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
PRG4	10216	hgsc.bcm.edu	37	1	186277976	186277979	+	Frame_Shift_Del	DEL	GAGT	GAGT	-	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	GAGT	GAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	105.0	18.0	118.0	0.0	0.171	.	.	.	none	PRG4,NS,adenoma,-1,1	PRG4	259	1	NM_005807	exon7	c.3124_3127del	p.1042_1043del	.	.	PASS	Pindel,Atlas-Indel
PCDH15	65217	hgsc.bcm.edu	37	10	55782809	55782811	+	In_Frame_Del	DEL	ACA	ACA	-	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	134.0	37.0	171.0	0.0	0.276	.	.	.	none	PCDH15_ENST00000417177,NS,carcinoma,-2,4	PCDH15	1715	4	NM_001142763	exon20	c.2383_2385del	p.795_795del	.	.	PASS	Pindel,Atlas-Indel
MBNL2	10150	hgsc.bcm.edu	37	13	97928659	97928660	+	Frame_Shift_Ins	INS	-	-	AA	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	106.0	37.0	147.0	0.0	0.349	.	.	.	none	.	MBNL2	84	.	NM_207304	exon2	c.170_171insAA	p.L57fs	.	.	PASS	Pindel,Atlas-Indel
SCN7A	6332	hgsc.bcm.edu	37	2	167313460	167313461	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	151.0	39.0	159.0	0.0	0.258	.	.	.	none	.	SCN7A	410	.	NM_002976	exon10	c.1210_1211del	p.404_404del	.	.	PASS	Pindel,Atlas-Indel
MLL2	8085	hgsc.bcm.edu	37	12	49433749	49433750	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	54.0	18.0	85.0	0.0	0.333	.	.	.	none	.	MLL2	1173	.	NM_003482	exon31	c.7804_7805del	p.2602_2602del	.	.	PASS	Pindel,Atlas-Indel
SPCS1	28972	hgsc.bcm.edu	37	3	52741760	52741760	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	202.0	43.0	331.0	0.0	0.213	.	.	.	none	.	SPCS1	20	.	NM_014041	exon4	c.441delT	p.V147fs	.	.	PASS	Pindel,Atlas-Indel
TBC1D10B	26000	hgsc.bcm.edu	37	16	30369466	30369486	+	In_Frame_Del	DEL	CCGCTCCTTCTCCTGTTTCTG	CCGCTCCTTCTCCTGTTTCTG	-	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	CCGCTCCTTCTCCTGTTTCTG	CCGCTCCTTCTCCTGTTTCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	131.0	21.0	284.0	0.0	0.160	.	.	.	none	.	TBC1D10B	32	.	NM_015527	exon9	c.2207_2227del	p.736_743del	.	.	PASS	Pindel,Atlas-Indel
ITPRIPL2	162073	hgsc.bcm.edu	37	16	19126354	19126354	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	4.0	4.0	5.0	0.0	1	0	.	.	none	.	ITPRIPL2	40	.	NM_001034841	exon1	c.C571T	p.R191W	GAGCCACGGAGCC	.	PASS	Atlas-SNP
R3HDM2	22864	hgsc.bcm.edu	37	12	57690294	57690294	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	69.0	17.0	134.0	0.0	0.246377	0	.	.	none	.	R3HDM2	125	.	NM_014925	exon7	c.C601T	p.R201W	GCATCCGGTGATA	.	PASS	Atlas-SNP
PCYT1B	9468	hgsc.bcm.edu	37	X	24608245	24608245	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	114.0	43.0	130.0	0.0	0.377193	0	.	.	none	.	PCYT1B	88	.	NM_004845	exon4	c.G381T	p.M127I	TTCATTCATCACG	.	PASS	Atlas-SNP
GSTA3	2940	hgsc.bcm.edu	37	6	52764808	52764808	+	Missense_Mutation	SNP	C	C	A	rs45602042	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	147.0	55.0	175.0	0.0	0.37415	0	C|0.989;T|0.011	.	alt	GSTA3,caecum,carcinoma,-1,1	GSTA3	21	1	NM_000847	exon5	c.G338T	p.R113L	TCAGGTCGACATA	.	PASS	Atlas-SNP
ADAM23	8745	hgsc.bcm.edu	37	2	207437855	207437855	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	100.0	4.0	119.0	0.0	0.04	0	.	.	none	.	ADAM23	239	.	NM_003812	exon18	c.A1673G	p.Y558C	GAGGGTATGAATG	.	PASS	Atlas-SNP
FAM118B	79607	hgsc.bcm.edu	37	11	126110774	126110774	+	Silent	SNP	A	A	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	71.0	33.0	146.0	1.0	0.464789	0.00684932	.	.	none	FAM118B,caecum,carcinoma,0,1	FAM118B	29	1	NM_024556	exon4	c.A174G	p.Q58Q	GCCCCAAGTTCCA	.	scavenged	Atlas-SNP
BIVM-ERCC5	0	hgsc.bcm.edu	37	13	103515306	103515306	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	95.0	30.0	124.0	0.0	0.315789	0	.	.	none	.	.	.	.	NM_001204425	exon16	c.G3169A	p.V1057M	GAAAATGTGGTGT	.	PASS	Atlas-SNP
ZNF319	57567	hgsc.bcm.edu	37	16	58032032	58032032	+	Silent	SNP	G	G	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	32.0	9.0	40.0	0.0	0.28125	0	.	.	none	.	ZNF319	42	.	NM_020807	exon2	c.C138A	p.G46G	GGCACAGCCCAGG	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	4494939	4494939	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	78.0	39.0	144.0	0.0	0.5	0	.	.	none	.	CSMD1	1469	.	NM_033225	exon2	c.C227A	p.T76N	GCAAAGGTATGGA	.	PASS	Atlas-SNP
ZSCAN20	7579	hgsc.bcm.edu	37	1	33959918	33959918	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	169.0	73.0	240.0	0.0	0.431953	0	.	.	none	.	ZSCAN20	107	.	NM_145238	exon8	c.C1974T	p.C658C	TGTTTGCCAACCT	.	PASS	Atlas-SNP
PATE1	160065	hgsc.bcm.edu	37	11	125616559	125616559	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	128.0	44.0	174.0	0.0	0.34375	0	.	.	none	.	PATE1	21	.	NM_138294	exon2	c.T56C	p.L19S	CAGCATTATCTGG	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	4494914	4494914	+	Silent	SNP	A	A	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	64.0	34.0	109.0	0.0	0.53125	0	.	.	none	.	CSMD1	1469	.	NM_033225	exon2	c.T252C	p.D84D	TAAAATATCAAAA	.	PASS	Atlas-SNP
C2CD4C	126567	hgsc.bcm.edu	37	19	407323	407323	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	22.0	17.0	16.0	0.0	0.772727	0	.	.	none	.	C2CD4C	13	.	NM_001136263	exon2	c.G1039T	p.G347C	ACAGGCCCACGCA	.	PASS	Atlas-SNP
B2M	567	hgsc.bcm.edu	37	15	45007710	45007710	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	103.0	87.0	123.0	0.0	0.84466	0	.	.	none	B2M,colon,carcinoma,-2,1	B2M	99	1	NM_004048	exon2	c.T157A	p.S53T	CATCCATCCGACA	.	PASS	Atlas-SNP
KRTAP21-1	337977	hgsc.bcm.edu	37	21	32127679	32127679	+	Silent	SNP	G	G	A	rs147444076	bycluster;by1000genomes	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	34.0	19.0	41.0	0.0	0.558824	0	G|1.000;A|0.000	0.000	strong	KRTAP21-1,NS,carcinoma,0,1	KRTAP21-1	23	1	NM_181619	exon1	c.C18T	p.Y6Y	GTTGCCGTAGTAG	.	PASS	Atlas-SNP
ZNF438	220929	hgsc.bcm.edu	37	10	31138094	31138094	+	Silent	SNP	T	T	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	64.0	29.0	57.0	0.0	0.453125	0	.	.	none	.	ZNF438	90	.	NM_182755	exon7	c.A1240C	p.R414R	TTACTCTTTCTTT	.	PASS	Atlas-SNP
FAIM	55179	hgsc.bcm.edu	37	3	138341028	138341028	+	Splice_Site	SNP	A	A	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	24.0	6.0	26.0	0.0	0.25	0	.	.	none	.	FAIM	27	.	NM_001033032	exon3	c.112-2A>G	.	TTATGTAGGAAGA	.	PASS	Atlas-SNP
PFN1	5216	hgsc.bcm.edu	37	17	4849259	4849259	+	Missense_Mutation	SNP	T	T	G	rs199714966	bycluster;alternate_allele	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	195.0	71.0	331.0	0.0	0.364103	0	.	.	alt	.	PFN1	6	.	NM_005022	exon3	c.A359C	p.H120P	CCACCGTGGACAC	.	PASS	Atlas-SNP
HTR3A	3359	hgsc.bcm.edu	37	11	113848285	113848285	+	Silent	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	63.0	24.0	73.0	0.0	0.380952	0	.	.	none	.	HTR3A	93	.	NM_001161772	exon1	c.G9A	p.R3R	GCATAGGTCCTTT	.	PASS	Atlas-SNP
CHEK2	11200	hgsc.bcm.edu	37	22	29107902	29107902	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	65.0	4.0	102.0	0.0	0.0615385	0	.	.	none	.	CHEK2	438	.	NM_001005735	exon7	c.G916A	p.E306K	CTGCCTCTCTTGC	.	PASS	Atlas-SNP
PRAMEF4	400735	hgsc.bcm.edu	37	1	12942173	12942173	+	Missense_Mutation	SNP	C	C	G	rs71232900		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	33.0	4.0	61.0	0.0	0.121212	0	C|0.500;G|0.500	0.500	weak	PRAMEF4,NS,carcinoma,0,1	PRAMEF4	62	1	NM_001009611	exon3	c.G377C	p.C126S	AGGAAGCACCCAT	.	scavenged	Atlas-SNP
SHH	6469	hgsc.bcm.edu	37	7	155599176	155599176	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	94.0	4.0	151.0	0.0	0.0425532	0	.	.	none	.	SHH	34	.	NM_000193	exon2	c.G376A	p.E126K	AGCCCTCGGTCAC	.	PASS	Atlas-SNP
B2M	567	hgsc.bcm.edu	37	15	45007681	45007681	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	81.0	67.0	109.0	0.0	0.82716	0	.	.	none	B2M,colon,carcinoma,0,2	B2M	99	2	NM_004048	exon2	c.T128G	p.L43R	ATTTCCTGAATTG	.	PASS	Atlas-SNP
CEP290	80184	hgsc.bcm.edu	37	12	88483187	88483187	+	Silent	SNP	A	A	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	100.0	4.0	132.0	0.0	0.04	0	.	.	none	.	CEP290	195	.	NM_025114	exon31	c.T3651C	p.A1217A	ACCAAGAGCAGTA	.	PASS	Atlas-SNP
BCL6	604	hgsc.bcm.edu	37	3	187442783	187442783	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	88.0	32.0	143.0	0.0	0.363636	0	.	.	none	.	BCL6	107	.	NM_001706	exon9	c.C1923A	p.H641Q	CTGAAGGTGCCGG	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3242042	3242042	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	282.0	101.0	387.0	1.0	0.358156	0.00258398	.	.	none	.	MXRA5	815	.	NM_015419	exon5	c.G1684T	p.E562X	CCATTTCATCCCT	.	PASS	Atlas-SNP
PFN1	5216	hgsc.bcm.edu	37	17	4849260	4849260	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	196.0	72.0	330.0	0.0	0.367347	0	.	.	none	.	PFN1	6	.	NM_005022	exon3	c.C358G	p.H120D	CACCGTGGACACC	.	PASS	Atlas-SNP
UNKL	64718	hgsc.bcm.edu	37	16	1417803	1417803	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	127.0	73.0	146.0	0.0	0.574803	0	.	.	none	.	UNKL	46	.	NM_001193388	exon13	c.A1642G	p.S548G	AGGGGCTGGGGGA	.	PASS	Atlas-SNP
MLLT1	4298	hgsc.bcm.edu	37	19	6230658	6230658	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	39.0	26.0	78.0	0.0	0.666667	0	.	.	none	MLLT1,NS,carcinoma,+2,1	MLLT1	47	1	NM_005934	exon4	c.A343T	p.N115Y	GGTGGTTCACGGG	.	PASS	Atlas-SNP
ERC2	26059	hgsc.bcm.edu	37	3	56052950	56052950	+	Missense_Mutation	SNP	G	G	A	rs201400364	by1000genomes	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	148.0	57.0	212.0	0.0	0.385135	0	G|1.000;A|0.000	0.000	strong	.	ERC2	221	.	NM_015576	exon8	c.C1751T	p.A584V	AGCGTCGCCAGTG	.	PASS	Atlas-SNP
UBE2QL1	134111	hgsc.bcm.edu	37	5	6491453	6491453	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	68.0	30.0	88.0	0.0	0.441176	0	.	.	none	.	UBE2QL1	10	.	NM_001145161	exon2	c.C477T	p.S159S	CGTGTCCGACGGC	.	PASS	Atlas-SNP
KSR2	283455	hgsc.bcm.edu	37	12	117962801	117962801	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	84.0	38.0	139.0	0.0	0.452381	0	.	.	none	.	KSR2	208	.	NM_173598	exon14	c.G1988A	p.R663Q	ATCAGCCGGATGG	.	PASS	Atlas-SNP
C14orf28	122525	hgsc.bcm.edu	37	14	45370114	45370114	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	85.0	31.0	88.0	0.0	0.364706	0	.	.	none	C14orf28,NS,carcinoma,0,1	C14orf28	32	1	NM_001017923	exon2	c.G476A	p.R159Q	ACTGGCGATGCCC	.	PASS	Atlas-SNP
RBMX2	51634	hgsc.bcm.edu	37	X	129545348	129545348	+	Silent	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	99.0	48.0	107.0	0.0	0.484848	0	.	.	none	.	RBMX2	46	.	NM_016024	exon5	c.T330C	p.D110D	AGTGGATCATGTG	.	PASS	Atlas-SNP
DLGAP2	9228	hgsc.bcm.edu	37	8	1497731	1497731	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	65.0	13.0	86.0	0.0	0.2	0	.	.	none	.	DLGAP2	292	.	NM_004745	exon2	c.G872A	p.W291X	GCTCCTGGTCTAC	.	PASS	Atlas-SNP
ZNF676	163223	hgsc.bcm.edu	37	19	22363817	22363817	+	Silent	SNP	A	A	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	24.0	3.0	26.0	1.0	0.125	0.0384615	.	.	none	ZNF676,NS,carcinoma,-1,2	ZNF676	146	2	NM_001001411	exon3	c.T702C	p.F234F	TCGATTAAAAGCT	.	scavenged	Atlas-SNP
SLC6A3	6531	hgsc.bcm.edu	37	5	1406387	1406387	+	Silent	SNP	G	G	A	rs114563841	by1000genomes	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	84.0	26.0	160.0	0.0	0.309524	0	G|0.995;A|0.005	0.005	strong	.	SLC6A3	102	.	NM_001044	exon12	c.C1515T	p.S505S	GTCGTCGCTGAAC	.	PASS	Atlas-SNP
ARID1A	8289	hgsc.bcm.edu	37	1	27056217	27056217	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	269.0	99.0	376.0	1.0	0.36803	0.00265957	.	.	none	ARID1A,NS,carcinoma,0,1	ARID1A	842	1	NM_006015	exon2	c.C1213T	p.Q405X	CAGCAACAGGGAC	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103236931	103236931	+	Missense_Mutation	SNP	T	T	G	rs374443790	alternate_allele	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	187.0	46.0	188.0	0.0	0.245989	0	.	.	alt	.	RELN	593	.	NM_173054	exon25	c.A3511C	p.M1171L	AGTACATCTCTGC	.	PASS	Atlas-SNP
KPRP	448834	hgsc.bcm.edu	37	1	152732767	152732767	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	129.0	30.0	142.0	0.0	0.232558	0	.	.	none	.	KPRP	152	.	NM_001025231	exon2	c.C703T	p.Q235X	CAGTGCCAGACCC	.	PASS	Atlas-SNP
ATOH1	474	hgsc.bcm.edu	37	4	94750977	94750977	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	37.0	13.0	44.0	0.0	0.351351	0	.	.	none	.	ATOH1	40	.	NM_005172	exon1	c.C900T	p.S300S	GGACAGCGCCCTG	.	PASS	Atlas-SNP
PCDHA13	56136	hgsc.bcm.edu	37	5	140263476	140263476	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	24.0	14.0	55.0	0.0	0.583333	0	.	.	none	.	PCDHA13	213	.	NM_031865	exon1	c.C1623T	p.G541G	CTCTGGCGTGCCG	.	PASS	Atlas-SNP
HCRTR2	3062	hgsc.bcm.edu	37	6	55113583	55113583	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	142.0	59.0	211.0	0.0	0.415493	0	.	.	none	.	HCRTR2	112	.	NM_001526	exon2	c.C370A	p.Q124K	TTTGGACAGTCCC	.	PASS	Atlas-SNP
CACNA1F	778	hgsc.bcm.edu	37	X	49088337	49088337	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	70.0	19.0	102.0	0.0	0.271429	0	.	.	none	.	CACNA1F	218	.	NM_001256789	exon2	c.G78A	p.W26X	CAGCCCCCATTCG	.	PASS	Atlas-SNP
MUC12	10071	hgsc.bcm.edu	37	7	100634964	100634964	+	Missense_Mutation	SNP	C	C	A	rs4370452	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	3.0	3.0	0.0	0.0	1	.	C|0.492;A|0.508	0.508	strong	MUC12,NS,carcinoma,0,1	MUC12	140	1	NM_001164462	exon2	c.C1120A	p.P374T	CACTTCCCTGAAA	.	scavenged	Atlas-SNP
RNF145	153830	hgsc.bcm.edu	37	5	158630639	158630639	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	31.0	2.0	23.0	1.0	0.0645161	0.0434783	.	.	none	RNF145,caecum,carcinoma,0,4	RNF145	110	4	NM_001199380	exon2	c.A77G	p.K26R	TTTTTTTTCTTTT	.	scavenged	Atlas-SNP
CYP7A1	1581	hgsc.bcm.edu	37	8	59409213	59409213	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	64.0	4.0	80.0	0.0	0.0625	0	.	.	none	CYP7A1,NS,carcinoma,-1,2	CYP7A1	76	2	NM_000780	exon3	c.G858A	p.S286S	TGCTTGCGATGCC	.	PASS	Atlas-SNP
XPO1	7514	hgsc.bcm.edu	37	2	61726851	61726851	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	201.0	144.0	104.0	0.0	0.716418	0	.	.	none	.	XPO1	108	.	NM_003400	exon7	c.A587T	p.D196V	TGCCTGTCTTTTA	.	PASS	Atlas-SNP
PIGC	5279	hgsc.bcm.edu	37	1	172411314	172411314	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	114.0	61.0	123.0	0.0	0.535088	0	.	.	none	.	PIGC	24	.	NM_153747	exon2	c.A449G	p.Y150C	ATGGCATAGATGG	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90437660	90437660	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	61.0	28.0	79.0	0.0	0.459016	0	.	.	none	.	MDN1	478	.	NM_014611	exon37	c.G5364A	p.L1788L	TCCAAACAGGTCT	.	PASS	Atlas-SNP
MEF2BNB-MEF2B	4207	hgsc.bcm.edu	37	19	19260045	19260045	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	97.0	70.0	172.0	2.0	0.721649	0.0116279	.	.	none	MEF2BNB-MEF2B,NS,lymphoid_neoplasm,0,15	MEF2BNB-MEF2B	29	15	NM_005919	exon5	c.A248C	p.D83A	AGGATGTCAGTGT	.	scavenged	Atlas-SNP
HAUS6	54801	hgsc.bcm.edu	37	9	19058365	19058365	+	Silent	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	132.0	49.0	196.0	0.0	0.371212	0	.	.	none	.	HAUS6	66	.	NM_017645	exon16	c.A2400G	p.K800K	CTCCAGTTTAAAA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092950	1092950	+	Missense_Mutation	SNP	C	C	T	rs199605832	bycluster	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	55.0	3.0	149.0	1.0	0.0545455	0.00671141	.	.	weak	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon30	c.C4769T	p.T1590I	CCACCACTACGGT	.	scavenged	Atlas-SNP
ANK3	288	hgsc.bcm.edu	37	10	61946498	61946498	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	100.0	55.0	136.0	0.0	0.55	0	.	.	none	.	ANK3	703	.	NM_020987	exon17	c.A2060G	p.N687S	TTCGCATTTCTAC	.	PASS	Atlas-SNP
MINK1	50488	hgsc.bcm.edu	37	17	4797860	4797860	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	75.0	4.0	108.0	0.0	0.0533333	0	.	.	none	.	MINK1	110	.	NM_153827	exon24	c.C2849T	p.S950L	AGAGCTCGTTCAC	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128350377	128350377	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	63.0	22.0	116.0	0.0	0.349206	0	.	.	none	.	MYO7B	359	.	NM_001080527	exon17	c.C2001G	p.D667E	GTTCGACCGGGAG	.	PASS	Atlas-SNP
FUT5	2527	hgsc.bcm.edu	37	19	5867725	5867725	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	107.0	32.0	223.0	0.0	0.299065	0	.	.	none	.	FUT5	29	.	NM_002034	exon2	c.G12A	p.L4L	TGGGCCCAGGGGA	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57060777	57060777	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	161.0	103.0	145.0	0.0	0.639752	0	.	.	none	.	NLRC5	186	.	NM_032206	exon5	c.T1922G	p.F641C	TGCCCTTCCACAA	.	PASS	Atlas-SNP
KIAA0408	9729	hgsc.bcm.edu	37	6	127768258	127768258	+	Silent	SNP	A	A	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	80.0	31.0	77.0	0.0	0.3875	0	.	.	none	.	KIAA0408	61	.	NM_014702	exon5	c.T1206C	p.H402H	ATCAGGATGAGAT	.	PASS	Atlas-SNP
EZH2	2146	hgsc.bcm.edu	37	7	148508727	148508727	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	36.0	14.0	31.0	0.0	0.388889	0	.	.	none	EZH2_ENST00000350995,face,carcinoma,-1,214	EZH2	823	214	NM_004456	exon16	c.A1937T	p.Y646F	CCACAGTATTCTG	.	PASS	Atlas-SNP
NCKAP5	344148	hgsc.bcm.edu	37	2	133542832	133542832	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	129.0	46.0	157.0	0.0	0.356589	0	.	.	none	.	NCKAP5	322	.	NM_207363	exon14	c.A1552G	p.R518G	GTTTTCTGTTTGT	.	PASS	Atlas-SNP
LOXL4	84171	hgsc.bcm.edu	37	10	100017842	100017842	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	72.0	25.0	118.0	0.0	0.347222	0	.	.	none	.	LOXL4	60	.	NM_032211	exon7	c.C1001T	p.T334M	CAGACCGTGCCCC	.	PASS	Atlas-SNP
SMOC1	64093	hgsc.bcm.edu	37	14	70459149	70459149	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	79.0	4.0	110.0	0.0	0.0506329	0	.	.	none	.	SMOC1	61	.	NM_001034852	exon6	c.C542T	p.P181L	CTAAGCCGACACC	.	PASS	Atlas-SNP
SLFN12	55106	hgsc.bcm.edu	37	17	33738875	33738875	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	47.0	18.0	74.0	0.0	0.382979	0	.	.	none	SLFN12,colon,carcinoma,+2,1	SLFN12	56	1	NM_018042	exon4	c.A1219C	p.K407Q	ATTGCTTAAGTCC	.	PASS	Atlas-SNP
SPRED3	399473	hgsc.bcm.edu	37	19	38882747	38882747	+	Silent	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	79.0	35.0	110.0	0.0	0.443038	0	.	.	none	.	SPRED3	47	.	NM_001042522	exon2	c.G339A	p.L113L	CGCACTGGGTCGA	.	PASS	Atlas-SNP
ANKRD35	148741	hgsc.bcm.edu	37	1	145561654	145561654	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	148.0	44.0	124.0	0.0	0.297297	0	.	.	none	.	ANKRD35	96	.	NM_144698	exon10	c.G1342A	p.G448R	ACCAATGGGGCAC	.	PASS	Atlas-SNP
DAAM2	23500	hgsc.bcm.edu	37	6	39832772	39832772	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	105.0	37.0	189.0	0.0	0.352381	0	.	.	none	.	DAAM2	101	.	NM_015345	exon5	c.C350T	p.A117V	TGTACGCGTTTGA	.	PASS	Atlas-SNP
EGFR	1956	hgsc.bcm.edu	37	7	55214404	55214404	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	69.0	16.0	97.0	0.0	0.231884	0	.	.	none	.	EGFR	20426	.	NM_201283	exon4	c.C530T	p.S177L	ACATGTCGATGGA	.	PASS	Atlas-SNP
OR2L8	391190	hgsc.bcm.edu	37	1	248112914	248112914	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	208.0	45.0	234.0	0.0	0.216346	0	.	.	none	OR2L8,right_upper_lobe,carcinoma,0,1	OR2L8	92	1	NM_001001963	exon1	c.C755A	p.A252E	ACTATGCACCTTT	.	PASS	Atlas-SNP
RSPO3	84870	hgsc.bcm.edu	37	6	127476585	127476585	+	Splice_Site	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	50.0	24.0	59.0	0.0	0.48	0	.	.	none	RSPO3,NS,carcinoma,+2,1	RSPO3	32	1	NM_032784	exon4	c.634+2T>C	.	ACGAGGTACAATC	.	PASS	Atlas-SNP
AURKA	6790	hgsc.bcm.edu	37	20	54945628	54945628	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	92.0	31.0	126.0	0.0	0.336957	0	.	.	none	.	AURKA	42	.	NM_198437	exon8	c.C942G	p.S314R	TCCAAGGCTCCAG	.	PASS	Atlas-SNP
GJA9	81025	hgsc.bcm.edu	37	1	39341674	39341674	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	88.0	32.0	105.0	0.0	0.363636	0	.	.	none	GJA9,NS,carcinoma,+1,2	GJA9	55	2	NM_030772	exon2	c.C97T	p.R33X	GCATTCGAAATAT	.	PASS	Atlas-SNP
PLD2	5338	hgsc.bcm.edu	37	17	4718855	4718855	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	115.0	48.0	156.0	0.0	0.417391	0	.	.	none	PLD2_ENST00000263088,bladder,carcinoma,-2,2	PLD2	138	2	NM_001243108	exon13	c.C1258T	p.L420L	AGGGCGCTGATGC	.	PASS	Atlas-SNP
TSEN15	116461	hgsc.bcm.edu	37	1	184020964	184020964	+	Silent	SNP	C	C	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	41.0	13.0	38.0	0.0	0.317073	0	.	.	none	.	TSEN15	19	.	NM_001127394	exon1	c.C75A	p.G25G	CTTTGGCGACGGC	.	PASS	Atlas-SNP
SIPA1L1	26037	hgsc.bcm.edu	37	14	72190600	72190600	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	37.0	12.0	61.0	0.0	0.324324	0	.	.	none	.	SIPA1L1	219	.	NM_015556	exon16	c.G4508A	p.R1503K	ACACGAGAAAGTA	.	PASS	Atlas-SNP
MZF1	7593	hgsc.bcm.edu	37	19	59073591	59073591	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	47.0	23.0	94.0	0.0	0.489362	0	.	.	none	MZF1,NS,carcinoma,0,1	MZF1	37	1	NM_198055	exon6	c.G2053A	p.E685K	CACACTCAGGGCA	.	PASS	Atlas-SNP
EZH2	2146	hgsc.bcm.edu	37	7	148507460	148507460	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	61.0	22.0	79.0	0.0	0.360656	0	.	.	none	.	EZH2	823	.	NM_004456	exon17	c.A1994G	p.K665R	ATGTATTTATCAT	.	PASS	Atlas-SNP
PTBP2	58155	hgsc.bcm.edu	37	1	97243142	97243142	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	216.0	98.0	332.0	0.0	0.453704	0	.	.	none	.	PTBP2	62	.	NM_021190	exon6	c.G434A	p.R145H	TCCAGCGTGCTCA	.	PASS	Atlas-SNP
VANGL1	81839	hgsc.bcm.edu	37	1	116206595	116206595	+	Missense_Mutation	SNP	G	G	A	rs148341022		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	214.0	82.0	344.0	1.0	0.383178	0.00290698	G|1.000;A|0.000	0.000	weak	.	VANGL1	65	.	NM_138959	exon4	c.G518A	p.R173H	TTTTCCGCAAGCG	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126412678	126412678	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	141.0	60.0	148.0	0.0	0.425532	0	.	.	none	.	FAT4	1752	.	NM_024582	exon17	c.G14701A	p.G4901R	GAGGGAGGACCTG	.	PASS	Atlas-SNP
DNAH1	25981	hgsc.bcm.edu	37	3	52409342	52409342	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	36.0	17.0	78.0	0.0	0.472222	0	.	.	none	.	DNAH1	534	.	NM_015512	exon45	c.A7072G	p.M2358V	CGGCTGATGCGTC	.	PASS	Atlas-SNP
DCC	1630	hgsc.bcm.edu	37	18	50832066	50832066	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	88.0	35.0	121.0	0.0	0.397727	0	.	.	none	.	DCC	360	.	NM_005215	exon13	c.A2030G	p.N677S	AGCCAAACAACCT	.	PASS	Atlas-SNP
ADRA1D	146	hgsc.bcm.edu	37	20	4229009	4229009	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	83.0	32.0	135.0	0.0	0.385542	0	.	.	none	ADRA1D,NS,carcinoma,0,1	ADRA1D	36	1	NM_000678	exon1	c.G596A	p.R199H	GAGTGGCGCACGC	.	PASS	Atlas-SNP
GNAI2	2771	hgsc.bcm.edu	37	3	50294169	50294169	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	191.0	76.0	283.0	0.0	0.397906	0	.	.	none	.	GNAI2	42	.	NM_002070	exon6	c.G608A	p.G203D	ATGTGGGTGGTCA	.	PASS	Atlas-SNP
FAM194B	220081	hgsc.bcm.edu	37	13	46115752	46115752	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	153.0	48.0	219.0	0.0	0.313726	0	.	.	none	.	FAM194B	42	.	NM_182542	exon15	c.C1936T	p.P646S	CTGTTGGGCCGGG	.	PASS	Atlas-SNP
TRIM42	287015	hgsc.bcm.edu	37	3	140406661	140406661	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	126.0	57.0	174.0	0.0	0.452381	0	.	.	none	.	TRIM42	143	.	NM_152616	exon3	c.C1137T	p.G379G	AAATGGCTTTCTC	.	PASS	Atlas-SNP
KLHL6	89857	hgsc.bcm.edu	37	3	183273173	183273173	+	Missense_Mutation	SNP	A	A	G	rs140971016		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	147.0	58.0	206.0	0.0	0.394558	0	A|1.000;G|0.000	0.000	weak	.	KLHL6	100	.	NM_130446	exon1	c.T269C	p.L90P	GCGGCAAGCACCA	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48314642	48314642	+	Silent	SNP	T	T	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	157.0	44.0	123.0	0.0	0.280255	0	.	.	none	.	ABCA13	1192	.	NM_152701	exon17	c.T5379A	p.I1793I	CGCAATTGTGATA	.	PASS	Atlas-SNP
SEC16A	9919	hgsc.bcm.edu	37	9	139371030	139371030	+	Silent	SNP	A	A	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	87.0	40.0	96.0	0.0	0.45977	0	.	.	none	.	SEC16A	249	.	NM_014866	exon3	c.T1038G	p.R346R	GTGCGTACGGTTT	.	PASS	Atlas-SNP
AVL9	23080	hgsc.bcm.edu	37	7	32620454	32620454	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	178.0	33.0	159.0	0.0	0.185393	0	.	.	none	.	AVL9	66	.	NM_015060	exon15	c.G1783A	p.V595I	GGAAACGTCATGG	.	PASS	Atlas-SNP
HIST1H3D	8351	hgsc.bcm.edu	37	6	26197212	26197212	+	Silent	SNP	C	C	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	109.0	36.0	186.0	0.0	0.330275	0	.	.	none	HIST1H3D,colon,carcinoma,0,1	HIST1H3D	31	1	NM_003530	exon2	c.G267C	p.A89A	CATCACCGCCGAG	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151970845	151970845	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	404.0	21.0	704.0	0.0	0.0519802	0	.	.	none	MLL3_ENST00000355193,NS,carcinoma,-1,2	MLL3	1564	2	NM_170606	exon7	c.T957A	p.D319E	ACTGAAATCCTGA	.	PASS	Atlas-SNP
GRIA2	2891	hgsc.bcm.edu	37	4	158257596	158257596	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	197.0	84.0	270.0	1.0	0.426396	0.0037037	.	.	none	.	GRIA2	358	.	NM_000826	exon11	c.A1541C	p.K514T	TCTCAAAGCCCTT	.	PASS	Atlas-SNP
NLRP1	22861	hgsc.bcm.edu	37	17	5440172	5440172	+	Missense_Mutation	SNP	G	G	A	rs199748129		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	37.0	11.0	53.0	0.0	0.297297	0	.	.	weak	NLRP1,colon,carcinoma,0,1	NLRP1	358	1	NM_014922	exon8	c.C2959T	p.R987W	CTTACCGTCTGCT	.	PASS	Atlas-SNP
SERPINB7	8710	hgsc.bcm.edu	37	18	61471521	61471521	+	Silent	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	19.0	7.0	22.0	0.0	0.368421	0	.	.	none	.	SERPINB7	66	.	NM_001261830	exon8	c.G795A	p.R265R	TCCAAGGCGAATG	.	PASS	Atlas-SNP
USP29	57663	hgsc.bcm.edu	37	19	57640529	57640529	+	Silent	SNP	A	A	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	106.0	81.0	101.0	0.0	0.764151	0	.	.	none	.	USP29	186	.	NM_020903	exon4	c.A486G	p.L162L	GATATTAGAAAAT	.	PASS	Atlas-SNP
DAZAP1	26528	hgsc.bcm.edu	37	19	1434902	1434902	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	12.0	5.0	15.0	0.0	0.416667	0	.	.	none	.	DAZAP1	52	.	NM_018959	exon12	c.C1215G	p.Y405X	CCCCTACCGACGC	.	PASS	Atlas-SNP
SLC10A4	201780	hgsc.bcm.edu	37	4	48490448	48490448	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	44.0	14.0	61.0	0.0	0.318182	0	.	.	none	.	SLC10A4	23	.	NM_152679	exon3	c.C806T	p.S269F	AGGTTTCCCTGTG	.	PASS	Atlas-SNP
PRPF39	55015	hgsc.bcm.edu	37	14	45579854	45579854	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	135.0	62.0	194.0	0.0	0.459259	0	.	.	none	.	PRPF39	46	.	NM_017922	exon10	c.G1406A	p.G469E	GGCATGGAAATCT	.	PASS	Atlas-SNP
DSG2	1829	hgsc.bcm.edu	37	18	29098213	29098213	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	69.0	32.0	83.0	0.0	0.463768	0	.	.	none	.	DSG2	115	.	NM_001943	exon2	c.C57T	p.N19N	CTTTAACGTTGGA	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170127524	170127524	+	Missense_Mutation	SNP	G	G	A	rs201860953	bycluster	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	97.0	36.0	142.0	0.0	0.371134	0	G|0.999;A|0.001	0.001	weak	LRP2,rectum,carcinoma,0,2	LRP2	751	2	NM_004525	exon16	c.C2210T	p.S737L	TTCCCCGAAACTG	.	PASS	Atlas-SNP
L1CAM	3897	hgsc.bcm.edu	37	X	153128162	153128162	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	98.0	29.0	163.0	0.0	0.295918	0	.	.	none	.	L1CAM	189	.	NM_000425	exon28	c.T3730C	p.S1244P	CCCCTGAGCTGTC	.	PASS	Atlas-SNP
SATB2	23314	hgsc.bcm.edu	37	2	200193545	200193545	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	76.0	33.0	137.0	0.0	0.434211	0	.	.	none	SATB2,NS,carcinoma,+1,1	SATB2	134	1	NM_015265	exon9	c.T1262C	p.F421S	TTGAGGAAATTCT	.	PASS	Atlas-SNP
IQCF2	389123	hgsc.bcm.edu	37	3	51897174	51897174	+	Missense_Mutation	SNP	G	G	A	rs369181892		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	60.0	3.0	134.0	1.0	0.05	0.00746269	.	.	weak	IQCF2,mouth,carcinoma,0,1	IQCF2	21	1	NM_203424	exon3	c.G283A	p.A95T	CTGATCGCCTACG	.	scavenged	Atlas-SNP
HINT2	84681	hgsc.bcm.edu	37	9	35813717	35813717	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	76.0	30.0	120.0	0.0	0.394737	0	.	.	none	.	HINT2	15	.	NM_032593	exon2	c.G146A	p.G49E	GCTCCCCCAGGAG	.	PASS	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	114031393	114031393	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	146.0	54.0	220.0	0.0	0.369863	0	.	.	none	.	CSMD3	2325	.	NM_052900	exon6	c.T933A	p.N311K	TGGTATATTCATT	.	PASS	Atlas-SNP
ILF3	3609	hgsc.bcm.edu	37	19	10795539	10795539	+	Silent	SNP	T	T	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	94.0	76.0	119.0	0.0	0.808511	0	.	.	none	.	ILF3	99	.	NM_153464	exon18	c.T2064G	p.G688G	AGCAGGTTTTGTA	.	PASS	Atlas-SNP
PNLIPRP1	5407	hgsc.bcm.edu	37	10	118351352	118351352	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	61.0	20.0	89.0	0.0	0.327869	0	.	.	none	.	PNLIPRP1	82	.	NM_006229	exon3	c.G119A	p.R40K	CAATCAGGCCCCT	.	PASS	Atlas-SNP
HOXD4	3233	hgsc.bcm.edu	37	2	177016724	177016724	+	Silent	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	18.0	11.0	29.0	0.0	0.611111	0	.	.	none	.	HOXD4	32	.	NM_014621	exon1	c.G363A	p.P121P	GCAGCCGCCCTCC	.	PASS	Atlas-SNP
FAM102A	399665	hgsc.bcm.edu	37	9	130742408	130742408	+	Silent	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	59.0	25.0	82.0	0.0	0.423729	0	.	.	none	.	FAM102A	32	.	NM_001035254	exon1	c.C9T	p.F3F	CATCAAGAAAGCC	.	PASS	Atlas-SNP
ASIC3	9311	hgsc.bcm.edu	37	7	150746203	150746203	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	36.0	15.0	62.0	0.0	0.416667	0	.	.	none	.	.	.	.	NM_020322	exon1	c.T231G	p.D77E	CCTGGATGAGCGA	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130159037	130159037	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	117.0	52.0	146.0	0.0	0.444444	0	.	.	none	.	COL6A5	205	.	NM_153264	exon35	c.G5855A	p.R1952Q	GCATTCGAGAGGC	.	PASS	Atlas-SNP
RFX3	5991	hgsc.bcm.edu	37	9	3225259	3225259	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	61.0	24.0	94.0	0.0	0.393443	0	.	.	none	RFX3_ENST00000382004,NS,carcinoma,+1,1	RFX3	156	1	NM_134428	exon18	c.G2033A	p.S678N	ATTTCACTTTCTA	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238277339	238277339	+	Silent	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	110.0	42.0	159.0	0.0	0.381818	0	.	.	none	.	COL6A3	608	.	NM_004369	exon10	c.C4767T	p.D1589D	TCTGGGGTCATTG	.	PASS	Atlas-SNP
VPS13B	157680	hgsc.bcm.edu	37	8	100789120	100789120	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	203.0	76.0	292.0	1.0	0.374384	0.00342466	.	.	none	.	VPS13B	811	.	NM_017890	exon41	c.C7440T	p.C2480C	CCTTTGCGTTTCT	.	PASS	Atlas-SNP
LTB	4050	hgsc.bcm.edu	37	6	31550123	31550123	+	Silent	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	164.0	63.0	251.0	0.0	0.384146	0	.	.	none	.	LTB	19	.	NM_002341	exon1	c.A72G	p.A24A	GGCTCCTGCCACA	.	PASS	Atlas-SNP
MAG	4099	hgsc.bcm.edu	37	19	35793379	35793379	+	Silent	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	29.0	22.0	55.0	0.0	0.758621	0	.	.	none	.	MAG	172	.	NM_080600	exon7	c.G999A	p.G333G	GAACGGGACAATG	.	PASS	Atlas-SNP
ADCY9	115	hgsc.bcm.edu	37	16	4016487	4016487	+	Silent	SNP	C	C	T	rs371159341		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	76.0	20.0	80.0	0.0	0.263158	0	.	.	weak	.	ADCY9	151	.	NM_001116	exon11	c.G3351A	p.A1117A	CCCTGACGCCGCC	.	PASS	Atlas-SNP
NUDT6	11162	hgsc.bcm.edu	37	4	123814096	123814096	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	96.0	34.0	118.0	0.0	0.354167	0	.	.	none	.	NUDT6	50	.	NM_007083	exon5	c.G838A	p.D280N	TTTTGTCAAACCC	.	PASS	Atlas-SNP
OR4C16	219428	hgsc.bcm.edu	37	11	55340486	55340486	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	65.0	24.0	62.0	0.0	0.369231	0	.	.	none	.	OR4C16	104	.	NM_001004701	exon1	c.G883A	p.A295T	AAAAGTGCCATGA	.	PASS	Atlas-SNP
AATK	9625	hgsc.bcm.edu	37	17	79098649	79098649	+	Splice_Site	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	99.0	46.0	186.0	0.0	0.464646	0	.	.	none	.	AATK	102	.	NM_001080395	exon10	c.841-1G>A	.	GTCCTCCTGTTGG	.	PASS	Atlas-SNP
SLC6A11	6538	hgsc.bcm.edu	37	3	10976837	10976837	+	Silent	SNP	G	G	A	rs138273152		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	133.0	28.0	207.0	0.0	0.210526	0	G|1.000;A|0.000	0.000	weak	SLC6A11,NS,carcinoma,+1,2	SLC6A11	87	2	NM_014229	exon13	c.G1698A	p.P566P	CATCCCGCTCTGG	.	PASS	Atlas-SNP
ZNF675	171392	hgsc.bcm.edu	37	19	23869831	23869831	+	Splice_Site	SNP	A	A	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	26.0	7.0	59.0	0.0	0.269231	0	.	.	none	.	ZNF675	88	.	NM_138330	exon2	c.3+2T>G	.	ACTCTCACCATTT	.	PASS	Atlas-SNP
REV3L	5980	hgsc.bcm.edu	37	6	111694135	111694135	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	70.0	32.0	100.0	0.0	0.457143	0	.	.	none	.	REV3L	386	.	NM_002912	exon13	c.G5423A	p.G1808E	GACTGTCCCATTT	.	PASS	Atlas-SNP
EPHA7	2045	hgsc.bcm.edu	37	6	93982068	93982068	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	208.0	75.0	278.0	1.0	0.360577	0.00359712	.	.	none	.	EPHA7	251	.	NM_004440	exon6	c.C1397G	p.P466R	TGCTCTGGTTCCT	.	PASS	Atlas-SNP
KIAA1967	57805	hgsc.bcm.edu	37	8	22464810	22464810	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	15.0	2.0	30.0	0.0	0.133333	0	.	.	none	KIAA1967,NS,carcinoma,+2,1	KIAA1967	72	1	NM_021174	exon6	c.C459T	p.H153H	GCCTCACCGGATT	.	scavenged	Atlas-SNP
PRPF40B	25766	hgsc.bcm.edu	37	12	50026835	50026835	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	61.0	17.0	86.0	0.0	0.278689	0	.	.	none	.	PRPF40B	83	.	NM_001031698	exon7	c.C387T	p.R129R	TGGGCGCATCTAC	.	PASS	Atlas-SNP
PCDHGA1	56114	hgsc.bcm.edu	37	5	140711926	140711926	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	65.0	3.0	132.0	0.0	0.0461538	0	.	.	none	PCDHGA1_ENST00000517417,NS,carcinoma,0,4	PCDHGA1	397	4	NM_018912	exon1	c.G1675A	p.A559T	GACAACGCGCCCG	.	scavenged	Atlas-SNP
FRMD4B	23150	hgsc.bcm.edu	37	3	69230472	69230472	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	87.0	45.0	92.0	0.0	0.517241	0	.	.	none	.	FRMD4B	90	.	NM_015123	exon21	c.C2429T	p.T810I	TAGGGTGTGTACC	.	PASS	Atlas-SNP
ZNF559	84527	hgsc.bcm.edu	37	19	9449245	9449245	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	119.0	98.0	157.0	1.0	0.823529	0.00636943	.	.	none	.	ZNF559	77	.	NM_001202408	exon3	c.C212G	p.T71R	GGTTGACAAATTA	.	PASS	Atlas-SNP
HAUS6	54801	hgsc.bcm.edu	37	9	19058226	19058226	+	Missense_Mutation	SNP	T	T	G	rs201053056	by1000genomes;alternate_allele	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	135.0	57.0	197.0	0.0	0.422222	0	T|1.000;C|0.000	.	alt	.	HAUS6	66	.	NM_017645	exon16	c.A2539C	p.K847Q	CCCTTTTCTTGGA	.	PASS	Atlas-SNP
BCO2	83875	hgsc.bcm.edu	37	11	112071462	112071462	+	Missense_Mutation	SNP	C	C	T	rs141269805		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	92.0	33.0	80.0	0.0	0.358696	0	C|1.000;T|0.000	0.000	weak	.	BCO2	44	.	NM_031938	exon7	c.C992T	p.T331M	GTAATACGCGGTT	.	PASS	Atlas-SNP
AQPEP	0	hgsc.bcm.edu	37	5	115299001	115299001	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	38.0	16.0	59.0	0.0	0.421053	0	.	.	none	.	.	.	.	NM_173800	exon1	c.C687T	p.G229G	CCAGGGCGAGCGC	.	PASS	Atlas-SNP
PKD2L2	27039	hgsc.bcm.edu	37	5	137228235	137228235	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	86.0	34.0	122.0	0.0	0.395349	0	.	.	none	.	PKD2L2	68	.	NM_001258448	exon3	c.A200T	p.D67V	TTTTGGACACTTC	.	PASS	Atlas-SNP
ETS1	2113	hgsc.bcm.edu	37	11	128442997	128442997	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	70.0	21.0	101.0	0.0	0.3	0	.	.	none	.	ETS1	123	.	NM_001143820	exon2	c.G29A	p.S10N	GGGCTGCTCCCAG	.	PASS	Atlas-SNP
MACROD2	140733	hgsc.bcm.edu	37	20	15967421	15967421	+	Silent	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	121.0	50.0	178.0	0.0	0.413223	0	.	.	none	MACROD2,colon,carcinoma,+2,2	MACROD2	34	2	NM_080676	exon14	c.G1035A	p.S345S	AGAATCGCAGAGC	.	PASS	Atlas-SNP
MAP4K5	11183	hgsc.bcm.edu	37	14	50901153	50901153	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	68.0	32.0	88.0	0.0	0.470588	0	.	.	none	.	MAP4K5	48	.	NM_006575	exon27	c.A2123G	p.N708S	TTCAAATTGATTG	.	PASS	Atlas-SNP
TIRAP	114609	hgsc.bcm.edu	37	11	126162924	126162924	+	Missense_Mutation	SNP	G	G	A	rs199561634		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	77.0	36.0	90.0	0.0	0.467532	0	G|0.999;A|0.001	0.001	weak	.	TIRAP	37	.	NM_148910	exon5	c.G620A	p.R207H	GCTTTCGTCAAGT	.	PASS	Atlas-SNP
MCM4	4173	hgsc.bcm.edu	37	8	48875553	48875553	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	111.0	31.0	153.0	0.0	0.279279	0	.	.	none	.	MCM4	97	.	NM_182746	exon7	c.A646T	p.K216X	CACATCAAATCAT	.	PASS	Atlas-SNP
CCDC88C	440193	hgsc.bcm.edu	37	14	91770135	91770135	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	71.0	29.0	84.0	0.0	0.408451	0	.	.	none	CCDC88C_ENST00000389857,caecum,carcinoma,+1,2	CCDC88C	192	2	NM_001080414	exon20	c.C3545A	p.S1182X	TCGGCCGATTGCC	.	PASS	Atlas-SNP
KREMEN2	79412	hgsc.bcm.edu	37	16	3014557	3014557	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	136.0	35.0	144.0	0.0	0.257353	0	.	.	none	.	KREMEN2	13	.	NM_001253725	exon1	c.C36T	p.L12L	CTTTCTCCTCTTC	.	PASS	Atlas-SNP
MTMR8	55613	hgsc.bcm.edu	37	X	63574801	63574801	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	63.0	30.0	83.0	0.0	0.47619	0	.	.	none	.	MTMR8	178	.	NM_017677	exon4	c.T324A	p.D108E	ATAAAGATCTTCA	.	PASS	Atlas-SNP
ADCY2	108	hgsc.bcm.edu	37	5	7826845	7826845	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	60.0	22.0	104.0	0.0	0.366667	0	.	.	none	.	ADCY2	337	.	NM_020546	exon25	c.C3137T	p.T1046M	AGGAGACGAGCCT	.	PASS	Atlas-SNP
ZNF485	220992	hgsc.bcm.edu	37	10	44112510	44112510	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	34.0	13.0	70.0	0.0	0.382353	0	.	.	none	.	ZNF485	102	.	NM_145312	exon5	c.C1019G	p.S340C	GCTCATCCTTTGC	.	PASS	Atlas-SNP
ZNF608	57507	hgsc.bcm.edu	37	5	123984038	123984038	+	Missense_Mutation	SNP	G	G	A	rs186374145	bycluster;by1000genomes	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	147.0	71.0	185.0	0.0	0.482993	0	G|1.000;A|0.000	0.000	strong	.	ZNF608	117	.	NM_020747	exon4	c.C2039T	p.T680M	GCAGCCGTCATGT	.	PASS	Atlas-SNP
TMPO	7112	hgsc.bcm.edu	37	12	98931352	98931352	+	Splice_Site	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	68.0	27.0	71.0	0.0	0.397059	0	.	.	none	.	TMPO	111	.	NM_001032284	exon4	c.663+2T>C	.	ATCAGGTATCTTT	.	PASS	Atlas-SNP
EZH2	2146	hgsc.bcm.edu	37	7	148507461	148507461	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	63.0	23.0	78.0	0.0	0.365079	0	.	.	none	.	EZH2	823	.	NM_004456	exon17	c.A1993G	p.K665E	TGTATTTATCATA	.	PASS	Atlas-SNP
BCL2	596	hgsc.bcm.edu	37	18	60985444	60985444	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	128.0	50.0	190.0	0.0	0.390625	0	.	.	none	.	BCL2	272	.	NM_000633	exon2	c.G456A	p.E152E	ACCGAACTCAAAG	.	PASS	Atlas-SNP
PCDHA6	56142	hgsc.bcm.edu	37	5	140209668	140209668	+	Silent	SNP	G	G	A	rs141570762	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	56.0	29.0	94.0	0.0	0.517857	0	G|0.998;C|0.002	.	alt	.	PCDHA6	442	.	NM_018909	exon1	c.G1992A	p.T664T	GGCCACGGTTCTG	.	PASS	Atlas-SNP
GPR158	57512	hgsc.bcm.edu	37	10	25701364	25701364	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	88.0	35.0	159.0	0.0	0.397727	0	.	.	none	.	GPR158	255	.	NM_020752	exon4	c.G1297A	p.V433I	GACTTCGTTAGCA	.	PASS	Atlas-SNP
RUFY2	55680	hgsc.bcm.edu	37	10	70143622	70143622	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	74.0	41.0	103.0	0.0	0.554054	0	.	.	none	.	RUFY2	58	.	NM_017987	exon10	c.G977A	p.R326H	CCCTGACGAGAAT	.	PASS	Atlas-SNP
PCDHGA1	56114	hgsc.bcm.edu	37	5	140711925	140711925	+	Silent	SNP	C	C	T	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	65.0	20.0	133.0	1.0	0.307692	0.0075188	.	.	none	PCDHGA1_ENST00000517417,NS,carcinoma,0,4	PCDHGA1	397	4	NM_018912	exon1	c.C1674T	p.N558N	CGACAACGCGCCC	.	scavenged	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28366537	28366537	+	Silent	SNP	T	T	C	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	75.0	4.0	115.0	0.0	0.0533333	0	.	.	none	.	HERC2	501	.	NM_004667	exon86	c.A13227G	p.V4409V	ATCGCGTACCATA	.	PASS	Atlas-SNP
USF1	7391	hgsc.bcm.edu	37	1	161012436	161012436	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	145.0	31.0	148.0	0.0	0.213793	0	.	.	none	.	USF1	29	.	NM_001276373	exon4	c.C83T	p.P28L	CTGGTTGGGTCTT	.	PASS	Atlas-SNP
OR10A5	144124	hgsc.bcm.edu	37	11	6866966	6866966	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	220.0	85.0	273.0	0.0	0.386364	0	.	.	none	.	OR10A5	48	.	NM_178168	exon1	c.C53A	p.S18Y	GCTTCTCTTCCCT	.	PASS	Atlas-SNP
ATP9A	10079	hgsc.bcm.edu	37	20	50313972	50313972	+	Silent	SNP	G	G	A	rs376498362		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	94.0	34.0	143.0	0.0	0.361702	0	.	.	weak	.	ATP9A	135	.	NM_006045	exon5	c.C486T	p.I162I	TTCAACGATGATA	.	PASS	Atlas-SNP