEL	TCT	TCT	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	306.0	52.0	236.0	0.0	0.170	.	.	.	none	.	C22orf43	18	.	NM_016449	exon9	c.604_606del	p.202_202del	.	.	PASS	Pindel,Atlas-Indel
ASPM	259266	hgsc.bcm.edu	37	1	197070009	197070009	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	157.0	33.0	115.0	0.0	0.210191	0	.	.	none	ASPM,right_upper_lobe,carcinoma,0,1	ASPM	444	1	NM_018136	exon18	c.G8372T	p.G2791V	ATAACACCTTCAC	.	PASS	Atlas-SNP
UNC80	285175	hgsc.bcm.edu	37	2	210783352	210783352	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	167.0	39.0	141.0	0.0	0.233533	0	.	.	none	.	UNC80	280	.	NM_032504	exon32	c.G5110A	p.G1704R	TGCAGCGGGAGTG	.	PASS	Atlas-SNP
RAB8A	4218	hgsc.bcm.edu	37	19	16222712	16222712	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	102.0	13.0	41.0	0.0	0.127451	0	.	.	none	.	RAB8A	19	.	NM_005370	exon1	c.A1C	p.M1L	TGTAATATGGCGA	.	PASS	Atlas-SNP
VGLL3	389136	hgsc.bcm.edu	37	3	87018229	87018229	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	58.0	14.0	32.0	0.0	0.241379	0	.	.	none	.	VGLL3	62	.	NM_016206	exon3	c.T448G	p.F150V	TCCAAAAGGAAGT	.	PASS	Atlas-SNP
SFTPD	6441	hgsc.bcm.edu	37	10	81702261	81702261	+	Splice_Site	SNP	C	C	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	61.0	8.0	63.0	0.0	0.131148	0	.	.	none	.	SFTPD	43	.	NM_003019	exon5	c.317-1G>T	.	GAGGTCCTGAGCA	.	PASS	Atlas-SNP
ZFC3H1	196441	hgsc.bcm.edu	37	12	72022729	72022729	+	Silent	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	87.0	36.0	70.0	0.0	0.413793	0	.	.	none	.	ZFC3H1	172	.	NM_144982	exon20	c.T3915C	p.D1305D	TTCCTCATCACTA	.	PASS	Atlas-SNP
SH2D4B	387694	hgsc.bcm.edu	37	10	82329986	82329986	+	Silent	SNP	T	T	C	rs192169537	bycluster;by1000genomes;alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	127.0	22.0	135.0	0.0	0.173228	0	T|1.000;A|0.000	.	alt	.	SH2D4B	44	.	NM_207372	exon2	c.T261C	p.P87P	AGGCCCTGGTGAC	.	PASS	Atlas-SNP
PCDH17	27253	hgsc.bcm.edu	37	13	58208119	58208119	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	94.0	12.0	90.0	0.0	0.12766	0	.	.	none	.	PCDH17	304	.	NM_001040429	exon1	c.A1439G	p.Q480R	TGCTTCAGGTGCA	.	PASS	Atlas-SNP
SFTPD	6441	hgsc.bcm.edu	37	10	81702260	81702260	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	61.0	8.0	62.0	0.0	0.131148	0	.	.	none	.	SFTPD	43	.	NM_003019	exon4	c.G317A	p.G106E	GGAGGTCCTGAGC	.	PASS	Atlas-SNP
CD300LB	124599	hgsc.bcm.edu	37	17	72522004	72522004	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	280.0	64.0	248.0	0.0	0.228571	0	.	.	none	CD300LB,lower_third,carcinoma,0,1	CD300LB	38	1	NM_174892	exon2	c.C364T	p.R122C	ACGTGCGGTCTTT	.	PASS	Atlas-SNP
GLI2	2736	hgsc.bcm.edu	37	2	121747495	121747495	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	79.0	19.0	86.0	0.0	0.240506	0	.	.	none	.	GLI2	187	.	NM_005270	exon13	c.G4005C	p.E1335D	CCAGGAGGGCTAC	.	PASS	Atlas-SNP
GBP3	2635	hgsc.bcm.edu	37	1	89476655	89476655	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	333.0	64.0	339.0	0.0	0.192192	0	.	.	none	.	GBP3	53	.	NM_018284	exon8	c.T1294C	p.C432R	AGAGACAATAGCC	.	PASS	Atlas-SNP
ZG16	653808	hgsc.bcm.edu	37	16	29791721	29791721	+	Missense_Mutation	SNP	G	G	C	rs235638	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	7.0	7.0	0.0	0.0	1	.	G|0.120;C|0.880	0.880	strong	.	ZG16	14	.	NM_152338	exon4	c.G485C	p.S162T	ACCCCAGTAGCTG	.	PASS	Atlas-SNP
ZNF181	339318	hgsc.bcm.edu	37	19	35232469	35232469	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	122.0	19.0	137.0	0.0	0.155738	0	.	.	none	.	ZNF181	65	.	NM_001029997	exon4	c.C1183T	p.H395Y	ACTCGACATCAAA	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970774	45970774	+	Missense_Mutation	SNP	G	G	A	rs76536096	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	119.0	12.0	94.0	0.0	0.10084	0	G|0.917;A|0.083	0.083	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.C568T	p.P190S	AGACAGGCTTGCA	.	PASS	Atlas-SNP
NFASC	23114	hgsc.bcm.edu	37	1	204943936	204943936	+	Missense_Mutation	SNP	C	C	T	rs149731085	bycluster;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	116.0	30.0	131.0	0.0	0.258621	0	C|1.000;T|0.000	0.000	strong	.	NFASC	396	.	NM_015090	exon14	c.C1576T	p.R526C	CAAGTCCGCCTGG	.	PASS	Atlas-SNP
TMPRSS2	7113	hgsc.bcm.edu	37	21	42851153	42851153	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	88.0	4.0	102.0	0.0	0.0454545	0	.	.	none	.	TMPRSS2	148	.	NM_001135099	exon7	c.T740A	p.M247K	AGTTTCATAAAGC	.	PASS	Atlas-SNP
LTB	4050	hgsc.bcm.edu	37	6	31549632	31549632	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	82.0	13.0	99.0	0.0	0.158537	0	.	.	none	.	LTB	19	.	NM_002341	exon2	c.C167T	p.T56M	GTCTCCGTTACCT	.	PASS	Atlas-SNP
GNAT3	346562	hgsc.bcm.edu	37	7	80117974	80117974	+	Silent	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	143.0	26.0	113.0	0.0	0.181818	0	.	.	none	.	GNAT3	65	.	NM_001102386	exon3	c.T180G	p.G60G	ACTGTAACCATTC	.	PASS	Atlas-SNP
PCDH7	5099	hgsc.bcm.edu	37	4	30723952	30723952	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	64.0	6.0	78.0	0.0	0.09375	0	.	.	none	.	PCDH7	215	.	NM_032457	exon1	c.A908C	p.D303A	TGAACGACAACAG	.	PASS	Atlas-SNP
MUC12	10071	hgsc.bcm.edu	37	7	100648117	100648117	+	Missense_Mutation	SNP	C	C	G	rs11766125	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	11.0	4.0	4.0	1.0	0.363636	0.25	C|0.499;G|0.501	0.501	strong	MUC12,NS,carcinoma,0,1	MUC12	140	1	NM_001164462	exon2	c.C14273G	p.T4758R	GCATGACAAGCTC	.	scavenged	Atlas-SNP
GLYR1	84656	hgsc.bcm.edu	37	16	4882161	4882161	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	255.0	43.0	257.0	0.0	0.168627	0	.	.	none	.	GLYR1	49	.	NM_032569	exon5	c.G356A	p.R119K	TTTGGCCTACTTC	.	PASS	Atlas-SNP
NRG3	10718	hgsc.bcm.edu	37	10	84498369	84498369	+	Silent	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	213.0	40.0	191.0	0.0	0.187793	0	.	.	none	.	NRG3	301	.	NM_001165972	exon3	c.A990G	p.Q330Q	TGATCAATTTCTG	.	PASS	Atlas-SNP
SEL1L3	23231	hgsc.bcm.edu	37	4	25783964	25783964	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	175.0	45.0	184.0	1.0	0.257143	0.00543478	.	.	none	SEL1L3,NS,carcinoma,+1,2	SEL1L3	62	2	NM_015187	exon15	c.A2357T	p.Y786F	AACCAGTACTTTG	.	scavenged	Atlas-SNP
SOCS3	9021	hgsc.bcm.edu	37	17	76354959	76354959	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	84.0	20.0	62.0	0.0	0.238095	0	.	.	none	.	SOCS3	16	.	NM_003955	exon2	c.G218A	p.S73N	TCCGAGCTGTCGC	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82816658	82816658	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	84.0	22.0	63.0	0.0	0.261905	0	.	.	none	.	VCAN	498	.	NM_004385	exon7	c.A2533C	p.S845R	ATCCCAAGTTTCA	.	PASS	Atlas-SNP
HDDC2	51020	hgsc.bcm.edu	37	6	125621684	125621684	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	186.0	40.0	193.0	0.0	0.215054	0	.	.	none	.	HDDC2	21	.	NM_016063	exon2	c.G206A	p.R69Q	GCTTACCGGTCTT	.	PASS	Atlas-SNP
MPZL1	9019	hgsc.bcm.edu	37	1	167741720	167741720	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	186.0	30.0	160.0	0.0	0.16129	0	.	.	none	.	MPZL1	25	.	NM_024569	exon3	c.A467G	p.E156G	TCGTAGAAAAAGG	.	PASS	Atlas-SNP
NOX4	50507	hgsc.bcm.edu	37	11	89182653	89182653	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	120.0	28.0	140.0	0.0	0.233333	0	.	.	none	.	NOX4	101	.	NM_001143836	exon4	c.A304G	p.R102G	ATGTTCTGCTTTT	.	PASS	Atlas-SNP
KIF16B	55614	hgsc.bcm.edu	37	20	16348090	16348090	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	188.0	25.0	175.0	0.0	0.132979	0	.	.	none	.	KIF16B	305	.	NM_001199866	exon23	c.C3880T	p.P1294S	CCGGAGGAGGTAT	.	PASS	Atlas-SNP
CHTF18	63922	hgsc.bcm.edu	37	16	847932	847932	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	81.0	7.0	88.0	0.0	0.0864198	0	.	.	none	.	CHTF18	52	.	NM_022092	exon22	c.C2885G	p.S962C	GTGTCTCCAACGC	.	PASS	Atlas-SNP
SLC18A1	6570	hgsc.bcm.edu	37	8	20031913	20031913	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	139.0	24.0	144.0	0.0	0.172662	0	.	.	none	SLC18A1,NS,carcinoma,-1,1	SLC18A1	68	1	NM_001142324	exon6	c.G590A	p.R197Q	AGGGTTCGGGCCA	.	PASS	Atlas-SNP
NCAPD3	23310	hgsc.bcm.edu	37	11	134076494	134076494	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	284.0	63.0	259.0	0.0	0.221831	0	.	.	none	.	NCAPD3	141	.	NM_015261	exon8	c.G1016A	p.S339N	CTTCACCTGATAA	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970772	45970772	+	Silent	SNP	A	A	G	rs76021731	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	120.0	14.0	96.0	0.0	0.116667	0	A|0.908;G|0.092	0.092	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.T570C	p.P190P	GCAGACAGGCTTG	.	PASS	Atlas-SNP
C9orf169	375791	hgsc.bcm.edu	37	9	140120215	140120215	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	56.0	13.0	69.0	0.0	0.232143	0	.	.	none	.	C9orf169	6	.	NM_199001	exon2	c.G142A	p.G48R	CCAGTGGGGCCCT	.	PASS	Atlas-SNP
AMICA1	120425	hgsc.bcm.edu	37	11	118085545	118085545	+	Silent	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	46.0	7.0	37.0	0.0	0.152174	0	.	.	none	.	AMICA1	49	.	NM_001098526	exon2	c.T37C	p.L13L	CCAGTAACACTGG	.	PASS	Atlas-SNP
FLG2	388698	hgsc.bcm.edu	37	1	152328295	152328295	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	185.0	10.0	177.0	0.0	0.0540541	0	.	.	none	.	FLG2	431	.	NM_001014342	exon3	c.G1967C	p.G656A	TATTGGCCAAAGC	.	PASS	Atlas-SNP
SLC19A1	6573	hgsc.bcm.edu	37	21	46935613	46935613	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	86.0	4.0	90.0	0.0	0.0465116	0	.	.	none	.	SLC19A1	53	.	NM_194255	exon6	c.C1735T	p.Q579X	GACACTGCAAACC	.	PASS	Atlas-SNP
DTX2	113878	hgsc.bcm.edu	37	7	76132841	76132841	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	219.0	51.0	203.0	0.0	0.232877	0	.	.	none	.	DTX2	64	.	NM_001102594	exon9	c.G1488A	p.S496S	GATGTCGCTCCCC	.	PASS	Atlas-SNP
GBP3	2635	hgsc.bcm.edu	37	1	89476646	89476646	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	341.0	73.0	321.0	0.0	0.214076	0	.	.	none	.	GBP3	53	.	NM_018284	exon8	c.A1303G	p.I435V	TCTGAATAAAGAG	.	PASS	Atlas-SNP
MAGI2	9863	hgsc.bcm.edu	37	7	78636484	78636484	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	148.0	22.0	107.0	0.0	0.148649	0	.	.	none	MAGI2,caecum,carcinoma,0,1	MAGI2	246	1	NM_012301	exon2	c.T340G	p.L114V	ATCGTAAGTTGAG	.	PASS	Atlas-SNP
NLGN1	22871	hgsc.bcm.edu	37	3	173322630	173322630	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	64.0	11.0	56.0	0.0	0.171875	0	.	.	none	NLGN1,NS,carcinoma,+1,1	NLGN1	209	1	NM_014932	exon3	c.T242C	p.L81P	AATTTCTTGGGGT	.	PASS	Atlas-SNP
MAP3K12	7786	hgsc.bcm.edu	37	12	53880795	53880795	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	147.0	39.0	149.0	0.0	0.265306	0	.	.	none	.	MAP3K12	160	.	NM_001193511	exon2	c.C381T	p.C127C	GCGCAGGCAGCCA	.	PASS	Atlas-SNP
ENPEP	2028	hgsc.bcm.edu	37	4	111397599	111397599	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	212.0	31.0	184.0	0.0	0.146226	0	.	.	none	.	ENPEP	149	.	NM_001977	exon1	c.A29C	p.K10T	GCTCTAAGAGATA	.	PASS	Atlas-SNP
BIRC8	112401	hgsc.bcm.edu	37	19	53793122	53793122	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	110.0	17.0	116.0	0.0	0.154545	0	.	.	none	.	BIRC8	54	.	NM_033341	exon1	c.C506A	p.S169X	TGCAATGAAGTCT	.	PASS	Atlas-SNP
PROX1	5629	hgsc.bcm.edu	37	1	214171399	214171399	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	65.0	18.0	49.0	0.0	0.276923	0	.	.	none	.	PROX1	124	.	NM_001270616	exon2	c.A1521C	p.K507N	TGGAAAAGACAGA	.	PASS	Atlas-SNP
SRSF1	6426	hgsc.bcm.edu	37	17	56083867	56083867	+	Nonsense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	174.0	42.0	149.0	0.0	0.241379	0	.	.	none	.	SRSF1	41	.	NM_006924	exon2	c.T216G	p.Y72X	GCGACCATACACC	.	PASS	Atlas-SNP
LTB	4050	hgsc.bcm.edu	37	6	31549636	31549636	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	79.0	11.0	100.0	0.0	0.139241	0	.	.	none	.	LTB	19	.	NM_002341	exon2	c.G163C	p.V55L	CCGTTACCTGGTT	.	PASS	Atlas-SNP
NMBR	4829	hgsc.bcm.edu	37	6	142399929	142399929	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	176.0	37.0	145.0	0.0	0.210227	0	.	.	none	NMBR,NS,carcinoma,-2,1	NMBR	62	1	NM_002511	exon2	c.A534G	p.E178E	CACCGCTTCGGGA	.	PASS	Atlas-SNP
LOXL3	84695	hgsc.bcm.edu	37	2	74761669	74761669	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	114.0	6.0	153.0	0.0	0.0526316	0	.	.	none	.	LOXL3	73	.	NM_032603	exon10	c.C1812T	p.H604H	GCACTCGTGCCAC	.	PASS	Atlas-SNP
TOX3	27324	hgsc.bcm.edu	37	16	52478202	52478202	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	63.0	7.0	64.0	0.0	0.111111	0	.	.	none	.	TOX3	121	.	NM_001080430	exon6	c.A973G	p.S325G	CGAGGCTGGCCCT	.	PASS	Atlas-SNP
KIRREL3	84623	hgsc.bcm.edu	37	11	126294687	126294687	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	122.0	31.0	144.0	0.0	0.254098	0	.	.	none	KIRREL3_ENST00000525144,NS,carcinoma,0,2	KIRREL3	183	2	NM_032531	exon17	c.C2125T	p.R709W	ACTCCCGCTCACA	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230404	23230404	+	Missense_Mutation	SNP	A	A	G	rs115653109	byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	59.0	14.0	97.0	0.0	0.237288	0	A|0.999;G|0.001	0.001	strong	.	IGLL5	26	.	NM_001256296	exon1	c.A65G	p.E22G	AGTTGGAAGCAGC	.	PASS	Atlas-SNP
HSP90AA1	3320	hgsc.bcm.edu	37	14	102552577	102552577	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	117.0	30.0	125.0	0.0	0.25641	0	.	.	none	.	HSP90AA1	65	.	NM_001017963	exon3	c.G505C	p.E169Q	TGAGCTCTCTCAG	.	PASS	Atlas-SNP
DOCK5	80005	hgsc.bcm.edu	37	8	25198452	25198452	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	87.0	13.0	77.0	0.0	0.149425	0	.	.	none	.	DOCK5	167	.	NM_024940	exon23	c.T2387C	p.L796P	TATTTCTTGCTTT	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141356256	141356256	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	295.0	58.0	246.0	0.0	0.19661	0	.	.	none	LRP1B,NS,carcinoma,+1,3	LRP1B	1315	3	NM_018557	exon43	c.T7138C	p.S2380P	CATCTGAGAAATA	.	PASS	Atlas-SNP
USP44	84101	hgsc.bcm.edu	37	12	95926864	95926864	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	250.0	62.0	195.0	0.0	0.248	0	.	.	none	.	USP44	83	.	NM_032147	exon2	c.A1169G	p.Q390R	ATGACTTGGAACA	.	PASS	Atlas-SNP
RBMXL2	27288	hgsc.bcm.edu	37	11	7111451	7111451	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	67.0	14.0	68.0	0.0	0.208955	0	.	.	none	.	RBMXL2	47	.	NM_014469	exon1	c.G1100T	p.R367L	ACAGCCGGTCAGG	.	PASS	Atlas-SNP
IGSF9B	22997	hgsc.bcm.edu	37	11	133790483	133790483	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	151.0	39.0	113.0	0.0	0.258278	0	.	.	none	.	IGSF9B	290	.	NM_014987	exon18	c.C3137T	p.P1046L	CCGAAGGGGAATT	.	PASS	Atlas-SNP
CPXCR1	53336	hgsc.bcm.edu	37	X	88008609	88008609	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	57.0	17.0	82.0	0.0	0.298246	0	.	.	none	.	CPXCR1	83	.	NM_001184771	exon3	c.A194G	p.Q65R	TTCCTCAAGCAGC	.	PASS	Atlas-SNP
MYH1	4619	hgsc.bcm.edu	37	17	10409204	10409204	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	521.0	88.0	490.0	0.0	0.168906	0	.	.	none	MYH1,NS,carcinoma,+1,1	MYH1	403	1	NM_005963	exon19	c.A2099C	p.N700T	ACACCGTTACACC	.	PASS	Atlas-SNP
SLC22A25	387601	hgsc.bcm.edu	37	11	62997098	62997098	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	54.0	13.0	42.0	0.0	0.240741	0	.	.	none	SLC22A25,right_upper_lobe,carcinoma,-2,1	SLC22A25	87	1	NM_199352	exon1	c.A27C	p.Q9H	TCCAACTTGATCT	.	PASS	Atlas-SNP
MAML2	84441	hgsc.bcm.edu	37	11	95825407	95825407	+	Silent	SNP	C	C	T	rs61901862	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	180.0	23.0	192.0	0.0	0.127778	0	C|0.250;T|0.750	0.750	weak	MAML2,rectum,carcinoma,0,2	MAML2	94	2	NM_032427	exon2	c.G1788A	p.Q596Q	CTGCTGCTGCTGC	.	PASS	Atlas-SNP
ZNF546	339327	hgsc.bcm.edu	37	19	40504295	40504295	+	Missense_Mutation	SNP	C	C	T	rs139751800		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	103.0	31.0	107.0	0.0	0.300971	0	C|1.000;T|0.000	0.000	weak	.	ZNF546	93	.	NM_178544	exon3	c.C62T	p.P21L	TCATTCCTCTGCA	.	PASS	Atlas-SNP
ZBTB17	7709	hgsc.bcm.edu	37	1	16272337	16272337	+	Splice_Site	SNP	T	T	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	16.0	5.0	16.0	0.0	0.3125	0	.	.	none	.	ZBTB17	45	.	NM_003443	exon7	c.536-2A>T	.	TGCACCTGGGTGG	.	PASS	Atlas-SNP
UNC45B	146862	hgsc.bcm.edu	37	17	33497208	33497208	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	150.0	23.0	169.0	0.0	0.153333	0	.	.	none	.	UNC45B	133	.	NM_001267052	exon12	c.C1623T	p.D541D	GCTGGACGCTGAT	.	PASS	Atlas-SNP
AGAP1	116987	hgsc.bcm.edu	37	2	236715883	236715883	+	Missense_Mutation	SNP	T	T	C	rs202230563	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	57.0	5.0	38.0	0.0	0.0877193	0	T|0.998;C|0.002	0.002	strong	.	AGAP1	95	.	NM_014914	exon9	c.T958C	p.S320P	TTGCAGTCTCGGA	.	PASS	Atlas-SNP
CEPT1	10390	hgsc.bcm.edu	37	1	111724864	111724864	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	137.0	36.0	137.0	0.0	0.262774	0	.	.	none	.	CEPT1	25	.	NM_006090	exon6	c.G770A	p.G257E	TAGCAGGGACCAT	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970771	45970771	+	Missense_Mutation	SNP	C	C	T	rs200215960	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	125.0	12.0	100.0	0.0	0.096	0	C|0.956;T|0.044	0.044	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.G571A	p.V191I	AGCAGACAGGCTT	.	PASS	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	128807004	128807004	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	107.0	14.0	141.0	0.0	0.130841	0	.	.	none	.	DOCK1	188	.	NM_001380	exon11	c.G994A	p.V332I	ATGGATGTAACAG	.	PASS	Atlas-SNP
ARHGAP44	9912	hgsc.bcm.edu	37	17	12859254	12859254	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	210.0	38.0	236.0	0.0	0.180952	0	.	.	none	.	ARHGAP44	55	.	NM_014859	exon14	c.G1207A	p.A403T	AATATGGCAATTG	.	PASS	Atlas-SNP
RNF216	54476	hgsc.bcm.edu	37	7	5662542	5662542	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	51.0	8.0	47.0	0.0	0.156863	0	.	.	none	.	RNF216	71	.	NM_207111	exon17	c.G2721A	p.L907L	GTGCTCCAGGGGC	.	PASS	Atlas-SNP
OR5AP2	338675	hgsc.bcm.edu	37	11	56409697	56409697	+	Silent	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	102.0	15.0	82.0	0.0	0.147059	0	.	.	none	.	OR5AP2	69	.	NM_001002925	exon1	c.T219G	p.S73S	TACAAAAGAGAGG	.	PASS	Atlas-SNP
GNL2	29889	hgsc.bcm.edu	37	1	38032563	38032563	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	133.0	27.0	142.0	0.0	0.203008	0	.	.	none	.	GNL2	58	.	NM_013285	exon16	c.C2089T	p.R697C	AGTAGCGCACACC	.	PASS	Atlas-SNP
DDX42	11325	hgsc.bcm.edu	37	17	61895140	61895140	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	215.0	44.0	208.0	0.0	0.204651	0	.	.	none	.	DDX42	86	.	NM_203499	exon18	c.T2199C	p.S733S	GACTAGTGCAGGG	.	PASS	Atlas-SNP
TBC1D14	57533	hgsc.bcm.edu	37	4	7008366	7008366	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	125.0	26.0	98.0	0.0	0.208	0	.	.	none	.	TBC1D14	110	.	NM_001113361	exon9	c.T1359C	p.G453G	TGCTGGTTTTTCA	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494704	134494704	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	50.0	5.0	51.0	0.0	0.1	0	.	.	none	SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,6	SGK1	387	6	NM_001143676	exon6	c.C514G	p.P172A	GACTTGGCTAGAA	.	PASS	Atlas-SNP
PLOD2	5352	hgsc.bcm.edu	37	3	145841964	145841964	+	Silent	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	97.0	16.0	85.0	0.0	0.164948	0	.	.	none	PLOD2,colon,carcinoma,-2,5	PLOD2	81	5	NM_182943	exon2	c.A162C	p.R54R	CATAAATCGATGG	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124103697	124103697	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	279.0	52.0	277.0	0.0	0.18638	0	.	.	none	KALRN_ENST00000360013,NS,carcinoma,+1,4	KALRN	556	4	NM_003947	exon11	c.G1770A	p.T590T	GAATACGTACACC	.	PASS	Atlas-SNP
RHOA	387	hgsc.bcm.edu	37	3	49413009	49413009	+	Missense_Mutation	SNP	C	C	T	rs11552758		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	171.0	51.0	233.0	0.0	0.298246	0	.	.	weak	RHOA,NS,lymphoid_neoplasm,0,7	RHOA	46	7	NM_001664	exon2	c.G14A	p.R5Q	TTCTTCCGGATGG	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216221971	216221971	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	175.0	50.0	167.0	0.0	0.285714	0	.	.	none	.	USH2A	1168	.	NM_206933	exon31	c.T6068C	p.L2023P	AAGGGTAGCAAGC	.	PASS	Atlas-SNP
CD274	29126	hgsc.bcm.edu	37	9	5457196	5457196	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	130.0	20.0	93.0	0.0	0.153846	0	.	.	none	CD274,spleen,lymphoid_neoplasm,-1,1	CD274	26	1	NM_014143	exon3	c.G170A	p.W57X	TCTATTGGGAAAT	.	PASS	Atlas-SNP
MTNR1A	4543	hgsc.bcm.edu	37	4	187455075	187455075	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	137.0	14.0	131.0	0.0	0.10219	0	.	.	none	.	MTNR1A	46	.	NM_005958	exon2	c.A821G	p.E274G	AGCCACTCTGGGA	.	PASS	Atlas-SNP
C1orf87	127795	hgsc.bcm.edu	37	1	60491072	60491072	+	Splice_Site	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	79.0	20.0	77.0	0.0	0.253165	0	.	.	none	.	C1orf87	55	.	NM_152377	exon9	c.1127+1G>C	.	GACTTACTTTATT	.	PASS	Atlas-SNP
HIST1H2BL	8340	hgsc.bcm.edu	37	6	27775641	27775641	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	286.0	71.0	272.0	0.0	0.248252	0	.	.	none	.	HIST1H2BL	48	.	NM_003519	exon1	c.C44T	p.S15F	TTCTTGGAGCCCT	.	PASS	Atlas-SNP
ABR	29	hgsc.bcm.edu	37	17	970326	970326	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	76.0	21.0	110.0	0.0	0.276316	0	.	.	none	.	ABR	119	.	NM_021962	exon10	c.C1173T	p.I391I	CTTCTGGATTTCA	.	PASS	Atlas-SNP
CTTNBP2	83992	hgsc.bcm.edu	37	7	117368154	117368154	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	177.0	33.0	182.0	0.0	0.186441	0	.	.	none	.	CTTNBP2	200	.	NM_033427	exon17	c.A4044G	p.Q1348Q	TGTCACTTGGGCA	.	PASS	Atlas-SNP
SEC62	7095	hgsc.bcm.edu	37	3	169684611	169684611	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	173.0	33.0	214.0	0.0	0.190751	0	.	.	none	.	SEC62	27	.	NM_003262	exon1	c.A1G	p.M1V	GCCAACATGGCGG	.	PASS	Atlas-SNP
ZNF471	57573	hgsc.bcm.edu	37	19	57036891	57036891	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	61.0	7.0	64.0	0.0	0.114754	0	.	.	none	.	ZNF471	99	.	NM_020813	exon5	c.A1455C	p.K485N	TGAAAAACCCTAT	.	PASS	Atlas-SNP
COL4A3	1285	hgsc.bcm.edu	37	2	228173618	228173618	+	Missense_Mutation	SNP	C	C	A	rs200818438	bycluster;alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	105.0	33.0	103.0	0.0	0.314286	0	.	.	alt	.	COL4A3	293	.	NM_000091	exon49	c.C4466A	p.T1489N	TAGGAACTCTTGG	.	PASS	Atlas-SNP
SPATA31E1	286234	hgsc.bcm.edu	37	9	90499849	90499849	+	Silent	SNP	C	C	T	rs148586576	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	71.0	8.0	86.0	0.0	0.112676	0	C|1.000;T|0.000	0.000	weak	C9orf79,colon,carcinoma,0,1	.	.	1	NM_178828	exon4	c.C447T	p.G149G	CGCTGGCGAAGGC	.	PASS	Atlas-SNP
PDCL3	79031	hgsc.bcm.edu	37	2	101188050	101188050	+	Splice_Site	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	29.0	7.0	45.0	0.0	0.241379	0	.	.	none	PDCL3,NS,carcinoma,0,1	PDCL3	27	1	NM_024065	exon5	c.369-2A>G	.	TTTTATAGAATTC	.	PASS	Atlas-SNP
GABRG3	2567	hgsc.bcm.edu	37	15	27765242	27765242	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	124.0	26.0	112.0	0.0	0.209677	0	.	.	none	.	GABRG3	115	.	NM_033223	exon7	c.A837C	p.K279N	CAAAAAAGATGCT	.	PASS	Atlas-SNP
ZNF729	100287226	hgsc.bcm.edu	37	19	22496574	22496574	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	71.0	16.0	68.0	0.0	0.225352	0	.	.	none	.	ZNF729	78	.	NM_001242680	exon4	c.A355G	p.N119D	CATAAGAATTTAC	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495169	134495169	+	Missense_Mutation	SNP	G	G	C	rs141028225		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	110.0	22.0	109.0	0.0	0.2	0	G|1.000;C|0.000	0.000	weak	.	SGK1	387	.	NM_001143676	exon5	c.C487G	p.L163V	TCATAAGCTCAGG	.	PASS	Atlas-SNP
INSC	387755	hgsc.bcm.edu	37	11	15267551	15267551	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	214.0	40.0	199.0	0.0	0.186916	0	.	.	none	.	INSC	104	.	NM_001031853	exon13	c.T1705G	p.L569V	TCCTTCTTACTCT	.	PASS	Atlas-SNP
SLIT2	9353	hgsc.bcm.edu	37	4	20619095	20619095	+	Silent	SNP	G	G	A	rs61746361	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	261.0	54.0	330.0	0.0	0.206897	0	G|0.996;A|0.004	0.004	strong	.	SLIT2	290	.	NM_004787	exon36	c.G4170A	p.A1390A	CAATGCGTTCTCC	.	PASS	Atlas-SNP
CHRM3	1131	hgsc.bcm.edu	37	1	240071117	240071117	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	349.0	58.0	377.0	1.0	0.166189	0.00265252	.	.	none	CHRM3,NS,carcinoma,0,1	CHRM3	118	1	NM_000740	exon5	c.G366T	p.M122I	TTCAATGAATCTG	.	scavenged	Atlas-SNP
PRPH2	5961	hgsc.bcm.edu	37	6	42690015	42690015	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	133.0	38.0	116.0	0.0	0.285714	0	.	.	none	.	PRPH2	47	.	NM_000322	exon1	c.C58A	p.L20I	GCCAGAGCCCTTG	.	PASS	Atlas-SNP
PBX2	5089	hgsc.bcm.edu	37	6	32155509	32155509	+	Missense_Mutation	SNP	T	T	A	rs202223627		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	212.0	14.0	223.0	2.0	0.0660377	0.00896861	T|0.999;A|0.001	0.001	weak	PBX2,NS,carcinoma,0,4	PBX2	29	4	NM_002586	exon5	c.A785T	p.Y262F	TAGAAATACTCAT	.	scavenged	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152883856	152883856	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	96.0	21.0	77.0	0.0	0.21875	0	.	.	none	.	IVL	100	.	NM_005547	exon2	c.G1583A	p.G528E	AGGAGGGGCAGCT	.	PASS	Atlas-SNP
USP31	57478	hgsc.bcm.edu	37	16	23117736	23117736	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	249.0	40.0	201.0	0.0	0.160643	0	.	.	none	.	USP31	122	.	NM_020718	exon3	c.T844G	p.F282V	CTTGAAAGAGTTC	.	PASS	Atlas-SNP
OR52I2	143502	hgsc.bcm.edu	37	11	4608396	4608396	+	Silent	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	572.0	149.0	503.0	1.0	0.26049	0.00198807	.	.	none	.	OR52I2	50	.	NM_001005170	exon1	c.A354C	p.G118G	CTCAGGAGACAGC	.	PASS	Atlas-SNP
WHSC1	7468	hgsc.bcm.edu	37	4	1957912	1957912	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	18.0	6.0	18.0	0.0	0.333333	0	.	.	none	.	WHSC1	180	.	NM_133335	exon15	c.A2878C	p.N960H	TTCAAAAACGGTA	.	PASS	Atlas-SNP
TIAM1	7074	hgsc.bcm.edu	37	21	32554842	32554842	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	95.0	25.0	111.0	0.0	0.263158	0	.	.	none	.	TIAM1	522	.	NM_003253	exon16	c.C2783A	p.P928H	AGCTCGGGGTAGG	.	PASS	Atlas-SNP
B2M	567	hgsc.bcm.edu	37	15	45003745	45003745	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	169.0	49.0	140.0	1.0	0.289941	0.00714286	.	.	none	B2M,caecum,carcinoma,-2,17	B2M	99	17	NM_004048	exon1	c.A1G	p.M1V	GCCGAGATGTCTC	.	scavenged	Atlas-SNP
LAMP5	24141	hgsc.bcm.edu	37	20	9498795	9498795	+	Missense_Mutation	SNP	C	C	T	rs137866690		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	303.0	72.0	272.0	0.0	0.237624	0	C|1.000;T|0.000	0.000	weak	.	.	.	.	NM_012261	exon5	c.C584T	p.P195L	GTGATCCGCAGAA	.	PASS	Atlas-SNP
SYT16	83851	hgsc.bcm.edu	37	14	62536400	62536400	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	227.0	50.0	212.0	0.0	0.220264	0	.	.	none	.	SYT16	144	.	NM_031914	exon2	c.C603T	p.S201S	GATTTCCGTGTCC	.	PASS	Atlas-SNP
HIPK1	204851	hgsc.bcm.edu	37	1	114495495	114495495	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	144.0	27.0	165.0	0.0	0.1875	0	.	.	none	.	HIPK1	195	.	NM_198268	exon3	c.C1184G	p.A395G	CTGGTGCTTCAGA	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79399181	79399181	+	Silent	SNP	C	C	T	rs371145937		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	322.0	80.0	274.0	0.0	0.248447	0	.	.	weak	.	FRAS1	779	.	NM_025074	exon55	c.C8064T	p.S2688S	CGAGAGCGCTGGT	.	PASS	Atlas-SNP
RFC5	5985	hgsc.bcm.edu	37	12	118458748	118458748	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	83.0	19.0	84.0	0.0	0.228916	0	.	.	none	.	RFC5	35	.	NM_007370	exon4	c.G305A	p.R102Q	TCATTCGAGGACC	.	PASS	Atlas-SNP
LTA4H	4048	hgsc.bcm.edu	37	12	96409429	96409429	+	Nonsense_Mutation	SNP	C	C	A	rs138184255	bycluster;byfrequency;alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	73.0	4.0	61.0	0.0	0.0547945	0	C|0.999;T|0.001	.	alt	.	LTA4H	38	.	NM_000895	exon11	c.G991T	p.G331X	ATCGTCCGCAAAT	.	PASS	Atlas-SNP
PIWIL1	9271	hgsc.bcm.edu	37	12	130855827	130855827	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	202.0	39.0	187.0	0.0	0.193069	0	.	.	none	.	PIWIL1	157	.	NM_004764	exon20	c.C2428T	p.R810C	ATACAGCGCTTGA	.	PASS	Atlas-SNP
CDH20	28316	hgsc.bcm.edu	37	18	59195219	59195219	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	179.0	28.0	180.0	0.0	0.156425	0	.	.	none	.	CDH20	117	.	NM_031891	exon6	c.A1037G	p.K346R	AAAGCAAGAAAAG	.	PASS	Atlas-SNP
BRAF	673	hgsc.bcm.edu	37	7	140453134	140453134	+	Missense_Mutation	SNP	T	T	C	rs121913364	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	115.0	19.0	87.0	0.0	0.165217	0	.	.	weak	BRAF,NS,malignant_melanoma,0,81	BRAF	36346	81	NM_004333	exon15	c.A1801G	p.K601E	GAGATTTCACTGT	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92577819	92577819	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	451.0	80.0	399.0	0.0	0.177384	0	.	.	none	FAT3_ENST00000409404,colon,carcinoma,0,6	FAT3	1822	6	NM_001008781	exon18	c.C11286T	p.H3762H	TTCCCACGCGCTC	.	PASS	Atlas-SNP
ASUN	55726	hgsc.bcm.edu	37	12	27070328	27070328	+	Silent	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	168.0	40.0	117.0	0.0	0.238095	0	.	.	none	.	.	.	.	NM_018164	exon10	c.A1026C	p.V342V	ACTATTTACATCT	.	PASS	Atlas-SNP
SCUBE1	80274	hgsc.bcm.edu	37	22	43600118	43600118	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	192.0	46.0	212.0	0.0	0.239583	0	.	.	none	.	SCUBE1	105	.	NM_173050	exon22	c.C2852T	p.A951V	GGATGCGCCAGCA	.	PASS	Atlas-SNP
SLX4IP	128710	hgsc.bcm.edu	37	20	10603706	10603706	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	71.0	11.0	77.0	0.0	0.15493	0	.	.	none	.	.	.	.	NM_001009608	exon8	c.G906A	p.A302A	CTCTGCGGAAGAC	.	PASS	Atlas-SNP
UBA6	55236	hgsc.bcm.edu	37	4	68514904	68514904	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	197.0	55.0	205.0	0.0	0.279188	0	.	.	none	.	UBA6	98	.	NM_018227	exon14	c.A1130G	p.H377R	AGCCAATGCACAA	.	PASS	Atlas-SNP
FGGY	55277	hgsc.bcm.edu	37	1	60223665	60223665	+	Splice_Site	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	73.0	9.0	80.0	0.0	0.123288	0	.	.	none	.	FGGY	99	.	NM_001113411	exon16	c.1646+1G>T	.	TAAAAAGTAAGTG	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130128909	130128909	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	78.0	16.0	65.0	0.0	0.205128	0	.	.	none	.	COL6A5	205	.	NM_153264	exon19	c.A4599T	p.Q1533H	AGAACAAGGAAGA	.	PASS	Atlas-SNP
CHST9	83539	hgsc.bcm.edu	37	18	24496569	24496569	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	209.0	47.0	148.0	1.0	0.22488	0.00675676	.	.	none	CHST9_ENST00000284224,NS,carcinoma,0,2	CHST9	114	2	NM_031422	exon6	c.A986G	p.K329R	TTGAACTTGACTC	.	scavenged	Atlas-SNP
HIST1H1E	3008	hgsc.bcm.edu	37	6	26157012	26157012	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	73.0	15.0	103.0	0.0	0.205479	0	.	.	none	.	HIST1H1E	69	.	NM_005321	exon1	c.G394A	p.A132T	AAGCCAGCAGGAG	.	PASS	Atlas-SNP
LTBP2	4053	hgsc.bcm.edu	37	14	74971792	74971792	+	Silent	SNP	C	C	T	rs61738017	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	49.0	22.0	38.0	0.0	0.44898	0	C|0.979;T|0.021	0.021	strong	LTBP2,colon,carcinoma,-1,1	LTBP2	158	1	NM_000428	exon29	c.G4263A	p.A1421A	GCAGGGCGCATGG	.	PASS	Atlas-SNP
PGM1	5236	hgsc.bcm.edu	37	1	64104389	64104389	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	302.0	18.0	368.0	0.0	0.0596026	0	.	.	none	.	PGM1	75	.	NM_001172818	exon7	c.G1116A	p.E372E	GTATGAGACCCCA	.	PASS	Atlas-SNP
EPB41L5	57669	hgsc.bcm.edu	37	2	120799656	120799656	+	Silent	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	241.0	36.0	219.0	0.0	0.149378	0	.	.	none	.	EPB41L5	98	.	NM_020909	exon3	c.T255G	p.G85G	TTTTGGTCTGAGA	.	PASS	Atlas-SNP
BIRC6	57448	hgsc.bcm.edu	37	2	32724813	32724813	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	286.0	65.0	210.0	2.0	0.227273	0.00952381	.	.	none	BIRC6_ENST00000421745,NS,carcinoma,-1,4	BIRC6	838	4	NM_016252	exon46	c.C8668T	p.R2890X	GGTGCTCGAGCAT	.	scavenged	Atlas-SNP
TRPC3	7222	hgsc.bcm.edu	37	4	122846198	122846198	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	212.0	11.0	205.0	0.0	0.0518868	0	.	.	none	.	TRPC3	201	.	NM_001130698	exon3	c.T1151G	p.L384R	ATGGCAAGTTTGA	.	PASS	Atlas-SNP
WDR72	256764	hgsc.bcm.edu	37	15	54025345	54025345	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	67.0	14.0	89.0	0.0	0.208955	0	.	.	none	.	WDR72	177	.	NM_182758	exon2	c.T2G	p.M1R	GTCCTCATTTTGG	.	PASS	Atlas-SNP
HSD3B7	80270	hgsc.bcm.edu	37	16	30997460	30997460	+	Missense_Mutation	SNP	C	C	T	rs371576756		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	355.0	74.0	318.0	0.0	0.208451	0	.	.	weak	.	HSD3B7	33	.	NM_025193	exon3	c.C257T	p.T86M	TCCACACGGCTGG	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230315	23230315	+	Silent	SNP	C	C	T	rs148489860	by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	68.0	20.0	45.0	0.0	0.294118	0	C|1.000;T|0.000	0.000	strong	.	IGLL5	26	.	NM_001178126	exon1	c.C82T	p.L28L	CTGCTGCTGCTGG	.	PASS	Atlas-SNP
NYNRIN	57523	hgsc.bcm.edu	37	14	24878537	24878537	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	102.0	13.0	110.0	0.0	0.127451	0	.	.	none	.	NYNRIN	120	.	NM_025081	exon4	c.G1537A	p.A513T	GGACCCGCTCCAG	.	PASS	Atlas-SNP
POU2AF1	5450	hgsc.bcm.edu	37	11	111249896	111249896	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	366.0	82.0	313.0	0.0	0.224044	0	.	.	none	.	POU2AF1	23	.	NM_006235	exon1	c.T7C	p.W3R	TTTGCCAGAGCAT	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23907902	23907902	+	Silent	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	96.0	20.0	90.0	0.0	0.208333	0	.	.	none	SACS_ENST00000382298,NS,carcinoma,0,2	SACS	871	2	NM_014363	exon10	c.T10113G	p.T3371T	TGTTGAAGTTTGG	.	PASS	Atlas-SNP
ST7L	54879	hgsc.bcm.edu	37	1	113153627	113153627	+	Splice_Site	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	92.0	20.0	85.0	0.0	0.217391	0	.	.	none	.	ST7L	31	.	NM_138728	exon4	c.289-2A>G	.	AATATCTATGACA	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124340397	124340397	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	784.0	158.0	726.0	2.0	0.201531	0.00275482	.	.	none	DMBT1_ENST00000368915,NS,carcinoma,-1,13	DMBT1	677	13	NM_007329	exon11	c.C1019T	p.P340L	CCCGGCCGACACC	.	scavenged	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230318	23230318	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	62.0	18.0	39.0	0.0	0.290323	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.C85G	p.L29V	CTGCTGCTGGGTC	.	PASS	Atlas-SNP
NECAP1	25977	hgsc.bcm.edu	37	12	8245311	8245311	+	Silent	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	138.0	40.0	104.0	0.0	0.289855	0	.	.	none	.	NECAP1	21	.	NM_015509	exon5	c.A423G	p.Q141Q	ATCTCAAGAAATG	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	89948249	89948249	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	153.0	31.0	168.0	0.0	0.202614	0	.	.	none	.	GPR98	605	.	NM_032119	exon19	c.A3503T	p.E1168V	GGCAGGAGTTCTA	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230283	23230283	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	142.0	38.0	107.0	0.0	0.267606	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.G50A	p.G17D	AGCTGGGCCCTGG	.	PASS	Atlas-SNP
RABEP2	79874	hgsc.bcm.edu	37	16	28935738	28935738	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	81.0	10.0	73.0	0.0	0.123457	0	.	.	none	.	RABEP2	48	.	NM_024816	exon2	c.A260G	p.Q87R	ATGGCCTGCAGCG	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186276981	186276981	+	Silent	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	118.0	5.0	123.0	0.0	0.0423729	0	.	.	none	PRG4,NS,carcinoma,0,6	PRG4	259	6	NM_005807	exon7	c.A2130G	p.K710K	CCCTAAAGGGACT	.	scavenged	Atlas-SNP
SCN1A	6323	hgsc.bcm.edu	37	2	166847770	166847770	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	55.0	16.0	45.0	0.0	0.290909	0	.	.	none	SCN1A_ENST00000303395,NS,carcinoma,-1,2	SCN1A	641	2	NM_001165963	exon26	c.A6015C	p.K2005N	TTTGGCTTTTTCA	.	PASS	Atlas-SNP
WASF3	10810	hgsc.bcm.edu	37	13	27239258	27239258	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	110.0	34.0	79.0	0.0	0.309091	0	.	.	none	.	WASF3	68	.	NM_006646	exon4	c.T227C	p.L76P	ATCGCCTTGCTGT	.	PASS	Atlas-SNP
ATG2B	55102	hgsc.bcm.edu	37	14	96771961	96771961	+	Silent	SNP	T	T	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	51.0	18.0	65.0	0.0	0.352941	0	.	.	none	.	ATG2B	169	.	NM_018036	exon31	c.A4698T	p.G1566G	GACTATTCCAAAA	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39262561	39262561	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	132.0	28.0	109.0	0.0	0.212121	0	.	.	none	.	FREM2	385	.	NM_207361	exon1	c.T1080C	p.T360T	CCTTACTTCTCCA	.	PASS	Atlas-SNP
CPNE6	9362	hgsc.bcm.edu	37	14	24544773	24544773	+	Silent	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	191.0	32.0	162.0	0.0	0.167539	0	.	.	none	CPNE6,mouth,carcinoma,+1,1	CPNE6	40	1	NM_006032	exon9	c.A837C	p.S279S	GAGCTCAGGGACG	.	PASS	Atlas-SNP
ZNF454	285676	hgsc.bcm.edu	37	5	178392474	178392474	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	49.0	5.0	63.0	0.0	0.102041	0	.	.	none	.	ZNF454	99	.	NM_001178089	exon5	c.G1069A	p.E357K	CCCTTTGAATGTA	.	PASS	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9887155	9887155	+	Missense_Mutation	SNP	A	A	G	rs200725516	by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	137.0	9.0	109.0	0.0	0.0656934	0	A|1.000;G|0.000	0.000	strong	TXNDC2_ENST00000306084,NS,carcinoma,0,2	TXNDC2	168	2	NM_001098529	exon2	c.A679G	p.T227A	GCCAAGACCTCAG	.	PASS	Atlas-SNP
OR4C3	256144	hgsc.bcm.edu	37	11	48347041	48347041	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	361.0	26.0	347.0	0.0	0.0720222	0	.	.	none	.	OR4C3	75	.	NM_001004702	exon1	c.T549C	p.V183V	ATTGGTTCAGCTC	.	PASS	Atlas-SNP
PDLIM1	9124	hgsc.bcm.edu	37	10	96998439	96998439	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	225.0	46.0	248.0	0.0	0.204444	0	.	.	none	.	PDLIM1	33	.	NM_020992	exon6	c.A689G	p.D230G	TTGGGATCCCCTG	.	PASS	Atlas-SNP
TSPAN19	144448	hgsc.bcm.edu	37	12	85421763	85421763	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	119.0	22.0	108.0	0.0	0.184874	0	.	.	none	TSPAN19_ENST00000532498,NS,carcinoma,+2,2	TSPAN19	23	2	NM_001100917	exon4	c.T178G	p.L60V	CAATCAAAATTTG	.	PASS	Atlas-SNP
PENK	5179	hgsc.bcm.edu	37	8	57354094	57354094	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	116.0	20.0	104.0	0.0	0.172414	0	.	.	none	PENK,NS,carcinoma,0,1	PENK	59	1	NM_001135690	exon4	c.G541A	p.E181K	TCACTTCTTCCTC	.	PASS	Atlas-SNP
ZNF629	23361	hgsc.bcm.edu	37	16	30795076	30795076	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	20.0	7.0	16.0	0.0	0.35	0	.	.	none	ZNF629,colon,carcinoma,-1,1	ZNF629	44	1	NM_001080417	exon3	c.G573A	p.S191S	CAGGTGCGAGCTC	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14859353	14859353	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	130.0	25.0	125.0	0.0	0.192308	0	.	.	none	.	FREM1	261	.	NM_144966	exon5	c.G459A	p.A153A	ATCAATCGCTTGG	.	PASS	Atlas-SNP
LYN	4067	hgsc.bcm.edu	37	8	56910951	56910951	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	287.0	73.0	227.0	0.0	0.254355	0	.	.	none	.	LYN	54	.	NM_002350	exon11	c.G1097A	p.R366Q	TTCACCGGGACCT	.	PASS	Atlas-SNP
ALX1	8092	hgsc.bcm.edu	37	12	85674196	85674196	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	66.0	12.0	73.0	1.0	0.181818	0.0136986	.	.	none	ALX1,lower_third,carcinoma,-2,1	ALX1	61	1	NM_006982	exon1	c.T157G	p.F53V	CAGGCCTTCGGAC	.	scavenged	Atlas-SNP
MUC12	10071	hgsc.bcm.edu	37	7	100635679	100635679	+	Missense_Mutation	SNP	C	C	G	rs10953314	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	5.0	4.0	2.0	0.0	0.8	0	C|0.505;G|0.495	0.495	strong	.	MUC12	140	.	NM_001164462	exon2	c.C1835G	p.T612S	GCAGCACCAGATC	.	PASS	Atlas-SNP
GOLGA4	2803	hgsc.bcm.edu	37	3	37368928	37368928	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	71.0	18.0	75.0	0.0	0.253521	0	.	.	none	.	GOLGA4	173	.	NM_001172713	exon15	c.A5617T	p.I1873F	TGTCAGATTTTGG	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495658	134495658	+	Missense_Mutation	SNP	G	G	A	rs375777416		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	88.0	14.0	86.0	0.0	0.159091	0	.	.	weak	.	SGK1	387	.	NM_001143676	exon4	c.C428T	p.A143V	TTGCATGCATAGG	.	PASS	Atlas-SNP
PAX1	5075	hgsc.bcm.edu	37	20	21687153	21687153	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	27.0	8.0	22.0	0.0	0.296296	0	.	.	none	.	PAX1	152	.	NM_006192	exon2	c.C364T	p.R122C	CGCTTGCGCATTG	.	PASS	Atlas-SNP
TMX4	56255	hgsc.bcm.edu	37	20	8000141	8000141	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	40.0	11.0	14.0	0.0	0.275	0	.	.	none	.	TMX4	39	.	NM_021156	exon1	c.G120A	p.Q40Q	CATGGGCTGGACC	.	PASS	Atlas-SNP
ROPN1B	152015	hgsc.bcm.edu	37	3	125702141	125702141	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	137.0	19.0	114.0	0.0	0.138686	0	.	.	none	.	ROPN1B	16	.	NM_001012337	exon6	c.A617G	p.N206S	CCCAAAACCCCAG	.	PASS	Atlas-SNP
ASIC1	41	hgsc.bcm.edu	37	12	50467769	50467769	+	Silent	SNP	G	G	A	rs706793	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	4.0	4.0	2.0	0.0	1	0	G|0.753;A|0.247	0.247	strong	.	.	.	.	NM_001256830	exon1	c.G402A	p.P134P	CTTCCCGGCAGTC	.	PASS	Atlas-SNP
SCN9A	6335	hgsc.bcm.edu	37	2	167168208	167168208	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	81.0	19.0	90.0	0.0	0.234568	0	.	.	none	SCN9A,colon,carcinoma,+1,2	SCN9A	296	2	NM_002977	exon2	c.T59C	p.L20P	AGGGCAAGAGACT	.	PASS	Atlas-SNP
PTPRT	11122	hgsc.bcm.edu	37	20	40709537	40709537	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	31.0	7.0	39.0	0.0	0.225806	0	.	.	none	PTPRT,upper_back,malignant_melanoma,-2,1	PTPRT	372	1	NM_133170	exon32	c.A4365T	p.E1455D	TAAATATTCCAGT	.	PASS	Atlas-SNP
KIRREL3	84623	hgsc.bcm.edu	37	11	126299148	126299148	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	108.0	36.0	158.0	0.0	0.333333	0	.	.	none	.	KIRREL3	183	.	NM_032531	exon15	c.C1732T	p.R578X	CCACTCGGATATC	.	PASS	Atlas-SNP
MAP2K3	5606	hgsc.bcm.edu	37	17	21206529	21206529	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	98.0	12.0	89.0	0.0	0.122449	0	.	.	none	.	MAP2K3	135	.	NM_145109	exon7	c.T551C	p.L184P	GCAAGCTGTCGGT	.	PASS	Atlas-SNP
GRK6	2870	hgsc.bcm.edu	37	5	176863212	176863212	+	Missense_Mutation	SNP	G	G	A	rs200870863		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	122.0	6.0	132.0	1.0	0.0491803	0.00757576	.	.	weak	GRK6,NS,carcinoma,0,1	GRK6	48	1	NM_002082	exon12	c.G1196A	p.R399Q	TGGAGCGGCTGGT	.	scavenged	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82833506	82833506	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	73.0	16.0	51.0	0.0	0.219178	0	.	.	none	.	VCAN	498	.	NM_004385	exon8	c.T4684G	p.F1562V	ATAGCCTTTGCAA	.	PASS	Atlas-SNP
ABCE1	6059	hgsc.bcm.edu	37	4	146033391	146033391	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	101.0	12.0	96.0	0.0	0.118812	0	.	.	none	.	ABCE1	47	.	NM_002940	exon9	c.T711C	p.I237I	TCATAGTTTCATG	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32020562	32020562	+	Silent	SNP	G	G	A	rs375459891		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	41.0	5.0	58.0	0.0	0.121951	0	.	.	weak	.	TNXB	553	.	NM_019105	exon26	c.C8994T	p.G2998G	CTCCTCGCCCCTG	.	PASS	Atlas-SNP
ZBBX	79740	hgsc.bcm.edu	37	3	167023655	167023655	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	42.0	9.0	54.0	0.0	0.214286	0	.	.	none	.	ZBBX	299	.	NM_024687	exon17	c.T1501C	p.S501P	CAAAGGAGGTGCT	.	PASS	Atlas-SNP
FCN2	2220	hgsc.bcm.edu	37	9	137779176	137779176	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	164.0	19.0	149.0	0.0	0.115854	0	.	.	none	.	FCN2	55	.	NM_004108	exon8	c.G857A	p.S286N	ATGGCAGCTTTGC	.	PASS	Atlas-SNP
PPFIA1	8500	hgsc.bcm.edu	37	11	70171055	70171055	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	95.0	22.0	93.0	0.0	0.231579	0	.	.	none	.	PPFIA1	114	.	NM_177423	exon4	c.G469A	p.E157K	TCCAGCGAAGTGG	.	PASS	Atlas-SNP
MAZ	4150	hgsc.bcm.edu	37	16	29821438	29821438	+	Silent	SNP	G	G	A	rs199924629	bycluster;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	69.0	3.0	63.0	1.0	0.0434783	0.015873	G|0.993;A|0.007	0.007	strong	MAZ_ENST00000322945,caecum,carcinoma,0,2	MAZ	48	2	NM_002383	exon5	c.G1320A	p.A440A	GGCAGCGGCGGCA	.	scavenged	Atlas-SNP
ARHGAP29	9411	hgsc.bcm.edu	37	1	94670633	94670633	+	Missense_Mutation	SNP	T	T	G	rs201001778	by1000genomes;alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	140.0	18.0	133.0	0.0	0.128571	0	T|1.000;C|0.000	.	alt	.	ARHGAP29	132	.	NM_004815	exon7	c.A681C	p.E227D	CTTTTTTTCAACC	.	PASS	Atlas-SNP
ZNF592	9640	hgsc.bcm.edu	37	15	85328068	85328068	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	286.0	54.0	250.0	0.0	0.188811	0	.	.	none	.	ZNF592	95	.	NM_014630	exon4	c.G2162A	p.R721Q	AGATGCGGGACTA	.	PASS	Atlas-SNP
GSDMA	284110	hgsc.bcm.edu	37	17	38122591	38122591	+	Missense_Mutation	SNP	C	C	T	rs140044904	bycluster;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	278.0	54.0	298.0	0.0	0.194245	0	C|0.991;T|0.009	0.009	strong	.	GSDMA	26	.	NM_178171	exon3	c.C293T	p.T98M	CAAAGACGGTGAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507985	195507985	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	536.0	29.0	538.0	0.0	0.0541045	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.T10466C	p.L3489P	ACATGAAGAGGGG	.	PASS	Atlas-SNP