Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov_SOL	TVarCov_SOL	TVaf_SOL	NTotCov_SOL	NVarCov_SOL	NVaf_SOL	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	Ttot_rna	Tvar_rna	Tvaf_rna	note	germline-maf-frequency	IGV
C1orf170	84808	bcgsc.ca	37	1	915450	915450	+	Silent	SNP	G	G	A	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	C1orf170	.	.	.	.	CGGCTCGGAGGCA		109	8	0.07	130	0	0		5		0	0				
.	284498	bcgsc.ca	37	1	11832311	11832311	+	Silent	SNP	G	G	C	rs10779764	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTGGCTGTGCAGG		277	12	0.04	308	3	0.0097402597				0	0				
.	284498	bcgsc.ca	37	1	11836682	11836682	+	Missense_Mutation	SNP	C	C	T	rs7538516	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTCCAGCGCCAGT		221	12	0.05	259	1	0.0038610039				0	0				
.	284498	bcgsc.ca	37	1	11838848	11838848	+	Missense_Mutation	SNP	G	G	T	rs6697244	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GCAGCAGCACACT		281	13	0.05	297	0	0				0	0				
.	284498	bcgsc.ca;mdanderson.org	37	1	11844330	11844330	+	Silent	SNP	C	C	T	rs10864543	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGGGGCCGTGTTT		158	13	0.08	196	0	0				2	0	0.00			
.	0	bcgsc.ca	37	1	12898512	12898512	+	RNA	SNP	G	G	T	rs116549626	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CGTGGAGGTCTCA		155	10	0.06	241	2	0.0082987552				0	0				
.	0	bcgsc.ca	37	1	12898517	12898517	+	RNA	SNP	C	C	G	rs72472679	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AGGTCTCATTTCC		157	10	0.06	227	0	0				0	0				
.	0	bcgsc.ca	37	1	12898551	12898551	+	RNA	SNP	A	A	G	rs117657781	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CTGGGAACAGTGG		174	11	0.06	219	1	0.00456621				0	0				
.	0	bcgsc.ca	37	1	13172124	13172124	+	RNA	SNP	C	C	G	rs75049200		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TACTGTCTGGGTA		539	46	0.09	624	3	0.0048076923				0	0				
PRAMEF19	391003	bcgsc.ca;mdanderson.org	37	1	13474974	13474974	+	Silent	SNP	G	G	A	rs4462137	bycluster	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	PRAMEF19	NM_001099790	exon3	c.C1155T	p.H385H	ATTGCCGTGAAAG		930	40	0.04	1083	0	0		6		0	0				
.	780789	bcgsc.ca	37	1	14507057	14507057	+	Missense_Mutation	SNP	A	A	G	rs10928050	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CATGATATTGATG		370	17	0.05	466	0	0				0	0				
FAM46B	115572	bcgsc.ca	37	1	27332465	27332466	+	Missense_Mutation	DNP	GT	GT	AC	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	GT	GT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	FAM46B	NM_052943	exon2	c.A1247G	p.H416R	ATAGGCGTGAGCC		206	17	0.08	319	4	0.012539185		44		745	0	0.00			
.	0	bcgsc.ca	37	1	59097172	59097172	+	RNA	SNP	C	C	T	rs232916	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GACACTCGGGTTC		251	23	0.09	270	1	0.0037037037				1	0	0.00			
.	0	bcgsc.ca	37	1	65450611	65450611	+	RNA	SNP	C	C	T	rs61734444	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTTCAGCCACAAT		63	5	0.08	53	0	0				0	0				
.	100505741	bcgsc.ca	37	1	85009894	85009894	+	RNA	SNP	A	A	G	rs12143652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	SPATA1,NS,carcinoma,0,1	.	.	.	.	.	GCTGAAAAAGAGT		230	11	0.05	262	0	0			1	2	0	0.00			
.	0	bcgsc.ca	37	1	100797449	100797449	+	RNA	SNP	A	A	T	rs614766	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AAGGCCATCACGC		236	12	0.05	246	0	0				0	0				
.	0	bcgsc.ca	37	1	100797473	100797473	+	RNA	SNP	T	T	C	rs614805	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTGAACTAGAAGA		211	11	0.05	222	3	0.0135135135				0	0				
NOTCH2NL	388677	broad.mit.edu	37	1	145273262	145273263	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	NOTCH2NL_ENST00000362074,caecum,carcinoma,+1,7	NOTCH2NL	NM_203458	exon3	c.116_117insT	p.T39fs	GTGGGACTTGTGT		1319	6	0.00	1189	0	0		100	7	80	0	0.00			
RPTN	126638	broad.mit.edu;bcgsc.ca;mdanderson.org	37	1	152127944	152127944	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	RPTN	NM_001122965	exon3	c.G1631T	p.S544I	TGGGAACTCTGGC		263	22	0.08	160	1	0.00625		123		0	0				
.	0	bcgsc.ca	37	1	157679691	157679691	+	RNA	SNP	C	C	T	rs17676303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGATGCCTGGGCT		313	30	0.10	263	1	0.0038022814				49	0	0.00			
.	0	bcgsc.ca	37	1	157679783	157679783	+	RNA	SNP	A	A	G	rs17727309	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTGCCCAACCTGG		375	23	0.06	280	0	0				5	0	0.00			
.	0	bcgsc.ca	37	1	160865612	160865612	+	RNA	SNP	A	A	C	rs112211905	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTTCCAATCTCCA		273	25	0.09	237	0	0				191	0	0.00			
.	441915	bcgsc.ca	37	1	172718250	172718250	+	RNA	SNP	C	C	T	rs184779733	by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGGCACCGGGGCC		113	5	0.04	77	0	0				1	0	0.00			
.	646891	bcgsc.ca	37	1	175013936	175013936	+	RNA	SNP	T	T	A	rs3737935	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CACCACTGTCAGG		155	10	0.06	115	1	0.0086956522				1	0	0.00			
.	0	bcgsc.ca	37	1	192216349	192216349	+	RNA	SNP	T	T	G	rs139697927	by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTTTCATGTAGTA		381	19	0.05	353	1	0.0028328612				4	0	0.00			
.	0	bcgsc.ca	37	1	192216500	192216500	+	RNA	SNP	C	C	A	rs1175146	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTTCCCCCAGCAT		202	8	0.04	210	0	0				4	0	0.00			
HHAT	55733	hgsc.bcm.edu;bcgsc.ca	37	1	210577807	210577807	+	Splice_Site	SNP	G	G	C	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	NM_001122834	exon6	c.469-1G>C	.	TTTGTAGAGAAGG		94	7	0.07	116	0	0				0	0				
LYPLAL1	127018	ucsc.edu	37	1	219347266	219347266	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	LYPLAL1	NM_138794	exon1	c.T34C	p.C12R	CAGCGCTGTATCG		46	4	0.09	36	0	0		17		93	0	0.00			
OBSCN	84033	ucsc.edu;bcgsc.ca	37	1	228412227	228412228	+	Missense_Mutation	DNP	TG	TG	CA	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	TG	TG					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	OBSCN	NM_001271223	exon10	c.G2998A	p.A908T	AGCCAGTGCCACA		151	16	0.11	127	1	0.0078740157		2142		2	0	0.00			
.	0	bcgsc.ca	37	1	240136251	240136251	+	RNA	SNP	C	C	G	rs4659558	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CACTGGCCGACTG		42	4	0.10	48	0	0				0	0				
.	0	broad.mit.edu;ucsc.edu	37	1	246939513	246939513	+	RNA	SNP	G	G	A	rs3795467	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AGTTGCGCAGTCA		109	11	0.10	110	1	0.0090909091				0	0				
.	0	bcgsc.ca	37	1	246942159	246942159	+	Silent	SNP	G	G	A	rs7512440	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTTGACGCCAAGG		143	9	0.06	137	1	0.0072992701				0	0				
.	81458	bcgsc.ca	37	1	248605395	248605395	+	RNA	SNP	T	T	G	rs28631666	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGTTGTTGGGAGG		146	12	0.08	157	0	0				0	0				
.	0	bcgsc.ca	37	10	30986348	30986348	+	RNA	SNP	G	G	A	rs4749588	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AGCTTCGGCGCTC		62	5	0.08	54	0	0				2	0	0.00			
.	143341	bcgsc.ca	37	10	43062433	43062433	+	RNA	SNP	G	G	A	rs210224	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GATGCTGCGCATG		71	5	0.07	88	0	0				57	0	0.00			
FAM21C	253725	bcgsc.ca;mdanderson.org	37	10	46245557	46245557	+	Missense_Mutation	SNP	T	T	C	rs190175456	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	FAM21C	NM_015262	exon9	c.T746C	p.M249T	CACAAATGAGTGA		610	22	0.04	691	0	0		68		18	0	0.00			
.	0	bcgsc.ca	37	10	79492768	79492768	+	RNA	SNP	T	T	C	rs12782219	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGGAGCTGGCACA		193	10	0.05	270	1	0.0037037037				2	0	0.00			
.	0	bcgsc.ca	37	10	79492827	79492827	+	RNA	SNP	C	C	A	rs12780841	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CGGCTCCTTTAAG		195	9	0.05	246	0	0				1	0	0.00			
.	0	bcgsc.ca	37	10	79492970	79492970	+	RNA	SNP	C	C	T	rs12761718	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CAGATACACGTGG		80	5	0.06	85	0	0				0	0				
BMPR1A	657	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	88676951	88676951	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	BMPR1A_ENST00000224764,NS,carcinoma,0,2	BMPR1A_ENST00000224764	NM_004329	exon9	c.G736A	p.G246R	CGATATGGAGAAG		232	21	0.09	206	1	0.0048543689		0	2	5	1	0.20			
.	340970	bcgsc.ca	37	11	49010832	49010832	+	RNA	SNP	A	A	G	rs10431006	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTCAGCATGTGCA		623	23	0.04	834	1	0.0011990408				0	0				
.	0	bcgsc.ca	37	11	49329521	49329521	+	RNA	SNP	T	T	C	rs1164671	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGGTCATAAGTCA		209	10	0.05	199	1	0.0050251256				1	0	0.00			
.	401696	bcgsc.ca	37	11	59259846	59259846	+	RNA	SNP	C	C	T	rs3862659	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCTGCACCTCCCA		85	5	0.06	81	0	0				0	0				
.	0	bcgsc.ca	37	11	62815424	62815424	+	RNA	SNP	C	C	T	rs7126542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCTGCCCGGGCCA		39	5	0.13	49	0	0				0	0				
INTS4	92105	broad.mit.edu	37	11	77635831	77635832	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	INTS4	NM_033547	exon12	c.1479_1480insT	p.L493fs	CTTGGTTAAATTT		395	6	0.02	603	0	0		89		19	0	0.00			
ARHGAP42	143872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	100814536	100814536	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	NM_152432	exon10	c.G980C	p.C327S	AATCTTGTATCCG		74	14	0.19	123	0	0				15	13	0.87			
NCAM1	4684	hgsc.bcm.edu	37	11	113078059	113078059	+	Silent	SNP	C	C	T	rs376337341		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	NCAM1_ENST00000401611,NS,carcinoma,0,3	NCAM1_ENST00000401611	NM_001242608	exon7	c.C705T	p.C235C	GGTGTGCGATGCC		69	4	0.06	82	0	0		0	3	0	0				
AKAP3	10566	bcgsc.ca	37	12	4735968	4735969	+	Missense_Mutation	DNP	AG	AG	CA	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	AKAP3	NM_006422	exon4	c.C2099T	p.S700L	ATCTCCAGACTTG		175	8	0.05	122	0	0		212		9	0	0.00			
ANO2	57101	broad.mit.edu	37	12	5841706	5841707	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	ANO2	NM_020373	exon15	c.1525_1526insC	p.T509fs	CCGTCGTGTTTGT		139	7	0.05	91	0	0		309		6	0	0.00			
.	0	bcgsc.ca	37	12	6587668	6587668	+	RNA	SNP	C	C	G	rs7301945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GCAGGGCTCACCG		60	10	0.17	33	1	0.0303030303				2	0	0.00			
.	0	bcgsc.ca	37	12	7757084	7757084	+	RNA	SNP	T	T	C	rs11054742	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GATTTTTGTCTCT		43	9	0.21	30	0	0				4	0	0.00			
CPNE8	144402	broad.mit.edu	37	12	39118673	39118673	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	CPNE8	NM_153634	exon12	c.827delA	p.K276fs	TTTTTCTTTTTTC		1131	7	0.01	1160	0	0		66		2	0	0.00			
.	283463	bcgsc.ca;mdanderson.org	37	12	40821867	40821867	+	Missense_Mutation	SNP	G	G	A	rs7958987	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGAGAAGTCCGAG		251	15	0.06	229	3	0.0131004367				0	0				
.	283463	bcgsc.ca	37	12	40832126	40832126	+	Silent	SNP	C	C	T	rs10878584	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CATAAACGACGAG		107	8	0.07	104	0	0				0	0				
.	283463	bcgsc.ca	37	12	40834376	40834376	+	Missense_Mutation	SNP	C	C	G	rs10878592	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTCCAGCGTCTGT		494	35	0.07	508	1	0.0019685039				0	0				
.	283463	bcgsc.ca;mdanderson.org	37	12	40835734	40835734	+	Missense_Mutation	SNP	C	C	G	rs7966110	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCACATCTATGGG		229	18	0.08	285	0	0				0	0				
.	283463	bcgsc.ca;mdanderson.org	37	12	40838216	40838216	+	Missense_Mutation	SNP	T	T	C	rs10784621	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	ATGATGTGTGCAT		201	13	0.06	213	0	0				0	0				
.	283463	bcgsc.ca	37	12	40840325	40840325	+	Silent	SNP	T	T	C	rs10878597	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCTTACTTGGATG		195	10	0.05	231	1	0.0043290043				0	0				
.	283463	bcgsc.ca	37	12	40857943	40857943	+	Missense_Mutation	SNP	A	A	C	rs2933353	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CTGGAGAAACCCC		137	5	0.04	113	0	0				0	0				
.	283463	bcgsc.ca	37	12	40951596	40951596	+	Silent	SNP	A	A	G	rs3751167	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTTTCCACTTTTC		198	14	0.07	208	0	0				0	0				
.	283463	bcgsc.ca	37	12	40951605	40951605	+	Silent	SNP	G	G	A	rs3751168	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTTCTTGATTTGC		209	14	0.07	211	1	0.0047393365				0	0				
.	0	bcgsc.ca	37	12	43965108	43965108	+	RNA	SNP	T	T	A	rs11611126	bycluster;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CTCCAATACAGTT		137	8	0.06	148	3	0.0202702703				0	0				
DYRK2	8445	hgsc.bcm.edu	37	12	68051843	68051844	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	DYRK2,NS,carcinoma,0,1	DYRK2	NM_006482	exon3	c.1156_1157insG	p.R386fs	CAGTCGCGTTTTT		131	11	0.08	114	0	0		63		34	0	0.00			
.	144453	bcgsc.ca;mdanderson.org	37	12	70037520	70037520	+	Missense_Mutation	SNP	G	G	A	rs61747221	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGGAGTGGGATTT		200	13	0.07	243	0	0				0	0				
TRAFD1	10906	broad.mit.edu	37	12	112589651	112589652	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	TRAFD1	NM_001143906	exon10	c.1326_1327insA	p.A442fs	AACAGCTAATGGG		385	6	0.02	364	0	0		42		113	0	0.00			
NCOR2	9612	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	124887093	124887093	+	Silent	SNP	C	C	T	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	NCOR2_ENST00000405201,NS,carcinoma,0,11	NCOR2_ENST00000405201	NM_006312	exon16	c.G1497A	p.Q499Q	CTGCTGCTGTTGT		56	10	0.18	58	0	0		0	11	3	0	0.00			
.	100128337	bcgsc.ca	37	13	24696846	24696846	+	RNA	SNP	G	G	A	rs17458394	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AATTACGAAGGAG		21	4	0.19	44	0	0				0	0				
.	0	bcgsc.ca	37	13	24983385	24983385	+	RNA	SNP	G	G	T	rs79891959		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTAAATGAGTGGA		453	23	0.05	605	0	0				0	0				
UFM1	51569	hgsc.bcm.edu	37	13	38934869	38934869	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	NM_016617	exon6	c.G212T	p.G71V	AACATGGTTCAGA		74	3	0.04	116	0	0				97	0	0.00			
.	81993	bcgsc.ca	37	13	47065127	47065127	+	RNA	SNP	G	G	A	rs200135094		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GCTGAAGCCCTGC		271	20	0.07	362	5	0.0138121547				4	0	0.00			
DACH1	1602	broad.mit.edu	37	13	72440446	72440446	+	Silent	SNP	G	G	A	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	DACH1	NM_080759	exon1	c.C462T	p.S154S	ACTACTGCTGCTG		27	3	0.11	21	0	0		123		0	0				
.	0	bcgsc.ca	37	14	22053729	22053729	+	RNA	SNP	G	G	A	rs17182620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTGAGAGGATGTC		34	4	0.12	50	1	0.02				0	0				
.	0	bcgsc.ca	37	14	22080350	22080350	+	RNA	SNP	G	G	T	rs79459924		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CATTGCGTATTCT		115	7	0.06	152	0	0				0	0				
.	0	bcgsc.ca	37	14	22080368	22080368	+	RNA	SNP	T	T	C	rs7152539	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AAGGAATAGTTCA		111	6	0.05	151	0	0				0	0				
.	319089	bcgsc.ca;mdanderson.org	37	14	38266074	38266074	+	Silent	SNP	C	C	T	rs9805910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	TTC6,NS,carcinoma,0,1	.	.	.	.	.	CTTGGACGGAATC		151	12	0.08	188	0	0			1	0	0				
MIA2	0	broad.mit.edu	37	14	39716475	39716475	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	MIA2	NM_054024	exon4	c.697delC	p.Q233fs	GGAGAACAAGCTG		209	7	0.03	214	0	0		82		0	0				
.	0	bcgsc.ca	37	14	45329930	45329930	+	RNA	SNP	A	A	G	rs8016855	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTCCACATAAACA		148	7	0.05	201	0	0				0	0				
.	0	bcgsc.ca	37	14	45330315	45330315	+	RNA	SNP	A	A	G	rs17633092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTCGCCATACCAA		449	16	0.04	508	2	0.0039370079				0	0				
.	0	bcgsc.ca	37	14	45330721	45330721	+	RNA	SNP	A	A	T	rs7149683	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TCTTCAACTATAT		143	9	0.06	161	0	0				0	0				
.	0	bcgsc.ca	37	14	45331290	45331290	+	RNA	SNP	C	C	T	rs73345244	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	ACCTCACAGCAAA		194	17	0.09	195	0	0				0	0				
.	0	bcgsc.ca	37	14	45331397	45331397	+	RNA	SNP	T	T	C	rs12323568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTCAGATTGTCCA		301	17	0.06	297	1	0.0033670034				0	0				
.	0	bcgsc.ca	37	14	45331633	45331633	+	RNA	SNP	T	T	G	rs12323575	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TAAGATTCTGAAG		309	30	0.10	373	0	0				0	0				
.	0	bcgsc.ca	37	14	45332387	45332387	+	RNA	SNP	C	C	G	rs7161626	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GAAGTACACCAAA		284	25	0.09	322	0	0				0	0				
.	0	bcgsc.ca	37	14	45332752	45332752	+	RNA	SNP	G	G	A	rs74700367	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GCCTTGGGAAATC		132	8	0.06	173	2	0.0115606936				0	0				
.	0	bcgsc.ca	37	14	45333584	45333584	+	RNA	SNP	T	T	C	rs17115667	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTTTAATCTCATC		172	8	0.05	233	0	0				1	0	0.00			
.	0	bcgsc.ca	37	14	45334503	45334503	+	RNA	SNP	C	C	A	rs8014660	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTACATCAAATAA		160	10	0.06	194	3	0.0154639175				0	0				
.	0	bcgsc.ca	37	14	45334686	45334686	+	RNA	SNP	C	C	T	rs17633300	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TCCAACCTCTGAA		292	16	0.05	333	2	0.006006006				0	0				
.	0	bcgsc.ca	37	14	65066986	65066986	+	RNA	SNP	T	T	C	rs61987039	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AAAATTTTGTGCA		233	10	0.04	263	1	0.0038022814				9	0	0.00			
.	317775	bcgsc.ca	37	14	90203530	90203530	+	RNA	SNP	G	G	C	rs72689476	bycluster;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GCTATTGCTTCTA		40	5	0.13	45	0	0				0	0				
AKT1	207	bcgsc.ca	37	14	105236681	105236681	+	Silent	SNP	G	G	T	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	AKT1	NM_005163	exon14	c.C1440A	p.A480A	GCCTCAGGCCGTG		29	4	0.14	28	0	0		379		185	0	0.00			
AHNAK2	113146	broad.mit.edu	37	14	105418489	105418490	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	AHNAK2	NM_138420	exon7	c.3299_3300insC	p.Q1100fs	TCCACCTGGGGGC		175	5	0.03	181	0	0		719		0	0				
.	3493	bcgsc.ca	37	14	106174261	106174261	+	RNA	SNP	C	C	G	rs1407	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTCACGCTCAGGT		146	8	0.05	216	0	0				753	1	0.00			
.	28474	bcgsc.ca;mdanderson.org	37	14	106452766	106452766	+	RNA	SNP	T	T	A	rs112806369	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGACCCTGCCCTG		518	24	0.05	618	0	0				563	3	0.01			
.	28429	bcgsc.ca	37	14	106866588	106866588	+	RNA	SNP	T	T	C	rs73379082	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGCGGATCCAGCT		127	12	0.09	163	1	0.0061349693				0	0				
.	28426	bcgsc.ca;mdanderson.org	37	14	106926223	106926223	+	RNA	SNP	T	T	C	rs2467912	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCTCAGTTCTCAG		182	12	0.07	205	1	0.0048780488				57	0	0.00			
.	28426	bcgsc.ca;mdanderson.org	37	14	106926287	106926287	+	RNA	SNP	G	G	A	rs2467911	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GAATCGGCCCTTC		143	14	0.10	156	0	0				66	0	0.00			
.	28461	bcgsc.ca;mdanderson.org	37	14	107170005	107170005	+	RNA	SNP	T	T	C	rs1141720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGGATTTGTCCGC		105	7	0.07	105	1	0.0095238095				200	1	0.01			
.	28454	bcgsc.ca	37	14	107178938	107178938	+	RNA	SNP	T	T	C	rs17113976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTGCTGTAGTATT		263	7	0.03	344	0	0				19	0	0.00			
.	390561	bcgsc.ca	37	15	31129037	31129037	+	RNA	SNP	G	G	A	rs11070624	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGTTCCGGAGGTA		339	19	0.06	352	7	0.0198863636				4	0	0.00			
AGBL1	123624	broad.mit.edu	37	15	87066164	87066165	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	AGBL1	NM_152336	exon18	c.2541_2542insC	p.S847fs	CCGAAGTCCCGTG		243	6	0.02	257	0	0		151		0	0				
.	0	bcgsc.ca	37	15	93974276	93974276	+	RNA	SNP	C	C	G	rs28539148	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGCTCCCAGAAAC		137	10	0.07	117	0	0				0	0				
.	0	broad.mit.edu	37	15	102312710	102312710	+	RNA	SNP	A	A	G	rs116458034	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTTCACATCTCGG		23	3	0.13	27	0	0				3	0	0.00			
C16orf90	0	broad.mit.edu	37	16	3546140	3546141	+	RNA	INS	-	-	A	rs200618809		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	C16orf90	.	.	.	.	CCGTCTCAAAAAA		5	2	0.40	5	0	0		16		0	0				
CNGB1	1258	ucsc.edu;mdanderson.org	37	16	57937856	57937856	+	Silent	SNP	C	C	T	rs413562	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	CNGB1	NM_001297	exon27	c.C2664A	p.A888A	CTGTCCGGCGGTG		81	9	0.11	74	0	0		105		0	0				
HYDIN	54768	bcgsc.ca	37	16	71101279	71101279	+	Silent	SNP	G	G	T	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	HYDIN	NM_001198542	exon15	c.C2070A	p.S690S	AGTGTTGGAGCAT		50	4	0.08	59	1	0.0169491525		788		3	0	0.00			
PKD1L2	114780	broad.mit.edu	37	16	81155069	81155069	+	RNA	DEL	A	A	-	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	PKD1L2	.	.	.	.	CATCTCAAAAAAA		6	3	0.50	7	0	0		361		1	0	0.00			
VMO1	284013	bcgsc.ca	37	17	4689195	4689195	+	Splice_Site	DEL	C	C	-	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	VMO1	NM_001144939	exon3	c.347+1G>-	.	GACATACCATCAC		95	10	0.11	96	0	0		19		0	0				
.	0	bcgsc.ca	37	17	16796691	16796691	+	RNA	SNP	C	C	T	rs6502530	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCTCCACGGCAGG		69	8	0.12	88	0	0				0	0				
.	0	broad.mit.edu	37	17	18996545	18996545	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AGACCTGCTTGTT		927	10	0.01	1048	0	0				0	0				
LOC100287072	0	bcgsc.ca	37	17	20619842	20619842	+	RNA	SNP	A	A	G	rs112468000	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AAGCAGAATGGAA		245	8	0.03	280	0	0				5	0	0.00			
.	284203	bcgsc.ca	37	17	20805348	20805348	+	RNA	SNP	A	A	G	rs57960567	bycluster;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTGTTGATCACCT		206	10	0.05	190	0	0				5	0	0.00			
.	645668	bcgsc.ca	37	17	25409812	25409812	+	RNA	SNP	G	G	A	rs2061899	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGTGAAGCACTGG		123	6	0.05	98	1	0.0102040816				0	0				
.	645740	bcgsc.ca	37	17	25982851	25982851	+	Splice_Site	SNP	A	A	T	rs9897292	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTGCTTACTTCCG		78	9	0.12	54	0	0				0	0				
KRT32	3882	bcgsc.ca	37	17	39619093	39619094	+	Missense_Mutation	DNP	GT	GT	AC	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	GT	GT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	KRT32	NM_002278	exon6	c.A1205G	p.N402S	GTCCTCGTTCTCC		115	10	0.09	160	0	0		57		6	0	0.00			
.	644157	bcgsc.ca	37	17	43663247	43663247	+	RNA	SNP	C	C	A	rs1724390	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AGTCCACGCGGGA		35	12	0.34	32	0	0				0	0				
.	0	bcgsc.ca	37	17	44336943	44336943	+	RNA	SNP	C	C	T	rs62623402	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCTCAGCCCCAGC		216	18	0.08	221	0	0				58	0	0.00			
.	0	bcgsc.ca	37	17	44337209	44337209	+	RNA	SNP	C	C	T	rs112008792		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTAGCCCGAGCCC		205	9	0.04	156	0	0				33	0	0.00			
.	0	bcgsc.ca	37	17	44344738	44344749	+	RNA	DEL	GCTGGTGACCCT	GCTGGTGACCCT	-	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	GCTGGTGACCCT	GCTGGTGACCCT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CATCTGGCTGGTG		90	3	0.03	92	0	0				5	0	0.00			
.	0	bcgsc.ca	37	17	44344822	44344822	+	RNA	SNP	G	G	A	rs76934998	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TCTTCCGAGTCCA		128	13	0.10	151	1	0.0066225166				10	0	0.00			
.	0	bcgsc.ca	37	17	44344858	44344858	+	RNA	SNP	A	A	G	rs74358353	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GCTGCAATAAACC		111	13	0.12	138	0	0				4	0	0.00			
TBC1D3P1-DHX40P1	0	broad.mit.edu	37	17	58054437	58054438	+	RNA	INS	-	-	A	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CTTACAGAAAAAA		12	2	0.17	10	0	0				0	0				
.	284167	bcgsc.ca	37	17	60214389	60214389	+	RNA	SNP	G	G	A	rs72844475	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GCTTGGGCACCGC		65	5	0.08	51	0	0				70	0	0.00			
ZNF44	51710	hgsc.bcm.edu;broad.mit.edu	37	19	12384353	12384353	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	ZNF44	NM_001164276	exon5	c.862delT	p.Y288fs	TAGATAGGAACTG		157	11	0.07	162	0	0		55		36	0	0.00			
ZNF799	90576	broad.mit.edu	37	19	12501744	12501745	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	ZNF799	NM_001080821	exon4	c.1468_1469insA	p.Y490fs	AAAGGTATTGGAA		226	7	0.03	215	0	0		111		16	0	0.00			
.	100506916	bcgsc.ca	37	19	16091763	16091763	+	RNA	SNP	T	T	C	rs8103740	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TCTCTCTTTGCTA		48	5	0.10	43	0	0				0	0				
GPI	2821	bcgsc.ca	37	19	34856274	34856274	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	GPI	NM_001184722	exon2	c.G220T	p.D74Y	AACAAGGACCGCT		21	4	0.19	32	0	0		63		224	0	0.00			
.	0	bcgsc.ca	37	19	36989005	36989005	+	RNA	SNP	C	C	T	rs2945970	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	ATCCAGCGGCGCC		61	5	0.08	51	0	0				0	0				
SUPT5H	6829	hgsc.bcm.edu	37	19	39944127	39944128	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	SUPT5H	NM_001130825	exon3	c.207_208insC	p.K69fs	CAAGAAACCCCGC		145	9	0.06	113	0	0		119		163	0	0.00			
.	171427	bcgsc.ca	37	19	41332171	41332171	+	RNA	SNP	C	C	T	rs78011401	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AGATGTCGTACAA		231	11	0.05	253	0	0				11	0	0.00			
.	1550	ucsc.edu	37	19	41531656	41531656	+	Missense_Mutation	SNP	A	A	C	rs7249735	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGGGATAGATGCT		41	4	0.10	41	0	0				0	0				
HIF3A	64344	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	46828803	46828803	+	Silent	SNP	A	A	G	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	HIF3A_ENST00000377670,NS,carcinoma,0,2	HIF3A_ENST00000377670	NM_152795	exon11	c.A1347G	p.P449P	TCTCCCAGATGAA		62	13	0.21	70	1	0.0142857143		0	2	4	0	0.00			
BIRC8	112401	bcgsc.ca	37	19	53792954	53792955	+	Missense_Mutation	DNP	GC	GC	AT	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	GC	GC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	BIRC8	NM_033341	exon1	c.G673A	p.A225M	ATAACCGCGCTGC		199	11	0.06	182	0	0		54		0	0				
.	653753	bcgsc.ca	37	19	53818603	53818603	+	RNA	SNP	G	G	A	rs10439122	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTTGGGGTTAGAT		153	12	0.08	153	0	0				0	0				
RDH13	112724	ucsc.edu;bcgsc.ca	37	19	55568084	55568085	+	Missense_Mutation	DNP	CG	CG	TT	rs36097401		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	CG	CG					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	RDH13_ENST00000415061,colon,carcinoma,-1,5	RDH13	NM_001145971	exon3	c.C276A	p.NA92KT	GCCGGGCGTTGAC		171	16	0.09	167	2	0.0119760479		43	5	26	0	0.00			
MATN3	4148	broad.mit.edu	37	2	20194085	20194085	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	MATN3	NM_002381	exon7	c.1380delG	p.S460fs	AAGATACGAGCTG		151	1	0.01	173	0	0		28		1	0	0.00			
AFTPH	54812	broad.mit.edu	37	2	64800144	64800144	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	AFTPH	NM_017657	exon6	c.2336delT	p.I779fs	CTTCCATCGGTCA		278	7	0.03	337	0	0		117		95	0	0.00			
.	116143	bcgsc.ca	37	2	68352515	68352515	+	RNA	SNP	A	A	C	rs6742154	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CTGAGCACTGGAG		74	7	0.09	79	0	0				0	0				
LOC285074	0	bcgsc.ca	37	2	87303060	87303060	+	RNA	SNP	C	C	G	rs79162177	bycluster;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGATCTCGTGCTT		26	4	0.15	30	0	0				8	0	0.00			
.	0	bcgsc.ca	37	2	87355925	87355925	+	RNA	SNP	G	G	A	rs77851313	bycluster;byfrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CTTCTCGTTCAGT		289	16	0.06	355	0	0				0	0				
.	28935	bcgsc.ca	37	2	89513365	89513365	+	RNA	SNP	A	A	G	rs181706250	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CTGAGCAGGGACC		157	9	0.06	200	3	0.015				246	1	0.00			
SNRNP200	23020	hgsc.bcm.edu	37	2	96940775	96940775	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	NM_014014	exon45	c.C6386G	p.A2129G	GTCTCAGCTTCTT		99	5	0.05	127	0	0				1354	1	0.00			
.	643445	bcgsc.ca	37	2	97695036	97695036	+	RNA	SNP	C	C	A	rs116171118	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTTGACCCAGCTT		246	12	0.05	297	2	0.0067340067				0	0				
.	0	bcgsc.ca	37	2	107107511	107107511	+	RNA	SNP	C	C	T	rs11124115	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGATTCCGCAAAA		193	16	0.08	221	2	0.0090497738				1	0	0.00			
.	0	bcgsc.ca	37	2	107107567	107107567	+	RNA	SNP	G	G	C	rs2228021	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGTTTCGGGATGC		179	14	0.08	191	0	0				5	0	0.00			
NEB	4703	broad.mit.edu	37	2	152364618	152364619	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	NEB	NM_001271208	exon163	c.23457_23458insA	p.K7819fs	CTTGTACTTTTTC		163	8	0.05	171	0	0		1697		22	0	0.00			
NOSTRIN	115677	broad.mit.edu	37	2	169699562	169699563	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	NOSTRIN	NM_001039724	exon8	c.565_566insA	p.Q189fs	TACTACCAAAAAA		408	0	0.00	495	0	0		68		18	0	0.00			
.	0	bcgsc.ca	37	2	184472711	184472711	+	RNA	SNP	T	T	G	rs61733051	bycluster;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GCGATTTCTGTTG		170	8	0.05	194	0	0				16	0	0.00			
.	0	bcgsc.ca;mdanderson.org	37	2	202939654	202939654	+	Missense_Mutation	SNP	T	T	C	rs10221698	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTCCTGTCAGCAA		155	10	0.06	220	1	0.0045454545				0	0				
CPS1	1373	hgsc.bcm.edu	37	2	211459325	211459325	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	NM_001122633	exon13	c.G1276T	p.V426F	TCTCGGGTTGAGG		96	5	0.05	110	0	0				1	0	0.00			
.	339766	bcgsc.ca;mdanderson.org	37	2	234717839	234717839	+	Missense_Mutation	SNP	C	C	A	rs188948269	bycluster;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGGCCTCCTACTG		140	13	0.09	196	1	0.0051020408				0	0				
.	0	bcgsc.ca;mdanderson.org	37	2	240500173	240500173	+	Silent	SNP	T	T	C	rs10187580	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	AC079612.1,NS,carcinoma,0,1	.	.	.	.	.	GTCGTCTGCAAGC		75	7	0.09	90	1	0.0111111111			1	0	0				
.	0	bcgsc.ca	37	2	241865156	241865156	+	Silent	SNP	T	T	C	rs4675847	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCTCTGTCAGGTG		351	15	0.04	353	0	0				0	0				
.	0	bcgsc.ca	37	2	241871956	241871956	+	RNA	SNP	G	G	T	rs12472087	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCTGCAGTGCACT		73	5	0.07	92	1	0.0108695652				0	0				
.	0	bcgsc.ca;mdanderson.org	37	2	241872597	241872597	+	Missense_Mutation	SNP	A	A	G	rs4441463	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTCTCCAGGAGCA		136	10	0.07	177	3	0.0169491525				0	0				
.	0	bcgsc.ca;mdanderson.org	37	20	4053254	4053254	+	Missense_Mutation	SNP	A	A	G	rs6139288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AAGGGAAACCAGG		115	14	0.12	111	0	0				0	0				
.	0	bcgsc.ca	37	20	6195664	6195664	+	RNA	SNP	C	C	G	rs3905165	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCCCCTCCAACAA		158	10	0.06	183	0	0				5	0	0.00			
C20orf112	140688	hgsc.bcm.edu	37	20	31062436	31062436	+	Missense_Mutation	SNP	C	C	T	rs139591950	bycluster	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	NM_001256798	exon5	c.G809A	p.R270Q	GGGCTCCGCATCC		50	4	0.08	60	0	0	0			6	0	0.00			
LOC149950	0	bcgsc.ca	37	20	31189411	31189411	+	Missense_Mutation	SNP	A	A	G	rs2029086	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AGCATGAAGCACC		84	7	0.08	93	1	0.0107526882				0	0				
.	391269	bcgsc.ca	37	21	15436741	15436741	+	RNA	SNP	C	C	T	rs1810864	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GCACTCCGAACTG		131	7	0.05	122	0	0				2	0	0.00			
PRODH	5625	bcgsc.ca	37	22	18900987	18900987	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	PRODH	NM_016335	exon14	c.C1579G	p.L527V	CTAGCAGCTGTCC		233	8	0.03	245	1	0.0040816327		42		3378	0	0.00			
.	373856	bcgsc.ca	37	22	20723832	20723832	+	Missense_Mutation	SNP	T	T	C	rs75178771	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCTTCATCCGGAT		223	11	0.05	251	5	0.0199203187				0	0				
.	645280	bcgsc.ca	37	22	20959252	20959252	+	RNA	SNP	A	A	G	rs526942	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GATGTGACTCTTC		62	5	0.08	34	0	0				0	0				
.	0	bcgsc.ca	37	22	51193227	51193227	+	RNA	SNP	T	T	G	rs34608236	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCAGAGTTGAAGC		249	20	0.08	212	2	0.0094339623				120	0	0.00			
.	0	bcgsc.ca	37	3	39255871	39255871	+	RNA	SNP	C	C	G	rs7622622	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTGTAACCATAAC		35	4	0.11	52	0	0				1	0	0.00			
LOC646498	0	ucsc.edu;bcgsc.ca;mdanderson.org	37	3	49215966	49215966	+	Silent	SNP	C	C	T	rs9837625	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	NM_001080528	exon3	c.G147A	p.P49P	CTGCGCCGGCTCC		57	6	0.11	68	0	0				0	0				
.	100289640	bcgsc.ca	37	3	87100447	87100447	+	RNA	SNP	G	G	A	rs9831869	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AATATCGTGCTTT		358	25	0.07	480	1	0.0020833333				19	0	0.00			
.	79289	bcgsc.ca	37	3	98031539	98031539	+	RNA	SNP	A	A	G	rs2316268	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	ATGTGCACCCTGC		78	4	0.05	84	0	0				0	0				
.	0	bcgsc.ca	37	3	98377789	98377789	+	RNA	SNP	C	C	G	rs3796137	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCACAACCTTTAC		72	11	0.15	59	0	0				0	0				
.	0	bcgsc.ca	37	3	98377862	98377862	+	RNA	SNP	G	G	C	rs3796138	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCAGAAGAACAAC		78	11	0.14	88	0	0				0	0				
.	339881	bcgsc.ca	37	3	122380614	122380614	+	RNA	SNP	C	C	A	rs790118	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTGCAGCGTCAGC		73	9	0.12	80	1	0.0125				0	0				
.	0	bcgsc.ca	37	3	132106634	132106634	+	RNA	SNP	G	G	A	rs10935006	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GCATACGTTATTG		124	10	0.08	133	0	0				0	0				
.	285329	bcgsc.ca	37	3	148703787	148703787	+	RNA	SNP	T	T	G	rs3732559	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CTCACTTCTGACG		128	7	0.05	153	0	0				4	0	0.00			
.	0	bcgsc.ca	37	3	180042256	180042256	+	RNA	SNP	A	A	G	rs9867767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AAGATTACACAAA		145	12	0.08	150	0	0				0	0				
.	0	bcgsc.ca	37	3	180042567	180042567	+	RNA	SNP	A	A	G	rs4854970	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	ACAGAGACAGAAC		65	6	0.09	63	0	0				0	0				
.	389197	broad.mit.edu;bcgsc.ca	37	4	5990110	5990110	+	Translation_Start_Site	SNP	C	C	A	rs4689287	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTGCCCCTGAGCC		102	8	0.08	131	0	0				1	0	0.00			
.	391672	bcgsc.ca	37	4	83323174	83323174	+	RNA	SNP	C	C	T	rs13144673	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AATATTCACAAAC		165	13	0.08	197	2	0.0101522843				1	0	0.00			
.	0	bcgsc.ca	37	4	138369443	138369443	+	RNA	SNP	A	A	T	rs9993896	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AGGAAGAGTGTCA		36	4	0.11	33	0	0				0	0				
.	0	bcgsc.ca	37	4	144832823	144832823	+	RNA	SNP	T	T	G	rs183478773	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AGAGTCTCCATTT		490	22	0.04	635	2	0.0031496063				0	0				
.	0	bcgsc.ca	37	4	144833153	144833154	+	RNA	DNP	CT	CT	GG	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	CT	CT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CTTCCCCTGCACC		129	8	0.06	167	0	0				8	0	0.00			
.	0	bcgsc.ca	37	4	166469496	166469496	+	RNA	SNP	G	G	A	rs17587610	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCTAGCGGGTTTC		28	4	0.14	43	0	0				0	0				
.	10934	bcgsc.ca;mdanderson.org	37	4	174537356	174537356	+	RNA	SNP	T	T	A	rs34402795	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	ATTTGTTGAGTAG		148	11	0.07	183	0	0				0	0				
TTC37	9652	broad.mit.edu	37	5	94850586	94850587	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	TTC37	NM_014639	exon26	c.2676_2677insC	p.P892fs	ATAAGATGGATCA		360	7	0.02	510	0	0		128		20	0	0.00			
MIR583	0	broad.mit.edu	37	5	95414786	95414787	+	RNA	INS	-	-	TAAAA	rs5869706	bycluster;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	ATGCACTTAAAGT		141	8	0.06	198	0	0				0	0				
WDR36	134430	bcgsc.ca	37	5	110436345	110436346	+	Missense_Mutation	DNP	AT	AT	CC	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	AT	AT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	WDR36	NM_139281	exon5	c.T636C	p.H212P	TTTTGCATCCAAG		482	19	0.04	630	8	0.0126984127		111		3	0	0.00			
CLINT1	9685	hgsc.bcm.edu;bcgsc.ca	37	5	157233045	157233046	+	Frame_Shift_Del	DEL	CA	CA	-	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	CLINT1	NM_014666	exon7	c.771_772del	p.257_258del	TGTCGTCACAGTC		210	24	0.11	281	0	0		86		39	0	0.00			
CDKAL1	54901	bcgsc.ca	37	6	21065449	21065450	+	Missense_Mutation	DNP	CA	CA	TG	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	CDKAL1,NS,carcinoma,0,1	CDKAL1	NM_017774	exon12	c.A1227G	p.P409L	AAGTTCCAGCACA		120	8	0.07	140	0	0		55	1	29	0	0.00			
BTN2A3P	0	broad.mit.edu	37	6	26426983	26426984	+	RNA	INS	-	-	T	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCTAGTCTTTTTT		9	3	0.33	5	0	0				0	0				
.	442188	bcgsc.ca	37	6	29149561	29149561	+	RNA	SNP	G	G	A	rs3116817	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTGTGGGAAAGAC		100	17	0.17	115	0	0				0	0				
.	442188	bcgsc.ca	37	6	29149605	29149605	+	RNA	SNP	G	G	T	rs3116818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TACTTTGTTCTCA		121	20	0.17	102	1	0.0098039216				0	0				
.	442188	bcgsc.ca	37	6	29149632	29149632	+	RNA	SNP	T	T	G	rs3129168	bycluster;byfrequency;by2hit2allele	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GAGTGTTTCCTAC		123	21	0.17	104	0	0				0	0				
.	442188	bcgsc.ca	37	6	29149645	29149645	+	RNA	SNP	C	C	T	rs3116819	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGGTGGCGATGTC		120	18	0.15	116	0	0				0	0				
.	26695	bcgsc.ca;mdanderson.org	37	6	29230577	29230577	+	RNA	SNP	C	C	A	rs3117328	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	ATATACCTATATC		87	7	0.08	106	0	0				0	0				
PRRT1	80863	broad.mit.edu	37	6	32118387	32118387	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	PRRT1	NM_030651	exon2	c.C316A	p.R106S	GCATGCGGGGCAA		14	2	0.14	25	0	0		14		0	0				
.	442204	bcgsc.ca	37	6	33306794	33306794	+	RNA	SNP	T	T	G	rs3130267	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AAAAGCTCCCTCA		87	6	0.07	71	0	0				0	0				
.	0	bcgsc.ca	37	6	99622711	99622711	+	RNA	SNP	C	C	T	rs13203293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AAGGTGCCAAAGT		144	9	0.06	146	0	0				0	0				
.	114182	bcgsc.ca	37	6	134924962	134924962	+	RNA	SNP	C	C	T	rs1977140	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CTGCTCCCCAAAT		51	4	0.08	93	0	0				0	0				
.	0	bcgsc.ca	37	7	1733182	1733182	+	Missense_Mutation	SNP	C	C	T	rs79496824	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CATACACGCCTGT		174	10	0.06	178	1	0.0056179775				0	0				
.	0	bcgsc.ca	37	7	1733192	1733192	+	Missense_Mutation	SNP	C	C	T	rs56130225	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGTGGACGTAGCC		175	10	0.06	171	1	0.0058479532				0	0				
.	0	bcgsc.ca	37	7	10491126	10491126	+	RNA	SNP	C	C	T	rs6970227	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	ATGAACCCCACCA		126	12	0.10	134	1	0.0074626866				7	0	0.00			
.	0	bcgsc.ca	37	7	10492136	10492136	+	RNA	SNP	C	C	T	rs4725276	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CTCTTTCCCTTGG		100	7	0.07	111	2	0.018018018				0	0				
.	0	bcgsc.ca	37	7	28319234	28319234	+	RNA	SNP	A	A	C	rs177484	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTGGAAACTTTTC		202	10	0.05	198	1	0.0050505051				0	0				
.	100128459	bcgsc.ca	37	7	56296969	56296969	+	RNA	SNP	C	C	T	rs816390	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	ATTGGCCAGCCGT		110	7	0.06	100	0	0				0	0				
.	27320	bcgsc.ca	37	7	63040467	63040467	+	RNA	SNP	G	G	A	rs1860493	bycluster;byhapmap	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GACCACGGTGCCT		52	6	0.12	53	0	0				0	0				
.	0	bcgsc.ca	37	7	63354705	63354705	+	RNA	SNP	C	C	A	rs73123056	bycluster;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTTAAGCTAAATC		257	14	0.05	222	0	0				0	0				
POMZP3	22932	broad.mit.edu	37	7	76247569	76247570	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	POMZP3	NM_152992	exon4	c.276_277insC	p.P92fs	GGGTCGAGGAACT		1742	12	0.01	1192	0	0		19		190	0	0.00			
.	0	bcgsc.ca	37	7	128220111	128220111	+	RNA	SNP	G	G	T	rs4294131	bycluster;byhapmap	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTGCACGATCCTC		695	29	0.04	822	7	0.0085158151				8	0	0.00			
.	155100	bcgsc.ca	37	7	152143744	152143744	+	RNA	SNP	A	A	G	rs6953943	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TACCACAGCATTG		104	8	0.08	113	0	0				0	0				
MCM4	4173	hgsc.bcm.edu	37	8	48874151	48874151	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	NM_182746	exon3	c.A146C	p.Q49P	AGTTGCAGCCGAT		76	8	0.11	72	0	0				73	11	0.15			
.	441391	bcgsc.ca	37	9	30690152	30690152	+	RNA	SNP	C	C	A	rs187211150	by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GCTTACCCCTTCT		418	18	0.04	481	1	0.0020790021				0	0				
.	0	bcgsc.ca	37	9	38453992	38453992	+	RNA	SNP	C	C	T	rs78688365	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	ATTGCTCCAGCTG		19	4	0.21	22	0	0				0	0				
.	0	bcgsc.ca	37	9	65632051	65632051	+	RNA	SNP	C	C	T	rs12684652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CACAGACTTCATC		496	16	0.03	635	5	0.0078740157				0	0				
.	0	bcgsc.ca	37	9	88990413	88990413	+	RNA	SNP	C	C	T	rs11141356	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CGGACACGGCCAT		25	4	0.16	19	0	0				0	0				
.	100129793	bcgsc.ca	37	9	125449495	125449499	+	RNA	DEL	AAAAC	AAAAC	-	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	AAAAC	AAAAC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AAAGGAAAAACAA		80	4	0.05	92	0	0				0	0				
.	256158	bcgsc.ca	37	9	133294244	133294244	+	Silent	SNP	G	G	A	rs13294886	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGGAGAGCCCACA		142	7	0.05	195	2	0.0102564103				1	0	0.00			
.	0	bcgsc.ca	37	X	35077823	35077823	+	RNA	SNP	T	T	C	rs3109859	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AAGTACTTGGAGT		43	5	0.12	35	0	0				0	0				
.	139163	bcgsc.ca	37	X	49431714	49431714	+	RNA	SNP	A	A	G	rs6608906	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GTTGGGAGCAATG		24	5	0.21	22	0	0				0	0				
.	139163	bcgsc.ca	37	X	49432879	49432880	+	RNA	DNP	CA	CA	TG	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGTGATCACTGAG		64	5	0.08	42	0	0				0	0				
.	139163	bcgsc.ca	37	X	49432943	49432943	+	RNA	SNP	T	T	C	rs6608907	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGGCTGTGGCTGG		42	4	0.10	36	0	0				0	0				
.	0	bcgsc.ca	37	X	53834482	53834482	+	RNA	SNP	A	A	C	rs10449002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGATTGAAGCTCC		25	5	0.20	25	0	0				1	1	1.00			
.	0	bcgsc.ca	37	X	68003320	68003320	+	RNA	SNP	T	T	C	rs12012713	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CATGCCTGGGCAC		67	9	0.13	53	1	0.0188679245				0	0				
.	0	bcgsc.ca	37	X	68004148	68004148	+	RNA	SNP	T	T	C	rs7061948	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCACCTTGTGAAC		113	12	0.11	110	0	0				0	0				
.	0	bcgsc.ca	37	X	68004230	68004230	+	RNA	SNP	A	A	C	rs7058210	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	ACCGACATATTCG		248	25	0.10	274	0	0				1	1	1.00			
.	0	bcgsc.ca	37	X	68004333	68004333	+	RNA	SNP	G	G	T	rs111708563	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGATAGGCATAGT		302	39	0.13	306	2	0.0065359477				59	0	0.00			
.	3947	bcgsc.ca	37	X	75556211	75556211	+	RNA	SNP	C	C	A	rs11798238	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CCGCAACTGGTAC		38	6	0.16	35	0	0				1	0	0.00			
.	254700	bcgsc.ca	37	X	89368606	89368606	+	RNA	SNP	G	G	T	rs5941478	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TATTGCGATAGTT		119	7	0.06	108	0	0				1	0	0.00			
.	0	bcgsc.ca	37	X	100212525	100212525	+	RNA	SNP	T	T	C	rs6616208	bycluster;byfrequency;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGTTGGTTGAAAT		54	7	0.13	52	0	0				3	0	0.00			
.	0	bcgsc.ca	37	X	101437635	101437635	+	RNA	SNP	A	A	G	rs5945049	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	ATCTCCAGGTAAG		433	39	0.09	502	3	0.0059760956				0	0				
.	84443	ucsc.edu;bcgsc.ca;mdanderson.org	37	X	106796084	106796084	+	Silent	SNP	T	T	C	rs12011630	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TGCTCTTGTCCTT		101	14	0.14	90	0	0				0	0				
.	84443	ucsc.edu;bcgsc.ca;mdanderson.org	37	X	106841068	106841068	+	Silent	SNP	G	G	A	rs61184704	bycluster;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGAGGAGGAGGAG		51	8	0.16	64	0	0				0	0				
.	392517	bcgsc.ca	37	X	107037795	107037795	+	Silent	SNP	C	C	A	rs5962885	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGATGTCGGTTTT		147	16	0.11	102	1	0.0098039216				0	0				
.	643873	bcgsc.ca	37	X	110863204	110863204	+	RNA	SNP	A	A	G	novel		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGAGCTACTTTTC		62	6	0.10	50	0	0				24	0	0.00			
.	0	bcgsc.ca	37	X	114659687	114659687	+	RNA	SNP	A	A	G	rs926705	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	AGTGGAATTGTAG		16	4	0.25	33	1	0.0303030303				0	0				
.	642812	bcgsc.ca	37	X	115239675	115239675	+	RNA	SNP	G	G	C	rs7057314	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CTCTACGTTCGGC		101	8	0.08	114	1	0.0087719298				0	0				
.	0	bcgsc.ca	37	X	118012888	118012888	+	RNA	SNP	G	G	A	rs261662	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TCTTCAGTGACGT		73	6	0.08	49	0	0				0	0				
.	0	bcgsc.ca	37	X	134345975	134345975	+	RNA	SNP	G	G	A	rs147984738	bycluster;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTAATTGGATGTG		317	24	0.08	310	1	0.0032258065				0	0				
.	0	bcgsc.ca	37	X	134741152	134741152	+	RNA	SNP	C	C	T	rs5929670	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	CAGATGCTGCAGT		164	17	0.10	158	1	0.0063291139				0	0				
.	0	bcgsc.ca	37	X	135027101	135027101	+	RNA	SNP	T	T	C	rs6528321	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	GGTGCATTGCTAC		87	7	0.08	99	1	0.0101010101				0	0				
.	100289259	bcgsc.ca	37	X	136742802	136742802	+	RNA	SNP	T	T	C	rs4240110	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TTCCTCTATTCTC		48	5	0.10	65	1	0.0153846154				0	0				
TMLHE-AS1	0	broad.mit.edu	37	X	154578866	154578866	+	RNA	DEL	T	T	-	rs67633161		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	.	.	.	.	.	.	TCTCTGTTTTTTT		13	6	0.46	8	0	0				0	0				
