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
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34803143	34803144	+	Frame_Shift_Ins	INS	-	-	CACA	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	120.0	18.0	114.0	0.0	0.15	0	.	.	none	.	UHRF1BP1	102	.	NM_017754	exon7	c.742_743insCACA	p.S248fs	.	.	PASS	Atlas-Indel
ERAP1	51752	hgsc.bcm.edu	37	5	96116871	96116871	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	128.0	31.0	87.0	0.0	0.242	.	.	.	none	.	ERAP1	59	.	NM_001198541	exon17	c.2480delT	p.I827fs	.	.	PASS	Pindel,Atlas-Indel
TNFAIP3	7128	hgsc.bcm.edu	37	6	138198372	138198376	+	Frame_Shift_Del	DEL	CTCAT	CTCAT	-	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	CTCAT	CTCAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	70.0	33.0	91.0	0.0	0.471	.	.	.	none	.	TNFAIP3	340	.	NM_001270508	exon6	c.964_968del	p.322_323del	.	.	PASS	Pindel,Atlas-Indel
NXPE2	120406	hgsc.bcm.edu	37	11	114576570	114576571	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	256.0	60.0	222.0	0.0	0.234	.	.	.	none	.	.	.	.	NM_182495	exon5	c.996_997insA	p.L332fs	.	.	PASS	Pindel,Atlas-Indel
ATXN2L	11273	hgsc.bcm.edu	37	16	28845868	28845884	+	Frame_Shift_Del	DEL	TCAGCCCCGCCGATGAT	TCAGCCCCGCCGATGAT	-	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	TCAGCCCCGCCGATGAT	TCAGCCCCGCCGATGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	24.0	11.0	34.0	0.0	0.458333	0	.	.	none	.	ATXN2L	159	.	NM_148416	exon18	c.2286_2302del	p.762_768del	.	.	PASS	Atlas-Indel
ABCC6	368	hgsc.bcm.edu	37	16	16244433	16244438	+	In_Frame_Del	DEL	ACCGGG	ACCGGG	-	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	ACCGGG	ACCGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	155.0	12.0	192.0	0.0	0.0774194	0	.	.	none	.	ABCC6	110	.	NM_001171	exon30	c.4401_4403del	p.1467_1468del	.	.	PASS	Atlas-Indel
MANSC4	100287284	hgsc.bcm.edu	37	12	27919655	27919656	+	Frame_Shift_Del	DEL	GT	GT	-	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	152.0	28.0	189.0	0.0	0.184211	0	.	.	none	.	MANSC4	9	.	NM_001146221	exon2	c.307_308del	p.103_103del	.	.	PASS	Atlas-Indel
MANSC4	100287284	hgsc.bcm.edu	37	12	27919648	27919652	+	Frame_Shift_Del	DEL	CTCTC	CTCTC	-	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	CTCTC	CTCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	162.0	28.0	184.0	0.0	0.17284	0	.	.	none	.	MANSC4	9	.	NM_001146221	exon2	c.311_315del	p.104_105del	.	.	PASS	Atlas-Indel
TENM4	26011	hgsc.bcm.edu	37	11	78437206	78437208	+	In_Frame_Del	DEL	TGT	TGT	-	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	255.0	39.0	237.0	0.0	0.153	.	.	.	none	.	.	.	.	NM_001098816	exon23	c.3467_3469del	p.1156_1157del	.	.	PASS	Pindel,Atlas-Indel
CIITA	4261	hgsc.bcm.edu	37	16	11010310	11010310	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	46.0	11.0	76.0	0.0	0.239	.	.	.	none	.	CIITA	92	.	NM_000246	exon15	c.3055delA	p.T1019fs	.	.	PASS	Pindel,Atlas-Indel
B2M	567	hgsc.bcm.edu	37	15	45003766	45003781	+	Frame_Shift_Del	DEL	GCTGTGCTCGCGCTAC	GCTGTGCTCGCGCTAC	-	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	GCTGTGCTCGCGCTAC	GCTGTGCTCGCGCTAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	68.0	25.0	93.0	0.0	0.368	.	.	.	none	B2M,NS,lymphoid_neoplasm,+1,1	B2M	99	1	NM_004048	exon1	c.21_36del	p.7_12del	.	.	PASS	Pindel,Atlas-Indel
MANSC4	100287284	hgsc.bcm.edu	37	12	27919649	27919656	+	Frame_Shift_Del	DEL	TCTCCAGT	TCTCCAGT	-	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	TCTCCAGT	TCTCCAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	164.0	35.0	187.0	0.0	0.213	.	.	.	none	.	MANSC4	9	.	NM_001146221	exon2	c.307_314del	p.103_105del	.	.	PASS	Pindel
SGCE	8910	hgsc.bcm.edu	37	7	94218023	94218023	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	94.0	4.0	68.0	0.0	0.0425532	0	.	.	none	.	SGCE	68	.	NM_001099401	exon11	c.G1350A	p.Q450Q	GGGAATCTGAGTC	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65300359	65300359	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	168.0	46.0	163.0	0.0	0.27381	0	.	.	none	.	EYS	527	.	NM_001142800	exon26	c.G5401C	p.A1801P	AAAGTGCTGGAGT	.	PASS	Atlas-SNP
PLXNB3	5365	hgsc.bcm.edu	37	X	153037066	153037066	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	79.0	17.0	151.0	0.0	0.21519	0	.	.	none	.	PLXNB3	208	.	NM_001163257	exon15	c.C2542T	p.P848S	TGCCCGCCGGGGG	.	PASS	Atlas-SNP
JAK3	3718	hgsc.bcm.edu	37	19	17948006	17948006	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	133.0	68.0	114.0	0.0	0.511278	0	.	.	none	JAK3,NS,lymphoid_neoplasm,0,5	JAK3	341	5	NM_000215	exon13	c.C1718T	p.A573V	AAGCTCGCTGCTT	.	PASS	Atlas-SNP
DYSF	8291	hgsc.bcm.edu	37	2	71748030	71748030	+	Missense_Mutation	SNP	C	C	T	rs115279465	bycluster;byfrequency;by1000genomes	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	213.0	74.0	207.0	0.0	0.347418	0	C|0.995;T|0.005	0.005	strong	DYSF_ENST00000410020,bladder,carcinoma,-1,2	DYSF	536	2	NM_001130982	exon12	c.C1145T	p.A382V	ACGAAGCGCCTGT	.	PASS	Atlas-SNP
USP17L2	377630	hgsc.bcm.edu	37	8	11994795	11994795	+	Missense_Mutation	SNP	G	G	A	rs201012791	bycluster	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	362.0	96.0	293.0	0.0	0.265193	0	.	.	weak	.	USP17L2	47	.	NM_201402	exon1	c.C1475T	p.T492M	CGGGTCGTCGAAG	.	PASS	Atlas-SNP
ZNF502	91392	hgsc.bcm.edu	37	3	44762425	44762425	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	96.0	21.0	87.0	0.0	0.21875	0	.	.	none	.	ZNF502	58	.	NM_001134440	exon4	c.G116C	p.G39A	CATCAGGGATAGT	.	PASS	Atlas-SNP
TBC1D12	23232	hgsc.bcm.edu	37	10	96259982	96259982	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	75.0	3.0	99.0	0.0	0.04	0	.	.	none	TBC1D12,NS,carcinoma,-1,1	TBC1D12	51	1	NM_015188	exon6	c.A1417G	p.S473G	AGGCGTAGTACAA	.	scavenged	Atlas-SNP
DPYSL5	56896	hgsc.bcm.edu	37	2	27147877	27147877	+	Silent	SNP	C	C	T	rs147434661		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	105.0	34.0	71.0	0.0	0.32381	0	C|1.000;T|0.000	0.000	weak	.	DPYSL5	69	.	NM_001253724	exon3	c.C384T	p.Y128Y	TGATTACGCCCTC	.	PASS	Atlas-SNP
NAP1L3	4675	hgsc.bcm.edu	37	X	92928124	92928124	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	63.0	10.0	56.0	0.0	0.15873	0	.	.	none	.	NAP1L3	81	.	NM_004538	exon1	c.C180A	p.S60R	GCTGCTGCTGCCG	.	PASS	Atlas-SNP
RSL1D1	26156	hgsc.bcm.edu	37	16	11944196	11944196	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	101.0	5.0	89.0	0.0	0.049505	0	.	.	none	.	RSL1D1	40	.	NM_015659	exon2	c.A185G	p.E62G	AAACTTTCATTCT	.	PASS	Atlas-SNP
SLC45A1	50651	hgsc.bcm.edu	37	1	8390740	8390740	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	59.0	17.0	125.0	0.0	0.288136	0	.	.	none	.	SLC45A1	85	.	NM_001080397	exon4	c.C1187T	p.P396L	GCGTCCCCAGGCC	.	PASS	Atlas-SNP
SHROOM1	134549	hgsc.bcm.edu	37	5	132159799	132159799	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	221.0	39.0	156.0	0.0	0.176471	0	.	.	none	.	SHROOM1	35	.	NM_133456	exon4	c.C1554T	p.P518P	GTGAGAGGGACCT	.	PASS	Atlas-SNP
ACTB	60	hgsc.bcm.edu	37	7	5568917	5568917	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	108.0	24.0	119.0	0.0	0.222222	0	.	.	none	.	ACTB	45	.	NM_001101	exon3	c.G238A	p.D80N	TGTCGTCCCAGTT	.	PASS	Atlas-SNP
DIS3L	115752	hgsc.bcm.edu	37	15	66621332	66621332	+	Silent	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	94.0	4.0	91.0	0.0	0.0425532	0	.	.	none	.	DIS3L	175	.	NM_001143688	exon13	c.T2226C	p.S742S	TGATTCTCTGGAT	.	PASS	Atlas-SNP
RIMS2	9699	hgsc.bcm.edu	37	8	104513283	104513283	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	197.0	68.0	198.0	0.0	0.345178	0	.	.	none	.	RIMS2	1357	.	NM_001100117	exon1	c.G169C	p.V57L	CAGTCCGTGCTCA	.	PASS	Atlas-SNP
RNMTL1	55178	hgsc.bcm.edu	37	17	685705	685705	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	35.0	21.0	40.0	0.0	0.6	0	.	.	none	.	RNMTL1	25	.	NM_018146	exon1	c.G87A	p.W29X	GCGCTGGGTCCGG	.	PASS	Atlas-SNP
TMEM229A	730130	hgsc.bcm.edu	37	7	123672815	123672815	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	60.0	36.0	64.0	0.0	0.6	0	.	.	none	.	TMEM229A	31	.	NM_001136002	exon1	c.G243A	p.P81P	CAGGTCCGGGCTG	.	PASS	Atlas-SNP
PPIB	5479	hgsc.bcm.edu	37	15	64455114	64455114	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	162.0	27.0	172.0	0.0	0.166667	0	.	.	none	.	PPIB	20	.	NM_000942	exon1	c.C72T	p.F24F	CAGCAGGAAGAAG	.	PASS	Atlas-SNP
ALKBH1	8846	hgsc.bcm.edu	37	14	78174250	78174250	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	93.0	4.0	81.0	0.0	0.0430108	0	.	.	none	.	ALKBH1	30	.	NM_006020	exon1	c.G98A	p.S33N	GGCCGGCTCTGAC	.	PASS	Atlas-SNP
SH3BP1	23616	hgsc.bcm.edu	37	22	38035817	38035817	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	61.0	7.0	75.0	0.0	0.114754	0	.	.	none	.	SH3BP1	41	.	NM_018957	exon1	c.G23A	p.R8H	TGCACCGCATGCG	.	PASS	Atlas-SNP
ZNF189	7743	hgsc.bcm.edu	37	9	104170651	104170651	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	132.0	55.0	106.0	0.0	0.416667	0	.	.	none	.	ZNF189	79	.	NM_003452	exon3	c.G601A	p.E201K	ACTGGGGAAAGGC	.	PASS	Atlas-SNP
FAM107B	83641	hgsc.bcm.edu	37	10	14816655	14816655	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	152.0	44.0	103.0	0.0	0.289474	0	.	.	none	.	FAM107B	43	.	NM_031453	exon1	c.C8T	p.T3M	TTCCACGTGGACA	.	PASS	Atlas-SNP
RECQL4	9401	hgsc.bcm.edu	37	8	145738768	145738768	+	Splice_Site	SNP	G	G	C	rs199605511	bycluster	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	34.0	7.0	102.0	0.0	0.205882	0	.	.	weak	.	RECQL4	75	.	NM_004260	exon15	c.2296+1C>G	.	CCACCCGGCAACT	.	PASS	Atlas-SNP
KDM4E	390245	hgsc.bcm.edu	37	11	94759726	94759726	+	Silent	SNP	C	C	T	rs76354273	bycluster;byfrequency;by1000genomes	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	12.0	6.0	6.0	0.0	0.5	0	C|0.947;T|0.053	0.053	strong	.	KDM4E	60	.	NM_001161630	exon1	c.C1005T	p.H335H	GAAACACAGGCAA	.	PASS	Atlas-SNP
PGR	5241	hgsc.bcm.edu	37	11	100922186	100922186	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	199.0	71.0	195.0	0.0	0.356784	0	.	.	none	.	PGR	115	.	NM_000926	exon5	c.C2326A	p.L776M	AATACAGCATCTG	.	PASS	Atlas-SNP
DHRS7B	25979	hgsc.bcm.edu	37	17	21092024	21092024	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	94.0	41.0	85.0	0.0	0.43617	0	.	.	none	.	DHRS7B	27	.	NM_015510	exon6	c.A620G	p.Y207C	GTGTAGATGCAGC	.	PASS	Atlas-SNP
KIF16B	55614	hgsc.bcm.edu	37	20	16360313	16360313	+	Silent	SNP	G	G	A	rs374151470	alternate_allele	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	202.0	73.0	147.0	0.0	0.361386	0	.	.	alt	.	KIF16B	305	.	NM_001199865	exon19	c.C2334T	p.L778L	CCGCAGGAGCTGG	.	PASS	Atlas-SNP
CD200	4345	hgsc.bcm.edu	37	3	112059764	112059764	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	94.0	24.0	127.0	0.0	0.255319	0	.	.	none	.	CD200	33	.	NM_001004196	exon3	c.T103G	p.F35V	ATGCCCTTCTCTC	.	PASS	Atlas-SNP
RBM20	282996	hgsc.bcm.edu	37	10	112572301	112572301	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	54.0	16.0	65.0	0.0	0.296296	0	.	.	none	.	RBM20	50	.	NM_001134363	exon9	c.C2146T	p.R716W	CACCCCCGGCAAC	.	PASS	Atlas-SNP
ACSS3	79611	hgsc.bcm.edu	37	12	81472143	81472143	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	56.0	20.0	49.0	0.0	0.357143	0	.	.	none	.	ACSS3	118	.	NM_024560	exon1	c.G244A	p.E82K	GCTGCCGAGCAGA	.	PASS	Atlas-SNP
PLCB4	5332	hgsc.bcm.edu	37	20	9374297	9374297	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	58.0	10.0	32.0	0.0	0.172414	0	.	.	none	.	PLCB4	204	.	NM_182797	exon16	c.C1386T	p.N462N	AAAAAACAAGCGG	.	PASS	Atlas-SNP
NPAT	4863	hgsc.bcm.edu	37	11	108044441	108044441	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	381.0	54.0	331.0	0.0	0.141732	0	.	.	none	.	NPAT	124	.	NM_002519	exon13	c.C1270T	p.Q424X	TTTTCTGTATGCT	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144993567	144993567	+	Silent	SNP	G	G	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	37.0	2.0	52.0	0.0	0.0540541	0	.	.	none	PLEC_ENST00000436759,bladder,carcinoma,-2,6	PLEC	1144	6	NM_201380	exon32	c.C10833A	p.I3611I	GTCGATGATGCCG	.	scavenged	Atlas-SNP
NBEA	26960	hgsc.bcm.edu	37	13	35691562	35691562	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	120.0	22.0	109.0	0.0	0.183333	0	.	.	none	.	NBEA	340	.	NM_015678	exon14	c.C2014T	p.P672S	CCCCGGCCATCAC	.	PASS	Atlas-SNP
LGI1	9211	hgsc.bcm.edu	37	10	95552602	95552602	+	Silent	SNP	C	C	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	134.0	61.0	100.0	0.0	0.455224	0	.	.	none	.	LGI1	69	.	NM_005097	exon6	c.C606A	p.G202G	CGAAGGCCCCCCA	.	PASS	Atlas-SNP
SCML4	256380	hgsc.bcm.edu	37	6	108070921	108070921	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	106.0	42.0	101.0	0.0	0.396226	0	.	.	none	.	SCML4	65	.	NM_198081	exon3	c.G253A	p.V85I	TGGGGACCGTGGC	.	PASS	Atlas-SNP
RAX	30062	hgsc.bcm.edu	37	18	56940307	56940307	+	Missense_Mutation	SNP	G	G	T	rs2271733	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	5.0	3.0	1.0	1.0	0.6	1	G|0.801;T|0.199	0.199	strong	RAX,NS,carcinoma,0,1	RAX	19	1	NM_013435	exon1	c.C132A	p.D44E	CCCGTCGTCCTTG	.	scavenged	Atlas-SNP
AFG3L2	10939	hgsc.bcm.edu	37	18	12356754	12356754	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	97.0	4.0	92.0	0.0	0.0412371	0	.	.	none	.	AFG3L2	60	.	NM_006796	exon9	c.C1103T	p.P368L	ATGAAGGGGACAT	.	PASS	Atlas-SNP
PIGW	284098	hgsc.bcm.edu	37	17	34894125	34894125	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	57.0	25.0	51.0	0.0	0.438596	0	.	.	none	.	PIGW	50	.	NM_178517	exon2	c.A1175G	p.D392G	TGGGTGATATAAT	.	PASS	Atlas-SNP
OR8K5	219453	hgsc.bcm.edu	37	11	55927379	55927379	+	Nonsense_Mutation	SNP	G	G	A	rs199580379	bycluster	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	80.0	4.0	103.0	0.0	0.05	0	.	.	weak	.	OR8K5	82	.	NM_001004058	exon1	c.C415T	p.R139X	ACAGTCGCTGAGA	.	PASS	Atlas-SNP
MUM1L1	139221	hgsc.bcm.edu	37	X	105449437	105449437	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	261.0	136.0	256.0	0.0	0.521073	0	.	.	none	.	MUM1L1	166	.	NM_152423	exon5	c.G12A	p.E4E	GTCTGAGTATGTC	.	PASS	Atlas-SNP
TRIM64C	646754	hgsc.bcm.edu	37	11	49075660	49075660	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	505.0	136.0	506.0	0.0	0.269307	0	.	.	none	.	TRIM64C	18	.	NM_001206631	exon6	c.T959C	p.M320T	GGATCCATGGGTG	.	PASS	Atlas-SNP
CARD10	29775	hgsc.bcm.edu	37	22	37912258	37912258	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	33.0	2.0	36.0	0.0	0.0606061	0	.	.	none	CARD10,NS,carcinoma,+1,1	CARD10	55	1	NM_014550	exon3	c.C421T	p.R141X	GCCGTCGCACCTC	.	scavenged	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225332227	225332227	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	111.0	20.0	96.0	0.0	0.18018	0	.	.	none	.	DNAH14	300	.	NM_001373	exon28	c.G4586A	p.R1529Q	CAGACCGATGCTG	.	PASS	Atlas-SNP
RAVER1	125950	hgsc.bcm.edu	37	19	10428229	10428229	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	67.0	4.0	89.0	0.0	0.0597015	0	.	.	none	.	RAVER1	67	.	NM_133452	exon13	c.G2172A	p.S724S	CTCGGGCGAGGGC	.	PASS	Atlas-SNP
PBDC1	51260	hgsc.bcm.edu	37	X	75395309	75395309	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	99.0	28.0	100.0	0.0	0.282828	0	.	.	none	.	.	.	.	NM_016500	exon4	c.T158C	p.L53P	CGCAGCTGATTTC	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88800422	88800422	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	73.0	38.0	90.0	0.0	0.520548	0	.	.	none	.	PIEZO1	79	.	NM_001142864	exon17	c.C2221T	p.Q741X	CCTGCTGCTCCTC	.	PASS	Atlas-SNP
HBS1L	10767	hgsc.bcm.edu	37	6	135358694	135358694	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	92.0	38.0	117.0	0.0	0.413043	0	.	.	none	.	HBS1L	75	.	NM_001145207	exon5	c.C901G	p.Q301E	TATTTTGAATATA	.	PASS	Atlas-SNP
JAKMIP3	282973	hgsc.bcm.edu	37	10	133962951	133962951	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	64.0	29.0	80.0	0.0	0.453125	0	.	.	none	.	JAKMIP3	69	.	NM_001105521	exon14	c.C1884T	p.H628H	CTTCCACCACACG	.	PASS	Atlas-SNP
DUSP2	1844	hgsc.bcm.edu	37	2	96810595	96810595	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	98.0	37.0	84.0	0.0	0.377551	0	.	.	none	.	DUSP2	20	.	NM_004418	exon2	c.T415G	p.C139G	CGGGACAGCAGCC	.	PASS	Atlas-SNP
GRAMD3	65983	hgsc.bcm.edu	37	5	125813449	125813449	+	Silent	SNP	C	C	T	rs375006587		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	146.0	35.0	107.0	0.0	0.239726	0	.	.	weak	.	GRAMD3	30	.	NM_001146319	exon6	c.C597T	p.N199N	GCCAAACGCCCTG	.	PASS	Atlas-SNP
CACNA1F	778	hgsc.bcm.edu	37	X	49061779	49061779	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	137.0	65.0	137.0	0.0	0.474453	0	.	.	none	.	CACNA1F	218	.	NM_005183	exon48	c.G5752A	p.V1918M	GGGCCACGAAACG	.	PASS	Atlas-SNP
PDGFB	5155	hgsc.bcm.edu	37	22	39627798	39627798	+	Silent	SNP	G	G	A	rs147036196		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	61.0	31.0	79.0	0.0	0.508197	0	G|1.000;A|0.000	0.000	weak	.	PDGFB	91	.	NM_002608	exon4	c.C285T	p.A95A	GCACTCGGCGATC	.	PASS	Atlas-SNP
DUOX2	50506	hgsc.bcm.edu	37	15	45403769	45403769	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	7.0	6.0	6.0	0.0	0.857143	0	.	.	none	.	DUOX2	137	.	NM_014080	exon6	c.G528A	p.T176T	CCAGCCCGTCACC	.	PASS	Atlas-SNP
MYCBP2	23077	hgsc.bcm.edu	37	13	77657173	77657173	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	141.0	56.0	150.0	0.0	0.397163	0	.	.	none	.	MYCBP2	1029	.	NM_015057	exon63	c.C11030T	p.A3677V	CTCAGGGCCATTT	.	PASS	Atlas-SNP
SPATA31A6	389730	hgsc.bcm.edu	37	9	43626815	43626815	+	Silent	SNP	G	G	A	rs76166720		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	41.0	4.0	46.0	1.0	0.097561	0.0217391	A|1.000;|0.000	1.000	weak	FAM75A6,NS,carcinoma,0,3	.	.	3	NM_001145196	exon4	c.C1872T	p.D624D	TGATTCGTCCCGA	.	scavenged	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140554429	140554429	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	37.0	19.0	73.0	0.0	0.513514	0	.	.	none	.	PCDHB7	231	.	NM_018940	exon1	c.G2013A	p.L671L	CTACCTGCGGCTC	.	PASS	Atlas-SNP
C11orf34	349633	hgsc.bcm.edu	37	11	112123070	112123070	+	Splice_Site	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	84.0	33.0	56.0	0.0	0.392857	0	.	.	none	.	C11orf34	6	.	NM_001145024	exon4	c.448+1G>A	.	AACTCACGTTTTT	.	PASS	Atlas-SNP
HECW2	57520	hgsc.bcm.edu	37	2	197298113	197298113	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	225.0	84.0	167.0	0.0	0.373333	0	.	.	none	.	HECW2	239	.	NM_020760	exon2	c.T35C	p.V12A	CGCCTCACAAAAA	.	PASS	Atlas-SNP
AIMP1	9255	hgsc.bcm.edu	37	4	107246152	107246152	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	295.0	69.0	349.0	0.0	0.233898	0	.	.	none	.	AIMP1	20	.	NM_001142416	exon2	c.C58T	p.R20C	TTCTGCCGTCTCT	.	PASS	Atlas-SNP
ZNF597	146434	hgsc.bcm.edu	37	16	3490834	3490834	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	70.0	3.0	65.0	0.0	0.0428571	0	.	.	none	ZNF597,NS,carcinoma,0,1	ZNF597	41	1	NM_152457	exon3	c.G133A	p.E45K	AAGACTCTTTTGT	.	scavenged	Atlas-SNP
SSX3	10214	hgsc.bcm.edu	37	X	48209473	48209473	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	825.0	350.0	858.0	1.0	0.424242	0.0011655	.	.	none	.	SSX3	64	.	NM_021014	exon6	c.C415T	p.L139L	GGCACAGCTGTTT	.	PASS	Atlas-SNP
THG1L	54974	hgsc.bcm.edu	37	5	157161623	157161623	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	209.0	82.0	203.0	0.0	0.392345	0	.	.	none	.	THG1L	31	.	NM_017872	exon3	c.C408G	p.S136R	CTCCAGCTATGTG	.	PASS	Atlas-SNP
MED26	9441	hgsc.bcm.edu	37	19	16687806	16687806	+	Missense_Mutation	SNP	G	G	A	rs201182566		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	103.0	18.0	131.0	0.0	0.174757	0	G|0.999;A|0.001	0.001	weak	MED26,colon,carcinoma,+1,1	MED26	25	1	NM_004831	exon3	c.C835T	p.R279W	CATGCCGTGAGTT	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186276981	186276981	+	Silent	SNP	A	A	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	198.0	10.0	179.0	2.0	0.050505	0.0111732	.	.	none	PRG4,NS,carcinoma,0,6	PRG4	259	6	NM_005807	exon7	c.A2130G	p.K710K	CCCTAAAGGGACT	.	scavenged	Atlas-SNP
BUB1B	701	hgsc.bcm.edu	37	15	40453452	40453452	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	78.0	17.0	91.0	0.0	0.217949	0	.	.	none	.	BUB1B	71	.	NM_001211	exon1	c.C31T	p.L11L	GGTGCTCTGAGGT	.	PASS	Atlas-SNP
FLG2	388698	hgsc.bcm.edu	37	1	152325925	152325925	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	314.0	149.0	307.0	0.0	0.474522	0	.	.	none	.	FLG2	431	.	NM_001014342	exon3	c.C4337T	p.T1446I	CCATGAGTTTGTT	.	PASS	Atlas-SNP
MED26	9441	hgsc.bcm.edu	37	19	16687805	16687805	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	102.0	17.0	129.0	0.0	0.166667	0	.	.	none	MED26,colon,carcinoma,0,1	MED26	25	1	NM_004831	exon3	c.G836T	p.R279L	TCATGCCGTGAGT	.	PASS	Atlas-SNP
P2RY8	286530	hgsc.bcm.edu	37	X	1584574	1584574	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	120.0	74.0	180.0	0.0	0.616667	0	.	.	none	.	P2RY8	53	.	NM_178129	exon2	c.A878T	p.Y293F	AAGTAATAAACAA	.	PASS	Atlas-SNP
TNRC6B	23112	hgsc.bcm.edu	37	22	40661027	40661027	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	71.0	37.0	65.0	0.0	0.521127	0	.	.	none	.	TNRC6B	195	.	NM_001162501	exon5	c.G793T	p.A265S	CCTAAGGCTAAAT	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110495331	110495331	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	103.0	32.0	83.0	0.0	0.31068	0	.	.	none	.	PKHD1L1	522	.	NM_177531	exon57	c.G9573T	p.W3191C	GGATTGGCAGGTA	.	PASS	Atlas-SNP
DNAJC13	23317	hgsc.bcm.edu	37	3	132245067	132245067	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	94.0	5.0	98.0	0.0	0.0531915	0	.	.	none	.	DNAJC13	253	.	NM_015268	exon53	c.T6323C	p.L2108P	TTGGTCTAGCCTG	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187629904	187629904	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	88.0	19.0	89.0	0.0	0.215909	0	.	.	none	.	FAT1	500	.	NM_005245	exon2	c.T1078G	p.F360V	CTTTGAACTGTGG	.	PASS	Atlas-SNP
HSPA2	3306	hgsc.bcm.edu	37	14	65008064	65008064	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	81.0	39.0	87.0	0.0	0.481481	0	.	.	none	HSPA2,NS,carcinoma,0,2	HSPA2	83	2	NM_021979	exon1	c.C497T	p.T166M	CCATCACGGGGCT	.	PASS	Atlas-SNP
NFKB2	4791	hgsc.bcm.edu	37	10	104160764	104160764	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	112.0	54.0	96.0	0.0	0.482143	0	.	.	none	.	NFKB2	48	.	NM_001077494	exon18	c.G2029A	p.G677R	GCAGCTGGACTGG	.	PASS	Atlas-SNP
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056488	26056488	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	144.0	61.0	136.0	0.0	0.423611	0	.	.	none	.	HIST1H1C	80	.	NM_005319	exon1	c.G169A	p.V57I	GAGAAACTCCGCT	.	PASS	Atlas-SNP
GLIS1	148979	hgsc.bcm.edu	37	1	53980302	53980302	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	161.0	29.0	143.0	0.0	0.180124	0	.	.	none	.	GLIS1	52	.	NM_147193	exon7	c.G1354A	p.D452N	ACCCATCCCGGGT	.	PASS	Atlas-SNP
PIGP	51227	hgsc.bcm.edu	37	21	38437947	38437947	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	191.0	45.0	143.0	0.0	0.235602	0	.	.	none	.	PIGP	9	.	NM_153681	exon4	c.A412T	p.I138F	TAGAAATATCTCT	.	PASS	Atlas-SNP
PRMT8	56341	hgsc.bcm.edu	37	12	3692249	3692249	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	102.0	22.0	85.0	0.0	0.215686	0	.	.	none	PRMT8,NS,carcinoma,-1,3	PRMT8	97	3	NM_019854	exon8	c.C854T	p.T285M	TGAAGACGGAAGA	.	PASS	Atlas-SNP
SYT7	9066	hgsc.bcm.edu	37	11	61291310	61291310	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	192.0	41.0	224.0	0.0	0.213542	0	.	.	none	.	SYT7	39	.	NM_001252065	exon8	c.G1121A	p.G374E	GTGCCCCCGATGT	.	PASS	Atlas-SNP
CUL4A	8451	hgsc.bcm.edu	37	13	113909104	113909104	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	70.0	17.0	91.0	1.0	0.242857	0.010989	.	.	none	CUL4A,NS,carcinoma,0,1	CUL4A	50	1	NM_001008895	exon17	c.C1850T	p.T617M	TGGCCACGGGGAT	.	scavenged	Atlas-SNP
PPP2R2B	5521	hgsc.bcm.edu	37	5	145969730	145969730	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	142.0	47.0	117.0	0.0	0.330986	0	.	.	none	PPP2R2B_ENST00000508545,NS,haematopoietic_neoplasm,-1,4	PPP2R2B	271	4	NM_181675	exon10	c.G1430A	p.R477H	ACATCACGCTTGG	.	PASS	Atlas-SNP
PTH2R	5746	hgsc.bcm.edu	37	2	209358138	209358138	+	Silent	SNP	A	A	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	165.0	26.0	154.0	0.0	0.157576	0	.	.	none	.	PTH2R	92	.	NM_005048	exon13	c.A1407C	p.T469T	CAGCACACGCATG	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48314897	48314897	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	138.0	26.0	144.0	0.0	0.188406	0	.	.	none	.	ABCA13	1192	.	NM_152701	exon17	c.C5634T	p.S1878S	AAGCTCCCGAATG	.	PASS	Atlas-SNP
PAX8	7849	hgsc.bcm.edu	37	2	114004442	114004442	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	168.0	71.0	122.0	0.0	0.422619	0	.	.	none	.	PAX8	42	.	NM_013952	exon3	c.C80T	p.P27L	ACTTCCGGCAGAG	.	PASS	Atlas-SNP
IGFBP4	3487	hgsc.bcm.edu	37	17	38612729	38612729	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	193.0	24.0	162.0	0.0	0.124352	0	.	.	none	.	IGFBP4	17	.	NM_001552	exon4	c.G671A	p.G224D	AGCGTGGCAAGTG	.	PASS	Atlas-SNP
C2CD4D	100191040	hgsc.bcm.edu	37	1	151810406	151810406	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	95.0	4.0	113.0	0.0	0.0421053	0	.	.	none	.	C2CD4D	3	.	NM_001136003	exon2	c.T1060C	p.X354Q	CAGGCTACAGGCT	.	PASS	Atlas-SNP
EML2	24139	hgsc.bcm.edu	37	19	46116911	46116911	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	113.0	18.0	107.0	0.0	0.159292	0	.	.	none	EML2,caecum,carcinoma,0,1	EML2	64	1	NM_001193268	exon21	c.C2315T	p.A772V	CCGTCCGCCCCCT	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101721960	101721960	+	Splice_Site	SNP	C	C	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	126.0	42.0	116.0	0.0	0.333333	0	.	.	none	.	PABPC1	76	.	NM_002568	exon9	c.973-1G>T	.	CATAACCTATTAA	.	PASS	Atlas-SNP
MAGEE1	57692	hgsc.bcm.edu	37	X	75648638	75648638	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	152.0	21.0	166.0	0.0	0.138158	0	.	.	none	.	MAGEE1	236	.	NM_020932	exon1	c.G315A	p.L105L	CGTGCTGCCCACC	.	PASS	Atlas-SNP
HYAL3	8372	hgsc.bcm.edu	37	3	50332345	50332345	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	211.0	88.0	208.0	0.0	0.417062	0	.	.	none	.	HYAL3	34	.	NM_001200030	exon2	c.A689C	p.Q230P	TGCAGTTGAGTGT	.	PASS	Atlas-SNP
LONRF3	79836	hgsc.bcm.edu	37	X	118109491	118109491	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	147.0	24.0	165.0	0.0	0.163265	0	.	.	none	.	LONRF3	138	.	NM_001031855	exon1	c.G748A	p.G250S	CACGAGGGCAACC	.	PASS	Atlas-SNP
OR2W3	343171	hgsc.bcm.edu	37	1	248059470	248059470	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	298.0	64.0	248.0	0.0	0.214765	0	.	.	none	OR2W3,right_lower_lobe,carcinoma,+2,1	OR2W3	113	1	NM_001001957	exon1	c.C582T	p.A194A	TGTGGCCATCGAA	.	PASS	Atlas-SNP
USP11	8237	hgsc.bcm.edu	37	X	47092477	47092477	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	83.0	24.0	120.0	0.0	0.289157	0	.	.	none	.	USP11	93	.	NM_004651	exon1	c.C164T	p.A55V	CTGCTGCGGCGGC	.	PASS	Atlas-SNP
MAATS1	89876	hgsc.bcm.edu	37	3	119466110	119466110	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	56.0	3.0	95.0	0.0	0.0535714	0	.	.	none	C3orf15,NS,carcinoma,+1,2	.	.	2	NM_033364	exon15	c.G2051A	p.R684H	AAAGCCGGTGTGT	.	scavenged	Atlas-SNP
DGAT2L6	347516	hgsc.bcm.edu	37	X	69424867	69424867	+	Missense_Mutation	SNP	G	G	A	rs35142503	bycluster	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	297.0	49.0	260.0	0.0	0.164983	0	G|0.987;A|0.013	0.013	weak	.	DGAT2L6	40	.	NM_198512	exon7	c.G925A	p.A309T	TATCACGCACTCT	.	PASS	Atlas-SNP
SLITRK2	84631	hgsc.bcm.edu	37	X	144904787	144904787	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	78.0	13.0	68.0	0.0	0.166667	0	.	.	none	.	SLITRK2	221	.	NM_001144005	exon5	c.G844A	p.V282I	ACCCACGTCCAAA	.	PASS	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140564228	140564228	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	55.0	19.0	86.0	0.0	0.345455	0	.	.	none	PCDHB16,colon,carcinoma,0,2	PCDHB16	159	2	NM_020957	exon1	c.G2094A	p.S698S	GGTGTCGTCGCTC	.	PASS	Atlas-SNP
ELF1	1997	hgsc.bcm.edu	37	13	41507882	41507882	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	137.0	62.0	118.0	0.0	0.452555	0	.	.	none	ELF1,NS,carcinoma,-2,1	ELF1	65	1	NM_172373	exon9	c.G1539A	p.Q513Q	AATGGTCTGAACA	.	PASS	Atlas-SNP
ANKRD53	79998	hgsc.bcm.edu	37	2	71212171	71212171	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	22.0	5.0	39.0	0.0	0.227273	0	.	.	none	.	ANKRD53	55	.	NM_001115116	exon6	c.C1334T	p.A445V	GGGTGGCGCCCGT	.	PASS	Atlas-SNP
GABRQ	55879	hgsc.bcm.edu	37	X	151820139	151820139	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	289.0	47.0	222.0	0.0	0.16263	0	.	.	none	.	GABRQ	131	.	NM_018558	exon8	c.A1052C	p.Y351S	TCAACTATCTTTT	.	PASS	Atlas-SNP
BMP5	653	hgsc.bcm.edu	37	6	55659189	55659189	+	Silent	SNP	G	G	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	52.0	9.0	75.0	0.0	0.173077	0	.	.	none	.	BMP5	94	.	NM_021073	exon3	c.C720A	p.A240A	AGCTTGGGCCTTT	.	PASS	Atlas-SNP
RIF1	55183	hgsc.bcm.edu	37	2	152300225	152300225	+	Splice_Site	SNP	T	T	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	74.0	28.0	64.0	0.0	0.378378	0	.	.	none	.	RIF1	244	.	NM_018151	exon18	c.1986+2T>G	.	ATCAGGTATGAAA	.	PASS	Atlas-SNP
KIAA1549	57670	hgsc.bcm.edu	37	7	138602479	138602479	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	71.0	11.0	69.0	0.0	0.15493	0	.	.	none	.	KIAA1549	314	.	NM_020910	exon2	c.G1893A	p.P631P	TTCCAGCGGGGGT	.	PASS	Atlas-SNP
SOCS1	8651	hgsc.bcm.edu	37	16	11348808	11348808	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	11.0	6.0	18.0	0.0	0.545455	0	.	.	none	SOCS1,lymph_node,lymphoid_neoplasm,0,1	SOCS1	84	1	NM_003745	exon2	c.G528A	p.E176E	GCACAGCTCCTGC	.	PASS	Atlas-SNP
LCMT1	51451	hgsc.bcm.edu	37	16	25186263	25186263	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	85.0	18.0	90.0	0.0	0.211765	0	.	.	none	.	LCMT1	22	.	NM_016309	exon10	c.A890G	p.E297G	GGATAGAATCACT	.	PASS	Atlas-SNP
SARM1	23098	hgsc.bcm.edu	37	17	26708753	26708753	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	38.0	4.0	40.0	0.0	0.105263	0	.	.	none	.	SARM1	40	.	NM_015077	exon3	c.C999T	p.L333L	GTTGCTCGACTCT	.	PASS	Atlas-SNP
GABRQ	55879	hgsc.bcm.edu	37	X	151820129	151820129	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	305.0	47.0	251.0	0.0	0.154098	0	.	.	none	.	GABRQ	131	.	NM_018558	exon8	c.T1042C	p.Y348H	TATGTCTACATCA	.	PASS	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	37	7	2976756	2976756	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	148.0	63.0	175.0	0.0	0.425676	0	.	.	none	.	CARD11	339	.	NM_032415	exon9	c.T1256G	p.I419S	ATCTCGATCCTCA	.	PASS	Atlas-SNP
STAT6	6778	hgsc.bcm.edu	37	12	57493818	57493818	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	152.0	56.0	137.0	0.0	0.368421	0	.	.	none	.	STAT6	69	.	NM_001178079	exon14	c.A1568G	p.D523G	GTGAGGTCCAGGA	.	PASS	Atlas-SNP
ITPKB	3707	hgsc.bcm.edu	37	1	226925148	226925148	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	33.0	7.0	32.0	0.0	0.212121	0	.	.	none	.	ITPKB	158	.	NM_002221	exon2	c.C12T	p.Y4Y	ATAGCAGTACACA	.	PASS	Atlas-SNP
AMBRA1	55626	hgsc.bcm.edu	37	11	46564251	46564251	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	172.0	38.0	162.0	0.0	0.22093	0	.	.	none	.	AMBRA1	201	.	NM_001267783	exon8	c.G1046A	p.R349K	CTGGTTCTGGGCG	.	PASS	Atlas-SNP
CNTRL	11064	hgsc.bcm.edu	37	9	123931934	123931934	+	Missense_Mutation	SNP	G	G	T	rs376768102	alternate_allele	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	96.0	41.0	76.0	0.0	0.427083	0	.	.	alt	.	CNTRL	161	.	NM_007018	exon37	c.G6116T	p.G2039V	AATCAGGTGAGCT	.	PASS	Atlas-SNP
SYMPK	8189	hgsc.bcm.edu	37	19	46352062	46352062	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	260.0	135.0	218.0	0.0	0.519231	0	.	.	none	.	SYMPK	104	.	NM_004819	exon6	c.C372T	p.N124N	CACCACGTTCACA	.	PASS	Atlas-SNP
KRT12	3859	hgsc.bcm.edu	37	17	39021152	39021152	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	148.0	26.0	125.0	0.0	0.175676	0	.	.	none	.	KRT12	53	.	NM_000223	exon3	c.T713A	p.V238E	TCCAGCACCCGGC	.	PASS	Atlas-SNP
PCM1	5108	hgsc.bcm.edu	37	8	17843569	17843569	+	Silent	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	97.0	4.0	100.0	0.0	0.0412371	0	.	.	none	.	PCM1	120	.	NM_006197	exon26	c.T4383C	p.P1461P	TACTCCTAGTGAG	.	PASS	Atlas-SNP
PRAC	84366	hgsc.bcm.edu	37	17	46799191	46799191	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	181.0	60.0	171.0	0.0	0.331492	0	.	.	none	.	PRAC	6	.	NM_032391	exon2	c.C146T	p.S49L	CCTCCCGAAATTC	.	PASS	Atlas-SNP
ZNF845	91664	hgsc.bcm.edu	37	19	53855284	53855284	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	77.0	4.0	48.0	0.0	0.0519481	0	.	.	none	ZNF845,NS,carcinoma,0,1	ZNF845	101	1	NM_138374	exon4	c.G1356A	p.S452S	CAAATCGAACCTT	.	scavenged	Atlas-SNP
PIK3AP1	118788	hgsc.bcm.edu	37	10	98369476	98369476	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	111.0	48.0	101.0	0.0	0.432432	0	.	.	none	.	PIK3AP1	111	.	NM_152309	exon14	c.C2163T	p.S721S	TGCTGTGCTGGAG	.	PASS	Atlas-SNP
UBE2A	7319	hgsc.bcm.edu	37	X	118715490	118715490	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	508.0	203.0	383.0	1.0	0.399606	0.00261097	.	.	none	.	UBE2A	43	.	NM_003336	exon4	c.G172T	p.E58X	ACAATAGAATTCA	.	PASS	Atlas-SNP
AURKAIP1	54998	hgsc.bcm.edu	37	1	1309461	1309461	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	73.0	29.0	63.0	0.0	0.39726	0	.	.	none	.	AURKAIP1	12	.	NM_001127230	exon3	c.C417T	p.N139N	GTGGTGGTTCATC	.	PASS	Atlas-SNP
DRP2	1821	hgsc.bcm.edu	37	X	100509422	100509422	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	351.0	67.0	314.0	0.0	0.190883	0	.	.	none	.	DRP2	98	.	NM_001939	exon18	c.C1986T	p.S662S	CACATCCAGTGAG	.	PASS	Atlas-SNP
C5orf38	153571	hgsc.bcm.edu	37	5	2752510	2752510	+	Silent	SNP	G	G	A	rs181498861	bycluster;by1000genomes;alternate_allele	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	51.0	17.0	58.0	0.0	0.333333	0	G|0.999;C|0.001	.	alt	.	C5orf38	20	.	NM_178569	exon1	c.G132A	p.A44A	CCTCGCGGTCCAC	.	PASS	Atlas-SNP
FNIP1	96459	hgsc.bcm.edu	37	5	131013444	131013444	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	126.0	37.0	96.0	0.0	0.293651	0	.	.	none	.	FNIP1	104	.	NM_133372	exon13	c.G1471C	p.D491H	ACATGTCCACACT	.	PASS	Atlas-SNP
ALDH8A1	64577	hgsc.bcm.edu	37	6	135271176	135271176	+	Missense_Mutation	SNP	C	C	T	rs150345681	bycluster;byfrequency;by1000genomes	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	109.0	5.0	111.0	0.0	0.0458716	0	C|0.999;T|0.001	0.001	strong	ALDH8A1,colon,carcinoma,0,1	ALDH8A1	68	1	NM_022568	exon1	c.G16A	p.A6T	AAAGTGCGTTTGT	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141259273	141259273	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	63.0	31.0	83.0	0.0	0.492063	0	.	.	none	.	LRP1B	1315	.	NM_018557	exon55	c.C8833T	p.L2945F	CCGGAAGGTCTTG	.	PASS	Atlas-SNP
TLE4	7091	hgsc.bcm.edu	37	9	82337469	82337469	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	129.0	46.0	127.0	0.0	0.356589	0	.	.	none	.	TLE4	187	.	NM_007005	exon18	c.T2090G	p.L697R	ACCAACTACATCT	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26164606	26164606	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	32.0	7.0	30.0	0.0	0.21875	0	.	.	none	.	MYO18B	322	.	NM_032608	exon4	c.G723A	p.V241V	CATAGTGGGGAAG	.	PASS	Atlas-SNP
CDH4	1002	hgsc.bcm.edu	37	20	60427856	60427856	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	133.0	45.0	114.0	0.0	0.338346	0	.	.	none	.	CDH4	172	.	NM_001794	exon6	c.C779T	p.P260L	AGAACCCCATCGA	.	PASS	Atlas-SNP
CTPS2	56474	hgsc.bcm.edu	37	X	16711587	16711587	+	Silent	SNP	G	G	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	156.0	44.0	188.0	0.0	0.282051	0	.	.	none	.	CTPS2	49	.	NM_001144002	exon5	c.C462A	p.I154I	TCCTTCGATGTCT	.	PASS	Atlas-SNP
ZNF846	162993	hgsc.bcm.edu	37	19	9873975	9873975	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	95.0	4.0	54.0	0.0	0.0421053	0	.	.	none	ZNF846,NS,carcinoma,0,1	ZNF846	61	1	NM_001077624	exon3	c.A125G	p.K42R	AGATTCTTGTAGT	.	PASS	Atlas-SNP
PLXNC1	10154	hgsc.bcm.edu	37	12	94543629	94543629	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	9.0	6.0	9.0	0.0	0.666667	0	.	.	none	.	PLXNC1	135	.	NM_005761	exon1	c.C882T	p.L294L	CCTGCTCCTCTCC	.	PASS	Atlas-SNP
MBD1	4152	hgsc.bcm.edu	37	18	47799097	47799097	+	Silent	SNP	A	A	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	105.0	27.0	114.0	0.0	0.257143	0	.	.	none	.	MBD1	228	.	NM_001204137	exon16	c.T1803C	p.I601I	GCTGAAAATCTCC	.	PASS	Atlas-SNP
CRISPLD1	83690	hgsc.bcm.edu	37	8	75898242	75898242	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	79.0	19.0	58.0	0.0	0.240506	0	.	.	none	.	CRISPLD1	94	.	NM_031461	exon2	c.A20T	p.E7V	CGCGGGAGTGGCT	.	PASS	Atlas-SNP
ZNF462	58499	hgsc.bcm.edu	37	9	109691621	109691621	+	Missense_Mutation	SNP	G	G	A	rs376844260		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	100.0	20.0	80.0	0.0	0.2	0	.	.	weak	ZNF462,NS,carcinoma,0,1	ZNF462	322	1	NM_021224	exon3	c.G5428A	p.V1810I	ACGGCCGTCTATG	.	PASS	Atlas-SNP
QRSL1	55278	hgsc.bcm.edu	37	6	107100238	107100238	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	212.0	44.0	203.0	0.0	0.207547	0	.	.	none	.	QRSL1	30	.	NM_018292	exon6	c.G712A	p.D238N	TGTGTGGATGATG	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46265035	46265035	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	123.0	22.0	104.0	0.0	0.178862	0	.	.	none	.	NCOA3	156	.	NM_001174088	exon12	c.C1935T	p.S645S	TCATTCCTCCTTG	.	PASS	Atlas-SNP
SLC25A37	51312	hgsc.bcm.edu	37	8	23429088	23429088	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	57.0	32.0	56.0	0.0	0.561404	0	.	.	none	.	SLC25A37	27	.	NM_016612	exon4	c.C737A	p.A246D	CCGGGGCCCTCGC	.	PASS	Atlas-SNP
C14orf37	145407	hgsc.bcm.edu	37	14	58598352	58598352	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	110.0	40.0	111.0	0.0	0.363636	0	.	.	none	C14orf37,NS,carcinoma,-1,1	C14orf37	87	1	NM_001001872	exon4	c.A1709G	p.E570G	CTGGGTTCCCCCA	.	PASS	Atlas-SNP
BLVRB	645	hgsc.bcm.edu	37	19	40964385	40964385	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	92.0	51.0	84.0	0.0	0.554348	0	.	.	none	.	BLVRB	12	.	NM_000713	exon2	c.C147T	p.H49H	TACCACGTGGGCC	.	PASS	Atlas-SNP
PCDHB4	56131	hgsc.bcm.edu	37	5	140503797	140503797	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	81.0	4.0	100.0	0.0	0.0493827	0	.	.	none	.	PCDHB4	177	.	NM_018938	exon1	c.C2217T	p.S739S	CGTAAGCGGCACC	.	PASS	Atlas-SNP
EBLN1	340900	hgsc.bcm.edu	37	10	22498749	22498749	+	Missense_Mutation	SNP	A	A	T	rs2478476	bycluster;byhapmap;by1000genomes	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	4.0	4.0	0.0	0.0	1	.	A|0.001;T|0.999	0.999	strong	.	.	.	.	NM_001199938	exon1	c.T164A	p.V55D	TCAATGACCTTAA	.	PASS	Atlas-SNP
CCDC87	55231	hgsc.bcm.edu	37	11	66359191	66359191	+	Silent	SNP	A	A	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	75.0	25.0	54.0	0.0	0.333333	0	.	.	none	.	CCDC87	83	.	NM_018219	exon1	c.T1296A	p.T432T	CTTCAAAGTAATG	.	PASS	Atlas-SNP
NEUROD1	4760	hgsc.bcm.edu	37	2	182543437	182543437	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	187.0	70.0	133.0	0.0	0.374332	0	.	.	none	NEUROD1,NS,carcinoma,0,1	NEUROD1	67	1	NM_002500	exon2	c.G151T	p.D51Y	GTGAGTCCTCCTC	.	PASS	Atlas-SNP
REL	5966	hgsc.bcm.edu	37	2	61147230	61147230	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	444.0	163.0	403.0	0.0	0.367117	0	.	.	none	.	REL	48	.	NM_002908	exon8	c.T908A	p.L303Q	AGAAACTGTGCCA	.	PASS	Atlas-SNP
GLTSCR1L	23506	hgsc.bcm.edu	37	6	42797411	42797411	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	89.0	46.0	73.0	0.0	0.516854	0	.	.	none	KIAA0240,NS,carcinoma,-1,1	.	.	1	NM_015349	exon5	c.A1340T	p.N447I	ACAGAAACTCTTC	.	PASS	Atlas-SNP
ANKHD1	54882	hgsc.bcm.edu	37	5	139917069	139917069	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	162.0	65.0	153.0	0.0	0.401235	0	.	.	none	.	ANKHD1	233	.	NM_017747	exon31	c.C7123T	p.R2375X	CTGGCCCGAATTC	.	PASS	Atlas-SNP
SLC25A17	10478	hgsc.bcm.edu	37	22	41188619	41188619	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	161.0	38.0	150.0	0.0	0.236025	0	.	.	none	.	SLC25A17	25	.	NM_006358	exon4	c.T244G	p.Y82D	AGAAATAGACAAA	.	PASS	Atlas-SNP
PRKD1	5587	hgsc.bcm.edu	37	14	30046446	30046446	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	205.0	49.0	212.0	0.0	0.239024	0	.	.	none	.	PRKD1	316	.	NM_002742	exon18	c.T2737A	p.X913R	GAACTCAGAGGAT	.	PASS	Atlas-SNP
IDNK	414328	hgsc.bcm.edu	37	9	86258428	86258428	+	Silent	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	152.0	31.0	116.0	0.0	0.203947	0	.	.	none	C9orf103,colon,carcinoma,+2,1	.	.	1	NM_001001551	exon5	c.T297C	p.D99D	AAAAGATGGTGTA	.	PASS	Atlas-SNP
PON3	5446	hgsc.bcm.edu	37	7	95025645	95025645	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	47.0	9.0	72.0	0.0	0.191489	0	.	.	none	PON3,NS,carcinoma,-1,1	PON3	59	1	NM_000940	exon1	c.G18A	p.A6A	GACCAGCGCCACG	.	PASS	Atlas-SNP
EIF3D	8664	hgsc.bcm.edu	37	22	36907798	36907798	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	194.0	90.0	180.0	0.0	0.463918	0	.	.	none	.	EIF3D	37	.	NM_003753	exon14	c.G1385A	p.R462H	ACGTGGCGTGAGG	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27373599	27373599	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	129.0	21.0	128.0	0.0	0.162791	0	.	.	none	.	IL4R	70	.	NM_000418	exon11	c.T926C	p.L309P	CCAAGCTCTTGCC	.	PASS	Atlas-SNP
ZNF101	94039	hgsc.bcm.edu	37	19	19790525	19790525	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	54.0	13.0	50.0	0.0	0.240741	0	.	.	none	.	ZNF101	43	.	NM_033204	exon4	c.C727T	p.H243Y	CAAATTCATGTTA	.	PASS	Atlas-SNP
MYH6	4624	hgsc.bcm.edu	37	14	23865523	23865523	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	136.0	63.0	121.0	0.0	0.463235	0	.	.	none	MYH6,NS,carcinoma,-1,1	MYH6	274	1	NM_002471	exon20	c.G2399A	p.R800H	TCAATGCGCATGA	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168107691	168107691	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	108.0	10.0	76.0	0.0	0.0925926	0	.	.	none	.	XIRP2	914	.	NM_152381	exon9	c.G9789T	p.R3263S	AATCAGGAAAGTG	.	PASS	Atlas-SNP
CDC42BPG	55561	hgsc.bcm.edu	37	11	64594201	64594201	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	16.0	10.0	49.0	0.0	0.625	0	.	.	none	.	CDC42BPG	101	.	NM_017525	exon35	c.G4455A	p.E1485E	CAACGCCTCGGAG	.	PASS	Atlas-SNP
CHD4	1108	hgsc.bcm.edu	37	12	6710854	6710854	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	221.0	75.0	174.0	1.0	0.339367	0.00574713	.	.	none	CHD4_ENST00000357008,NS,malignant_melanoma,0,3	CHD4	539	3	NM_001273	exon5	c.C517T	p.R173X	GGGTTCGATAATC	.	scavenged	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60892438	60892438	+	Missense_Mutation	SNP	C	C	T	rs373181217		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	25.0	9.0	39.0	0.0	0.36	0	.	.	weak	.	LAMA5	268	.	NM_005560	exon55	c.G7474A	p.A2492T	GCTGTGCGTGGGC	.	PASS	Atlas-SNP
PDZD7	79955	hgsc.bcm.edu	37	10	102778029	102778029	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	110.0	45.0	122.0	0.0	0.409091	0	.	.	none	.	PDZD7	101	.	NM_001195263	exon9	c.A1349C	p.E450A	GACTTCTCCTTCT	.	PASS	Atlas-SNP
ZSCAN32	54925	hgsc.bcm.edu	37	16	3434848	3434848	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	128.0	31.0	160.0	0.0	0.242188	0	.	.	none	.	.	.	.	NM_017810	exon5	c.A209G	p.Q70R	CTGTTCTGCTGAC	.	PASS	Atlas-SNP
NAP1L3	4675	hgsc.bcm.edu	37	X	92928107	92928107	+	Missense_Mutation	SNP	C	C	A	rs62635803	bycluster;by1000genomes	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	68.0	14.0	59.0	0.0	0.205882	0	C|0.992;A|0.008	0.008	strong	.	NAP1L3	81	.	NM_004538	exon1	c.G197T	p.G66V	GTGCTGCCGCTGC	.	PASS	Atlas-SNP
SAP130	79595	hgsc.bcm.edu	37	2	128758026	128758026	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	86.0	20.0	77.0	0.0	0.232558	0	.	.	none	.	SAP130	169	.	NM_001145928	exon8	c.G950A	p.R317K	GTTGGCCTACTGA	.	PASS	Atlas-SNP
TNFAIP8	25816	hgsc.bcm.edu	37	5	118728686	118728686	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	170.0	54.0	149.0	0.0	0.317647	0	.	.	none	.	TNFAIP8	12	.	NM_014350	exon2	c.G207A	p.E69E	GGCAGAGAAGATC	.	PASS	Atlas-SNP
LRRC15	131578	hgsc.bcm.edu	37	3	194080325	194080325	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	242.0	55.0	291.0	0.0	0.227273	0	.	.	none	.	LRRC15	137	.	NM_001135057	exon3	c.G1466C	p.S489T	GGGTAACTAGGCA	.	PASS	Atlas-SNP
ITPKB	3707	hgsc.bcm.edu	37	1	226924388	226924388	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	134.0	62.0	110.0	0.0	0.462687	0	.	.	none	.	ITPKB	158	.	NM_002221	exon2	c.G772C	p.E258Q	CCTTCTCCATCCT	.	PASS	Atlas-SNP
TIAM2	26230	hgsc.bcm.edu	37	6	155577707	155577707	+	Missense_Mutation	SNP	G	G	A	rs116807909	bycluster;byfrequency;by1000genomes	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	183.0	85.0	175.0	0.0	0.464481	0	G|0.998;A|0.002	0.002	strong	.	TIAM2	161	.	NM_012454	exon26	c.G4558A	p.E1520K	TCTGACGAGGGCA	.	PASS	Atlas-SNP
CELA3B	23436	hgsc.bcm.edu	37	1	22304901	22304901	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	239.0	45.0	232.0	0.0	0.188285	0	.	.	none	.	CELA3B	24	.	NM_007352	exon2	c.G83A	p.R28H	CCAGCCGCGTTGT	.	PASS	Atlas-SNP
CCDC64	92558	hgsc.bcm.edu	37	12	120518805	120518805	+	Missense_Mutation	SNP	G	G	A	rs373363052		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	29.0	9.0	33.0	0.0	0.310345	0	.	.	weak	.	CCDC64	40	.	NM_207311	exon7	c.G1423A	p.D475N	GACCGCGACGAGG	.	PASS	Atlas-SNP
KCNK1	3775	hgsc.bcm.edu	37	1	233802348	233802348	+	Silent	SNP	C	C	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	230.0	108.0	239.0	0.0	0.469565	0	.	.	none	KCNK1,colon,carcinoma,+1,1	KCNK1	36	1	NM_002245	exon2	c.C363G	p.G121G	TTATGGCCACACC	.	PASS	Atlas-SNP
MAML3	55534	hgsc.bcm.edu	37	4	140811099	140811099	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	94.0	4.0	86.0	2.0	0.0425532	0.0232558	.	.	none	MAML3_ENST00000509479,caecum,carcinoma,0,12	MAML3	192	12	NM_018717	exon2	c.G1491A	p.Q497Q	CTGCTGCTGCTGC	.	scavenged	Atlas-SNP
PRKD1	5587	hgsc.bcm.edu	37	14	30046591	30046591	+	Silent	SNP	A	A	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	189.0	37.0	199.0	0.0	0.195767	0	.	.	none	.	PRKD1	316	.	NM_002742	exon18	c.T2592C	p.S864S	GTCATCACTTTCA	.	PASS	Atlas-SNP
ZNF816	125893	hgsc.bcm.edu	37	19	53456125	53456125	+	Silent	SNP	G	G	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	49.0	14.0	43.0	0.0	0.285714	0	.	.	none	.	ZNF816	73	.	NM_001202457	exon3	c.C69G	p.R23R	AGTCAAGCGTCCC	.	PASS	Atlas-SNP
SKP1	6500	hgsc.bcm.edu	37	5	133494195	133494195	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	132.0	45.0	145.0	1.0	0.340909	0.00689655	.	.	none	SKP1,colon,carcinoma,-1,1	SKP1	10	1	NM_170679	exon5	c.G407A	p.R136H	GTCTTGCGAATCT	.	scavenged	Atlas-SNP
LAP3	51056	hgsc.bcm.edu	37	4	17606285	17606285	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	107.0	39.0	114.0	0.0	0.364486	0	.	.	none	.	LAP3	50	.	NM_015907	exon11	c.T1255C	p.F419L	AAACTCTTCGAGG	.	PASS	Atlas-SNP
NLRX1	79671	hgsc.bcm.edu	37	11	119045894	119045894	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	125.0	5.0	130.0	0.0	0.04	0	.	.	none	.	NLRX1	128	.	NM_024618	exon6	c.C1582T	p.R528C	GTGGGCCGTGTTG	.	PASS	Atlas-SNP
PPP1R42	286187	hgsc.bcm.edu	37	8	67922976	67922976	+	Missense_Mutation	SNP	C	C	T	rs200466525	by1000genomes	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	63.0	20.0	83.0	0.0	0.31746	0	C|1.000;T|0.000	0.000	strong	.	PPP1R42	2	.	NM_001013626	exon5	c.G526A	p.V176I	TGTCAACGGCTAT	.	PASS	Atlas-SNP
RPL3	6122	hgsc.bcm.edu	37	22	39714450	39714450	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	90.0	21.0	70.0	0.0	0.233333	0	.	.	none	.	RPL3	29	.	NM_001033853	exon2	c.G151A	p.A51T	TGCCAGCCTTGTA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092929	1092929	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	105.0	9.0	111.0	1.0	0.0857143	0.00900901	.	.	none	MUC2_ENST00000441003,rectum,carcinoma,+1,4	MUC2	614	4	NM_002457	exon30	c.C4748T	p.S1583L	CAACATCGACACC	.	scavenged	Atlas-SNP
SOCS1	8651	hgsc.bcm.edu	37	16	11349329	11349329	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	12.0	8.0	16.0	2.0	0.666667	0.125	.	.	none	SOCS1,NS,lymphoid_neoplasm,0,2	SOCS1	84	2	NM_003745	exon2	c.G7A	p.A3T	TGTGTGCTACCAT	.	scavenged	Atlas-SNP
PCDHB1	29930	hgsc.bcm.edu	37	5	140432615	140432615	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	143.0	62.0	94.0	0.0	0.433566	0	.	.	none	.	PCDHB1	148	.	NM_013340	exon1	c.G1560A	p.M520I	AACCATGGATTAT	.	PASS	Atlas-SNP
PPP2R5B	5526	hgsc.bcm.edu	37	11	64699058	64699058	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	47.0	25.0	40.0	0.0	0.531915	0	.	.	none	.	PPP2R5B	47	.	NM_006244	exon10	c.C973T	p.P325S	TACTGGCCAAAAA	.	PASS	Atlas-SNP
PLA2G4C	8605	hgsc.bcm.edu	37	19	48558246	48558246	+	Missense_Mutation	SNP	C	C	T	rs370150895		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	145.0	77.0	138.0	0.0	0.531034	0	.	.	weak	.	PLA2G4C	76	.	NM_001159322	exon15	c.G1348A	p.E450K	CAGCCTCTTCTAC	.	PASS	Atlas-SNP
FNBP4	23360	hgsc.bcm.edu	37	11	47744591	47744591	+	Silent	SNP	A	A	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	53.0	4.0	48.0	0.0	0.0754717	0	.	.	none	FNBP4,NS,carcinoma,0,1	FNBP4	99	1	NM_015308	exon15	c.T2742A	p.P914P	TGGTGGAGGAGGA	.	PASS	Atlas-SNP
MLL2	8085	hgsc.bcm.edu	37	12	49427679	49427679	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	44.0	3.0	54.0	0.0	0.0681818	0	.	.	none	MLL2_ENST00000301067,NS,carcinoma,0,2	MLL2	1173	2	NM_003482	exon39	c.G10809A	p.Q3603Q	CTGCTGCTGTTGT	.	scavenged	Atlas-SNP
UNC45B	146862	hgsc.bcm.edu	37	17	33504529	33504529	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	101.0	41.0	83.0	0.0	0.405941	0	.	.	none	UNC45B,NS,carcinoma,-1,2	UNC45B	133	2	NM_173167	exon17	c.C2161T	p.R721W	GTGGTGCGGCCCC	.	PASS	Atlas-SNP
AR	367	hgsc.bcm.edu	37	X	66905872	66905872	+	Missense_Mutation	SNP	G	G	A	rs137852569		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	59.0	4.0	60.0	0.0	0.0677966	0	.	.	weak	.	AR	249	.	NM_000044	exon3	c.G1789A	p.A597T	CTGTGCGCCAGCA	.	PASS	Atlas-SNP
BEST3	144453	hgsc.bcm.edu	37	12	70087575	70087575	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	162.0	60.0	138.0	0.0	0.37037	0	.	.	none	.	BEST3	129	.	NM_032735	exon4	c.C360T	p.H120H	GCGCCCGTGCTCG	.	PASS	Atlas-SNP
DACH1	1602	hgsc.bcm.edu	37	13	72440219	72440219	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	133.0	66.0	149.0	0.0	0.496241	0	.	.	none	.	DACH1	123	.	NM_080759	exon1	c.C689G	p.T230R	TAGACCGTATGCA	.	PASS	Atlas-SNP
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056385	26056385	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	188.0	87.0	171.0	0.0	0.462766	0	.	.	none	.	HIST1H1C	80	.	NM_005319	exon1	c.G272A	p.G91D	AGAGTGCCCTTGC	.	PASS	Atlas-SNP
CYP2C19	1557	hgsc.bcm.edu	37	10	96580331	96580331	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	102.0	30.0	103.0	0.0	0.294118	0	.	.	none	.	CYP2C19	88	.	NM_000769	exon6	c.G898A	p.E300K	GGGACAGAGACAA	.	PASS	Atlas-SNP
PMPCA	23203	hgsc.bcm.edu	37	9	139306549	139306549	+	Missense_Mutation	SNP	A	A	G	rs367845329		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	288.0	72.0	268.0	0.0	0.25	0	.	.	weak	.	PMPCA	29	.	NM_015160	exon2	c.A172G	p.T58A	TTTGCTACAGTTG	.	PASS	Atlas-SNP
CTR9	9646	hgsc.bcm.edu	37	11	10777233	10777233	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	116.0	48.0	139.0	0.0	0.413793	0	.	.	none	.	CTR9	94	.	NM_014633	exon4	c.G393T	p.L131F	CCATTTGTTGGGA	.	PASS	Atlas-SNP
OPN1LW	5956	hgsc.bcm.edu	37	X	153421999	153421999	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	464.0	71.0	409.0	0.0	0.153017	0	.	.	none	.	OPN1LW	87	.	NM_020061	exon5	c.G975A	p.M325I	CTTTATGAACCGG	.	PASS	Atlas-SNP
SERINC3	10955	hgsc.bcm.edu	37	20	43129937	43129937	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	103.0	50.0	78.0	0.0	0.485437	0	.	.	none	.	SERINC3	42	.	NM_006811	exon9	c.C1060T	p.R354C	AAGTGCGGATGCT	.	PASS	Atlas-SNP
GTF2H5	404672	hgsc.bcm.edu	37	6	158613139	158613139	+	Nonsense_Mutation	SNP	C	C	T	rs121434364		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	173.0	87.0	201.0	0.0	0.50289	0	.	.	weak	.	GTF2H5	1	.	NM_207118	exon3	c.C166T	p.R56X	CAGGAGCGAGTGG	.	PASS	Atlas-SNP
ABCA3	21	hgsc.bcm.edu	37	16	2338028	2338028	+	Silent	SNP	G	G	A	rs76519389	bycluster;byfrequency;by1000genomes	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	20.0	8.0	27.0	0.0	0.4	0	G|1.000;A|0.000	0.000	strong	.	ABCA3	176	.	NM_001089	exon21	c.C3003T	p.L1001L	CTTACCGAGCACC	.	PASS	Atlas-SNP
NKAIN2	154215	hgsc.bcm.edu	37	6	124676480	124676480	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	234.0	116.0	283.0	0.0	0.495726	0	.	.	none	.	NKAIN2	34	.	NM_153355	exon3	c.G260C	p.G87A	AGGCTGGGGACCT	.	PASS	Atlas-SNP
SEC22C	9117	hgsc.bcm.edu	37	3	42610481	42610481	+	Missense_Mutation	SNP	C	C	G	rs141431943	alternate_allele	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	168.0	30.0	178.0	0.0	0.178571	0	C|1.000;T|0.000	.	alt	.	SEC22C	27	.	NM_001201584	exon2	c.G58C	p.A20P	TAGAGGCTGAGAG	.	PASS	Atlas-SNP
USP17L10	100287144	hgsc.bcm.edu	37	4	9212697	9212697	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	19.0	10.0	20.0	0.0	0.526316	0	.	.	none	.	.	.	.	NM_001256852	exon1	c.C315T	p.A105A	ACTTGCCAACTAC	.	PASS	Atlas-SNP
SH3GL3	6457	hgsc.bcm.edu	37	15	84287010	84287010	+	Missense_Mutation	SNP	G	G	A	rs376114446		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	80.0	14.0	79.0	0.0	0.175	0	.	.	weak	SH3GL3_ENST00000427482,NS,carcinoma,0,2	SH3GL3	91	2	NM_003027	exon9	c.G1015A	p.V339M	AATTACGTGGAAG	.	PASS	Atlas-SNP
IQCA1	79781	hgsc.bcm.edu	37	2	237374287	237374287	+	Missense_Mutation	SNP	G	G	A	rs35814876	bycluster	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	255.0	40.0	202.0	1.0	0.156863	0.00495049	G|0.986;A|0.014	0.014	weak	IQCA1_ENST00000409907,NS,carcinoma,+1,4	IQCA1	170	4	NM_001270585	exon6	c.C808T	p.R270W	CATTCCGCAGGCG	.	scavenged	Atlas-SNP
CA10	56934	hgsc.bcm.edu	37	17	49713329	49713329	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	93.0	4.0	97.0	0.0	0.0430108	0	.	.	none	.	CA10	84	.	NM_001082534	exon8	c.T676C	p.Y226H	CTGGATATAGTTC	.	PASS	Atlas-SNP
SEMA6D	80031	hgsc.bcm.edu	37	15	48063877	48063877	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	146.0	8.0	146.0	0.0	0.0547945	0	.	.	none	.	SEMA6D	322	.	NM_153618	exon19	c.G3117A	p.R1039R	TCCTAGGACGGGA	.	PASS	Atlas-SNP
DBC1	1620	hgsc.bcm.edu	37	9	121929513	121929513	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	226.0	79.0	189.0	0.0	0.349558	0	.	.	none	DBC1,rectum,carcinoma,0,4	DBC1	194	4	NM_014618	exon8	c.C2135T	p.P712L	TTCCCCGGGGCCA	.	PASS	Atlas-SNP
NELL2	4753	hgsc.bcm.edu	37	12	44915940	44915940	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	64.0	3.0	52.0	0.0	0.046875	0	.	.	none	NELL2_ENST00000437801,colon,carcinoma,-1,2	NELL2	286	2	NM_001145107	exon19	c.G2168A	p.R723Q	ATCCGTCGACACA	.	scavenged	Atlas-SNP
CUX1	1523	hgsc.bcm.edu	37	7	101845432	101845432	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	96.0	4.0	125.0	0.0	0.0416667	0	.	.	none	.	CUX1	253	.	NM_001202543	exon18	c.T2888C	p.V963A	GGCAGGTTAAGGA	.	PASS	Atlas-SNP
GRN	2896	hgsc.bcm.edu	37	17	42430050	42430050	+	Missense_Mutation	SNP	C	C	T	rs63750116		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	62.0	30.0	51.0	0.0	0.483871	0	.	.	weak	.	GRN	51	.	NM_002087	exon13	c.C1666T	p.R556C	GATCGGCGCCACT	.	PASS	Atlas-SNP
CHTF18	63922	hgsc.bcm.edu	37	16	840179	840179	+	Silent	SNP	C	C	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	91.0	23.0	108.0	0.0	0.252747	0	.	.	none	.	CHTF18	52	.	NM_022092	exon5	c.C609T	p.G203G	ACAGGGCTCTCTC	.	PASS	Atlas-SNP
PITX2	5308	hgsc.bcm.edu	37	4	111539469	111539469	+	Missense_Mutation	SNP	C	C	T	rs149181425	alternate_allele	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	162.0	40.0	146.0	0.0	0.246914	0	C|1.000;A|0.000	.	alt	.	PITX2	73	.	NM_000325	exon3	c.G787A	p.A263T	GCACCGCGGAATT	.	PASS	Atlas-SNP
UBQLN2	29978	hgsc.bcm.edu	37	X	56591532	56591532	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	131.0	57.0	117.0	0.0	0.435115	0	.	.	none	.	UBQLN2	55	.	NM_013444	exon1	c.T1226C	p.M409T	CACAGATGATGCT	.	PASS	Atlas-SNP
SEMA5B	54437	hgsc.bcm.edu	37	3	122632728	122632728	+	Silent	SNP	G	G	A	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	80.0	38.0	143.0	0.0	0.475	0	.	.	none	.	SEMA5B	303	.	NM_001256347	exon15	c.C2271T	p.C757C	GCCCACGCAGATG	.	PASS	Atlas-SNP
SYT10	341359	hgsc.bcm.edu	37	12	33579301	33579301	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	135.0	21.0	113.0	0.0	0.155556	0	.	.	none	.	SYT10	109	.	NM_198992	exon2	c.C281A	p.T94N	AGCGTAGTGATGT	.	PASS	Atlas-SNP