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
RERE	473	hgsc.bcm.edu	hg19	1	8415616	8415616	+	Silent	SNP	G	G	T	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	RERE	NM_012102	exon23	c.C4530A	p.P1510P	TGACATGGGGGGT	.	36.0	9.0	39.0	0.0	.	129	.	.	.	none	.	.	PASS	Atlas-SNP
TSPAN2	10100	hgsc.bcm.edu	hg19	1	115601516	115601516	+	Silent	SNP	G	G	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	TSPAN2	NM_005725	exon5	c.C432T	p.T144T	GTGGAAGGTGATG	.	167.0	40.0	203.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
RGL1	23179	hgsc.bcm.edu	hg19	1	183885638	183885638	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	RGL1,NS,carcinoma,0,1	RGL1	NM_015149	exon17	c.G1912C	p.G638R	TCCTCAGGGATGT	.	169.0	47.0	153.0	0.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
TRAPPC12	51112	hgsc.bcm.edu	hg19	2	3483103	3483103	+	Silent	SNP	G	G	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	.	NM_016030	exon12	c.G2079A	p.V693V	GAGCGTGCTCTTC	.	124.0	30.0	160.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
RHOQ	23433	hgsc.bcm.edu	hg19	2	46803262	46803262	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	RHOQ_ENST00000238738,NS,carcinoma,0,1	RHOQ	NM_012249	exon3	c.A238G	p.M80V	TACCCAATGACCG	.	74.0	3.0	84.0	2.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
SESTD1	91404	hgsc.bcm.edu	hg19	2	180016091	180016091	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	SESTD1	NM_178123	exon6	c.A397T	p.T133S	AACGAGTCAATTT	.	41.0	17.0	46.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
CUL3	8452	hgsc.bcm.edu	hg19	2	225422410	225422410	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	CUL3	NM_001257198	exon2	c.T248C	p.L83P	TCTCTTAGTCCAG	.	53.0	16.0	35.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
CUL3	8452	hgsc.bcm.edu	hg19	2	225449722	225449722	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	CUL3	NM_003590	exon1	c.C5A	p.S2X	AGATTCGACATGG	.	33.0	8.0	39.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
CRBN	51185	hgsc.bcm.edu	hg19	3	3209360	3209360	+	Silent	SNP	T	T	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	CRBN	NM_016302	exon5	c.A645G	p.R215R	GTCTTCTCTTGAG	.	155.0	13.0	171.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
CAPN7	23473	hgsc.bcm.edu	hg19	3	15288291	15288291	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	CAPN7,NS,carcinoma,0,1	CAPN7	NM_014296	exon18	c.T2063C	p.L688S	ACACCTTATCAAA	.	37.0	2.0	39.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
ACAD9	28976	hgsc.bcm.edu	hg19	3	128612493	128612493	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	ACAD9,NS,carcinoma,0,1	ACAD9	NM_014049	exon3	c.G340C	p.E114Q	CCAGAAGAATATG	.	40.0	2.0	43.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
COMMD2	51122	hgsc.bcm.edu	hg19	3	149468478	149468478	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	COMMD2	NM_016094	exon4	c.G389A	p.R130Q	TCTAGTCGCCATT	.	123.0	25.0	103.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
FAM194A	131831	hgsc.bcm.edu	hg19	3	150421569	150421569	+	Silent	SNP	T	T	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	FAM194A,NS,carcinoma,0,2	FAM194A	NM_152394	exon1	c.A117G	p.E39E	CACCTCTTCCTCC	.	20.0	3.0	22.0	1.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
FETUB	26998	hgsc.bcm.edu	hg19	3	186362554	186362554	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	FETUB	NM_014375	exon4	c.A439G	p.I147V	AAAAAGATTTACA	.	106.0	27.0	156.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
EGF	1950	hgsc.bcm.edu	hg19	4	110865158	110865158	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	EGF	NM_001963	exon4	c.A670T	p.S224C	GAAGGAAGCAATT	.	70.0	20.0	75.0	0.0	.	113	.	.	.	none	.	.	PASS	Atlas-SNP
MND1	84057	hgsc.bcm.edu	hg19	4	154330168	154330168	+	Splice_Site	SNP	G	G	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	MND1,colon,carcinoma,0,1	MND1	NM_032117	exon7	c.511+1G>C	.	GGACTGGTATGTA	.	46.0	2.0	44.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	hg19	5	37187887	37187887	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	C5orf42	NM_023073	exon22	c.C3869G	p.S1290C	CTATAGGATAACT	.	26.0	5.0	56.0	0.0	.	422	.	.	.	none	.	.	PASS	Atlas-SNP
C7	730	hgsc.bcm.edu	hg19	5	40964972	40964972	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	C7	NM_000587	exon14	c.C1879G	p.Q627E	CATTGTCAGAGTG	.	159.0	8.0	180.0	0.0	.	136	.	.	.	none	.	.	PASS	Atlas-SNP
SPINK5	11005	hgsc.bcm.edu	hg19	5	147510840	147510840	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	SPINK5	NM_001127698	exon32	c.G3073C	p.D1025H	TGCAAAGACTACC	.	239.0	44.0	276.0	0.0	.	245	.	.	.	none	.	.	PASS	Atlas-SNP
SERPINB9	5272	hgsc.bcm.edu	hg19	6	2890546	2890546	+	Nonsense_Mutation	SNP	C	C	A	rs375600576	alternate_allele	TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	SERPINB9	NM_004155	exon7	c.G982T	p.E328X	CTGCCTCGGTGCC	.	125.0	10.0	91.0	0.0	.	37	.	.	.	alt	.	.	PASS	Atlas-SNP
HOXA1	3198	hgsc.bcm.edu	hg19	7	27134334	27134334	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	HOXA1	NM_005522	exon2	c.G733A	p.E245K	CCTTCTCCAGTTC	.	205.0	46.0	155.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
MAGI2	9863	hgsc.bcm.edu	hg19	7	78131031	78131031	+	Silent	SNP	C	C	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	MAGI2	NM_012301	exon5	c.G828T	p.V276V	ACTGTACACTGGT	.	105.0	22.0	77.0	0.0	.	246	.	.	.	none	.	.	PASS	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	hg19	7	82763823	82763823	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	PCLO	NM_014510	exon3	c.G3043C	p.A1015P	TTGGAGCTTGTTC	.	57.0	16.0	60.0	0.0	.	1506	.	.	.	none	.	.	PASS	Atlas-SNP
CYP3A7	1551	hgsc.bcm.edu	hg19	7	99328744	99328744	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	CYP3A7	NM_000765	exon2	c.A103T	p.K35X	CAAGCTTCTTAAA	.	152.0	56.0	104.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
CUX1	1523	hgsc.bcm.edu	hg19	7	101845410	101845410	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	CUX1	NM_001202543	exon18	c.A2866T	p.T956S	GTGGACACCATCG	.	230.0	78.0	172.0	0.0	.	253	.	.	.	none	.	.	PASS	Atlas-SNP
MET	4233	hgsc.bcm.edu	hg19	7	116417463	116417463	+	Missense_Mutation	SNP	C	C	T	rs121913244		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	MET,colon,carcinoma,0,2	MET	NM_001127500	exon16	c.C3334T	p.H1112Y	GTATATCATGGGA	.	181.0	62.0	161.0	0.0	.	412	.	.	.	weak	.	.	PASS	Atlas-SNP
C7orf55-LUC7L2	100996928	hgsc.bcm.edu	hg19	7	139030365	139030365	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	.	NM_001244584	exon2	c.A257T	p.K86M	ATGGCAAGGGTGA	.	81.0	16.0	68.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
KEL	3792	hgsc.bcm.edu	hg19	7	142658089	142658089	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	KEL	NM_000420	exon4	c.G326T	p.G109V	GCCCTTCCACAGG	.	208.0	40.0	191.0	0.0	.	128	.	.	.	none	.	.	PASS	Atlas-SNP
FBXO43	286151	hgsc.bcm.edu	hg19	8	101152996	101152996	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	FBXO43	NM_001029860	exon2	c.G1486C	p.D496H	AGATGTCCAGTTT	.	160.0	36.0	167.0	0.0	.	155	.	.	.	none	.	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	hg19	9	14801824	14801824	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	FREM1	NM_144966	exon21	c.G3520C	p.V1174L	GGTCCACAGCGCT	.	160.0	36.0	227.0	0.0	.	261	.	.	.	none	.	.	PASS	Atlas-SNP
FCN1	2219	hgsc.bcm.edu	hg19	9	137801883	137801883	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	FCN1	NM_002003	exon9	c.C742G	p.L248V	CCGTTAGAGAATT	.	253.0	53.0	283.0	0.0	.	62	.	.	.	none	.	.	PASS	Atlas-SNP
PLAU	5328	hgsc.bcm.edu	hg19	10	75672687	75672687	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	PLAU	NM_002658	exon5	c.T199A	p.S67T	GATAAGTCAAAAA	.	62.0	6.0	75.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
WDR74	54663	hgsc.bcm.edu	hg19	11	62606983	62606983	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	WDR74	NM_018093	exon2	c.G60C	p.L20F	ACCTTTCAAGATC	.	97.0	26.0	104.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
MMP13	4322	hgsc.bcm.edu	hg19	11	102822873	102822873	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	MMP13,NS,NS,0,1	MMP13	NM_002427	exon5	c.G667C	p.E223Q	CGAACTCATGCGC	.	179.0	32.0	175.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
FKBP4	2288	hgsc.bcm.edu	hg19	12	2910328	2910328	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	FKBP4	NM_002014	exon9	c.G1078A	p.G360R	CGCCGGGGAGAGG	.	150.0	33.0	115.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC23	10233	hgsc.bcm.edu	hg19	12	7023220	7023220	+	Silent	SNP	A	A	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	LRRC23	NM_006992	exon7	c.A924C	p.A308A	GGGTGCAGAATGG	.	170.0	65.0	153.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
CD163	9332	hgsc.bcm.edu	hg19	12	7640255	7640255	+	Missense_Mutation	SNP	G	G	A	rs373039092		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	CD163_ENST00000396620,NS,lymphoid_neoplasm,+1,1	CD163	NM_203416	exon8	c.C1750T	p.R584C	CCAAGCGAATTTC	.	166.0	9.0	114.0	0.0	.	221	.	.	.	weak	.	.	PASS	Atlas-SNP
KERA	11081	hgsc.bcm.edu	hg19	12	91449805	91449805	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	KERA	NM_007035	exon2	c.C254G	p.T85S	GGAATGGTTTCTA	.	115.0	19.0	116.0	0.0	.	62	.	.	.	none	.	.	PASS	Atlas-SNP
DDX54	79039	hgsc.bcm.edu	hg19	12	113610194	113610194	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	DDX54	NM_024072	exon11	c.T1243C	p.F415L	CGGGGAAGCTGTA	.	51.0	21.0	48.0	0.0	.	73	.	.	.	none	.	.	PASS	Atlas-SNP
CDK8	1024	hgsc.bcm.edu	hg19	13	26975738	26975738	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	CDK8	NM_001260	exon12	c.C1246A	p.L416I	GGTGGACTTATCA	.	97.0	12.0	117.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
DIAPH3	81624	hgsc.bcm.edu	hg19	13	60566699	60566699	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	DIAPH3	NM_001042517	exon10	c.A1033T	p.I345F	CATTGATGAGCTG	.	52.0	8.0	42.0	0.0	.	139	.	.	.	none	.	.	PASS	Atlas-SNP
CPNE6	9362	hgsc.bcm.edu	hg19	14	24545747	24545747	+	Silent	SNP	G	G	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	CPNE6	NM_006032	exon13	c.G1146A	p.P382P	TGACCCGGAAAAT	.	94.0	30.0	139.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
SEMA7A	8482	hgsc.bcm.edu	hg19	15	74708932	74708932	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	SEMA7A	NM_003612	exon7	c.T785G	p.V262G	TGGGCCACACGGG	.	63.0	18.0	68.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
ARID3B	10620	hgsc.bcm.edu	hg19	15	74884140	74884140	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	ARID3B	NM_006465	exon7	c.A1405G	p.R469G	AAGATCAGGATCA	.	114.0	5.0	109.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
PEAK1	0	hgsc.bcm.edu	hg19	15	77406689	77406689	+	Silent	SNP	G	G	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	.	NM_024776	exon8	c.C5050T	p.L1684L	GTACTAGGCTAGG	.	137.0	34.0	143.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF423	23090	hgsc.bcm.edu	hg19	16	49670185	49670185	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	ZNF423	NM_015069	exon4	c.A2878G	p.M960V	GACACATGTAGTG	.	62.0	12.0	61.0	0.0	.	463	.	.	.	none	.	.	PASS	Atlas-SNP
FLII	2314	hgsc.bcm.edu	hg19	17	18150655	18150655	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	FLII	NM_002018	exon21	c.T2504G	p.F835C	TTCTTGAACTTGG	.	109.0	18.0	119.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
ZPBP2	124626	hgsc.bcm.edu	hg19	17	38027753	38027753	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	ZPBP2	NM_199321	exon4	c.T281C	p.L94P	GACAGCTGATGGT	.	59.0	15.0	96.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
PLVAP	83483	hgsc.bcm.edu	hg19	19	17476968	17476968	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	PLVAP	NM_031310	exon2	c.A406G	p.I136V	AGATGATGGCAGC	.	191.0	52.0	196.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF780A	284323	hgsc.bcm.edu	hg19	19	40581903	40581903	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	ZNF780A	NM_001142577	exon6	c.C449G	p.P150R	TGAGTAGGCAGTT	.	76.0	17.0	97.0	0.0	.	156	.	.	.	none	.	.	PASS	Atlas-SNP
NLRP7	199713	hgsc.bcm.edu	hg19	19	55449434	55449434	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	NLRP7	NM_001127255	exon5	c.A2107T	p.T703S	GACAGGTGCTACG	.	418.0	101.0	421.0	0.0	.	411	.	.	.	none	.	.	PASS	Atlas-SNP
CHRNA4	1137	hgsc.bcm.edu	hg19	20	61982183	61982183	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	CHRNA4	NM_000744	exon5	c.A580G	p.M194V	TGTGCATGTTCAC	.	96.0	25.0	97.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
ARFRP1	10139	hgsc.bcm.edu	hg19	20	62333531	62333531	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	ARFRP1	NM_001134758	exon5	c.C303G	p.D101E	GGTGGAGTCAATG	.	69.0	20.0	75.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
ZDHHC8	29801	hgsc.bcm.edu	hg19	22	20130720	20130720	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	ZDHHC8	NM_001185024	exon10	c.C1567T	p.R523C	CTACCCCGCAGCT	.	56.0	14.0	74.0	0.0	.	77	.	.	.	none	.	.	PASS	Atlas-SNP
ADSL	158	hgsc.bcm.edu	hg19	22	40745897	40745897	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	ADSL	NM_001123378	exon2	c.T215A	p.I72N	AGAACATCGACTT	.	56.0	11.0	88.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
PARVG	64098	hgsc.bcm.edu	hg19	22	44581694	44581694	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	PARVG	NM_001254742	exon3	c.A287T	p.K96M	GAGGAAAGAAGAA	.	46.0	11.0	29.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
HDAC10	83933	hgsc.bcm.edu	hg19	22	50684494	50684494	+	Silent	SNP	A	A	G	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	HDAC10	NM_032019	exon18	c.T1678C	p.L560L	AGCCCAAGATGCA	.	47.0	5.0	48.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
PRKX	5613	hgsc.bcm.edu	hg19	X	3544550	3544550	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	PRKX	NM_005044	exon5	c.C725G	p.P242R	AACGGAGGAAACC	.	25.0	7.0	24.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA2022	340533	hgsc.bcm.edu	hg19	X	73961092	73961092	+	Silent	SNP	C	C	T	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	KIAA2022	NM_001008537	exon3	c.G3300A	p.E1100E	GACACCCTCTTGG	.	85.0	4.0	109.0	0.0	.	262	.	.	.	none	.	.	PASS	Atlas-SNP
TIMP2	7077	hgsc.bcm.edu	hg19	17	76867041	76867047	+	Frame_Shift_Del	DEL	GGGGGCC	GGGGGCC	-	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	GGGGGCC	GGGGGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	TIMP2	NM_003255	exon3	c.274_280del	p.92_94del	.	.	161.0	10.0	180.0	0.0	.	27	.	0.0621118	0	none	.	.	PASS	Atlas-INDEL
LARS	51520	hgsc.bcm.edu	hg19	5	145552256	145552256	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	LARS	NM_020117	exon3	c.208delT	p.C70fs	.	.	62.0	23.0	48.0	0.0	.	100	.	0.370968	0	none	.	.	PASS	Atlas-INDEL
ITGA1	3672	hgsc.bcm.edu	hg19	5	52204750	52204750	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	ITGA1	NM_181501	exon13	c.1477delA	p.I493fs	.	.	145.0	31.0	168.0	0.0	.	112	.	0.213793	0	none	.	.	PASS	Atlas-INDEL
ST6GAL1	6480	hgsc.bcm.edu	hg19	3	186790685	186790685	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	ST6GAL1	NM_003032	exon5	c.753delA	p.E251fs	.	.	142.0	29.0	145.0	0.0	.	36	.	0.204225	0	none	.	.	PASS	Atlas-INDEL
CDK8	1024	hgsc.bcm.edu	hg19	13	26975735	26975736	+	Frame_Shift_Del	DEL	GG	GG	-	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	CDK8	NM_001260	exon12	c.1242_1243del	p.414_415del	.	.	95.0	11.0	117.0	0.0	.	61	.	0.115789	0	none	.	.	PASS	Atlas-INDEL
ANKDD1A	348094	hgsc.bcm.edu	hg19	15	65214185	65214185	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	.	ANKDD1A	NM_182703	exon4	c.332delT	p.V111fs	.	.	80.0	17.0	76.0	0.0	.	47	.	0.2125	0	none	.	.	PASS	Atlas-INDEL
