Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	TVarRat	NVarRat	dbSNP_Strength	dbSNP_AF	dbSNP_PopFreq	Confidence	Algorithm
CSMD2	114784	hgsc.bcm.edu	hg19	1	34112388	34112388	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	CSMD2	NM_052896	exon29	c.G4514T	p.R1505L	GAGTCCCGTCCGT	.	54.0	4.0	74.0	0.0	.	946	.	.	.	none	.	.	PASS	Atlas-SNP
SASS6	163786	hgsc.bcm.edu	hg19	1	100572938	100572938	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	SASS6	NM_194292	exon11	c.G1318C	p.E440Q	CTTGCTCTTTAAT	.	88.0	13.0	143.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
RPTN	126638	hgsc.bcm.edu	hg19	1	152127802	152127802	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	RPTN	NM_001122965	exon3	c.A1773G	p.I591M	CCCTTGTATTTCC	.	769.0	224.0	594.0	0.0	.	123	.	.	.	none	.	.	PASS	Atlas-SNP
FAM129A	116496	hgsc.bcm.edu	hg19	1	184767228	184767228	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	FAM129A	NM_052966	exon13	c.G1651T	p.D551Y	TTTCATCAAGCAG	.	87.0	8.0	69.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
PTPN14	5784	hgsc.bcm.edu	hg19	1	214557259	214557259	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	PTPN14	NM_005401	exon13	c.A1939G	p.N647D	TGCTGTTCATCAC	.	169.0	55.0	71.0	0.0	.	168	.	.	.	none	.	.	PASS	Atlas-SNP
MARC1	64757	hgsc.bcm.edu	hg19	1	220971317	220971317	+	Silent	SNP	G	G	A	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	.	NM_022746	exon4	c.G714A	p.R238R	CTTCAGGCCCAAT	.	498.0	119.0	376.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
SLC35F3	148641	hgsc.bcm.edu	hg19	1	234458910	234458910	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	SLC35F3	NM_173508	exon8	c.A1394T	p.E465V	AGGAGGAGCCTGC	.	281.0	36.0	160.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
RAB11FIP5	26056	hgsc.bcm.edu	hg19	2	73315269	73315269	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	RAB11FIP5	NM_015470	exon3	c.G1477A	p.A493T	GGGAGGCCCCCAG	.	484.0	55.0	249.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
FAM124B	79843	hgsc.bcm.edu	hg19	2	225266233	225266233	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	FAM124B_ENST00000409685,NS,carcinoma,0,4	FAM124B	NM_024785	exon1	c.G253A	p.V85I	CCAGGACGCGAAA	.	145.0	20.0	105.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
PFKFB4	5210	hgsc.bcm.edu	hg19	3	48577177	48577177	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	PFKFB4	NM_004567	exon5	c.G406T	p.E136X	TCCGTTCTCGGGT	.	124.0	49.0	143.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
TKT	7086	hgsc.bcm.edu	hg19	3	53264627	53264627	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	TKT	NM_001258028	exon9	c.G977A	p.R326H	GCCTTGCGGGTGG	.	98.0	6.0	72.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
PPP4R2	151987	hgsc.bcm.edu	hg19	3	73110176	73110176	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	PPP4R2	NM_174907	exon5	c.T384A	p.N128K	GCAGAATGTGATG	.	34.0	8.0	68.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
MED12L	116931	hgsc.bcm.edu	hg19	3	151072983	151072983	+	Missense_Mutation	SNP	C	C	T	rs200848773	alternate_allele	TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	MED12L	NM_053002	exon16	c.C2368T	p.L790F	ACTAAACTCCAGC	.	61.0	17.0	151.0	0.0	.	271	.	.	.	alt	C|0.999;G|0.001	.	PASS	Atlas-SNP
HIST1H2BL	8340	hgsc.bcm.edu	hg19	6	27775403	27775403	+	Silent	SNP	C	C	T	rs141648774	alternate_allele	TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	HIST1H2BL	NM_003519	exon1	c.G282A	p.E94E	CTGGATCTCCCTG	.	197.0	143.0	176.0	0.0	.	48	.	.	.	alt	C|1.000;A|0.000	.	PASS	Atlas-SNP
MLIP	90523	hgsc.bcm.edu	hg19	6	53989447	53989447	+	Silent	SNP	T	T	C	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	MLIP	NM_138569	exon3	c.T396C	p.I132I	CCTTATTGTGGAC	.	166.0	127.0	250.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
NOS3	4846	hgsc.bcm.edu	hg19	7	150698913	150698913	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	NOS3	NM_001160111	exon12	c.G1507A	p.V503M	AGCGCCGTGAAGA	.	174.0	53.0	148.0	0.0	.	131	.	.	.	none	.	.	PASS	Atlas-SNP
OXR1	55074	hgsc.bcm.edu	hg19	8	107752622	107752622	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	OXR1	NM_001198532	exon13	c.T2218A	p.Y740N	CTTGTTTATGGTA	.	75.0	11.0	234.0	0.0	.	190	.	.	.	none	.	.	PASS	Atlas-SNP
AKNA	80709	hgsc.bcm.edu	hg19	9	117139726	117139726	+	Missense_Mutation	SNP	T	T	C	rs371041163	alternate_allele	TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	AKNA	NM_030767	exon3	c.A361G	p.T121A	CTTCAGTCATGTC	.	163.0	84.0	129.0	0.0	.	119	.	.	.	alt	.	.	PASS	Atlas-SNP
DBC1	1620	hgsc.bcm.edu	hg19	9	121930244	121930244	+	Silent	SNP	C	C	T	rs370346617		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	DBC1	NM_014618	exon8	c.G1404A	p.S468S	CCGCTCCGAGTCC	.	107.0	26.0	92.0	0.0	.	194	.	.	.	weak	.	.	PASS	Atlas-SNP
GTPBP4	23560	hgsc.bcm.edu	hg19	10	1043230	1043230	+	Silent	SNP	G	G	A	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	GTPBP4	NM_012341	exon5	c.G543A	p.K181K	TGGGAAGTCCAGC	.	456.0	204.0	390.0	1.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
PIK3C2A	5286	hgsc.bcm.edu	hg19	11	17190402	17190402	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	PIK3C2A	NM_002645	exon1	c.C887T	p.S296L	AAACTTGAAACAT	.	278.0	59.0	276.0	0.0	.	148	.	.	.	none	.	.	PASS	Atlas-SNP
MS4A12	54860	hgsc.bcm.edu	hg19	11	60268545	60268545	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	MS4A12	NM_017716	exon3	c.C304T	p.H102Y	TTGATGCACATTG	.	298.0	44.0	591.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
VWCE	220001	hgsc.bcm.edu	hg19	11	61026692	61026692	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	VWCE	NM_152718	exon20	c.G2323T	p.E775X	GGGCCTCAGTGTC	.	112.0	22.0	117.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
M6PR	4074	hgsc.bcm.edu	hg19	12	9096395	9096395	+	Splice_Site	SNP	A	A	G	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	M6PR	NM_002355	exon5	c.453+2T>C	.	TGCCTCACCGCTA	.	100.0	18.0	150.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
MEIS2	4212	hgsc.bcm.edu	hg19	15	37184626	37184626	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	MEIS2,right_lower_lobe,carcinoma,0,1	MEIS2	NM_170675	exon12	c.G1182T	p.Q394H	ACCACCCTGAGAA	.	214.0	59.0	591.0	1.0	.	99	.	.	.	none	.	.	PASS	Atlas-SNP
CRISPLD2	83716	hgsc.bcm.edu	hg19	16	84940197	84940197	+	Silent	SNP	G	G	A	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	CRISPLD2	NM_031476	exon15	c.G1443A	p.L481L	CAGCCTGGGGACT	.	282.0	59.0	256.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
NGFR	4804	hgsc.bcm.edu	hg19	17	47588006	47588006	+	Silent	SNP	G	G	T	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	NGFR	NM_002507	exon4	c.G801T	p.V267V	CCTTGTGGCCTAC	.	333.0	56.0	205.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
HRC	3270	hgsc.bcm.edu	hg19	19	49657602	49657602	+	Missense_Mutation	SNP	C	C	T	rs146437807		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	HRC	NM_002152	exon1	c.G893A	p.R298Q	TGGCTTCGGTGCC	.	164.0	88.0	95.0	0.0	.	85	.	.	.	weak	.	.	PASS	Atlas-SNP
MAOB	4129	hgsc.bcm.edu	hg19	X	43655071	43655071	+	Missense_Mutation	SNP	C	C	A	rs143144504	alternate_allele	TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	MAOB	NM_000898	exon7	c.G683T	p.R228L	TTCACTCGGTCTC	.	117.0	6.0	103.0	0.0	.	52	.	.	.	alt	C|1.000;T|0.000	.	PASS	Atlas-SNP
EPG5	57724	hgsc.bcm.edu	hg19	18	43514887	43514888	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	EPG5	NM_020964	exon11	c.2145_2146insT	p.L715fs	.	.	151.0	34.0	123.0	0.0	.	199	.	0.225166	0	none	.	.	PASS	Atlas-INDEL
HAVCR1	26762	hgsc.bcm.edu	hg19	5	156482352	156482362	+	Frame_Shift_Del	DEL	AATAGCTTATA	AATAGCTTATA	-	novel		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	AATAGCTTATA	AATAGCTTATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	.	HAVCR1	NM_001099414	exon3	c.230_240del	p.77_80del	.	.	271.0	52.0	128.0	0.0	.	84	.	0.191882	0	none	.	.	PASS	Atlas-INDEL