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
.	339457	ucsc.edu	37	1	1855319	1855319	+	Missense_Mutation	SNP	C	C	T	rs2295362	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GACGCCCTTGACG		116	14	0.12	115	3	0.0260869565				0	0				
.	339457	bcgsc.ca	37	1	1859176	1859176	+	Missense_Mutation	SNP	T	T	C	rs45489198	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCATATTCTTTCG		39	5	0.13	57	0	0				0	0				
.	284498	bcgsc.ca	37	1	11835556	11835556	+	Missense_Mutation	SNP	C	C	T	rs41275456	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCTGACCGCCGGA		137	8	0.06	166	0	0				0	0				
.	284498	bcgsc.ca	37	1	11836628	11836628	+	Missense_Mutation	SNP	T	T	C	rs6699881	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCCTGCTGGACAC		104	5	0.05	180	0	0				0	0				
.	284498	bcgsc.ca;mdanderson.org	37	1	11836670	11836670	+	Silent	SNP	C	C	A	rs41275458	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AAGATGCGGCTTT		172	17	0.10	248	0	0				0	0				
.	284498	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	11838762	11838762	+	Silent	SNP	G	G	A	rs72640211	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAGCCTGAGATGG		138	13	0.09	189	0	0				0	0				
.	284498	bcgsc.ca;mdanderson.org	37	1	11838841	11838841	+	Missense_Mutation	SNP	A	A	G	rs56001051	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCACTGAGCAGCA		227	15	0.07	310	0	0				1	0	0.00			
.	284498	bcgsc.ca	37	1	11839009	11839009	+	Silent	SNP	C	C	T	rs55685198	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCCGGACACTCTC		139	7	0.05	201	0	0				0	0				
.	0	bcgsc.ca	37	1	12898045	12898045	+	RNA	SNP	G	G	A	rs10158988	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GGGACCGAAGAAG		72	15	0.21	108	0	0				0	0				
.	0	bcgsc.ca	37	1	12898378	12898378	+	RNA	SNP	C	C	G	rs57957396	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCAGCCCTAATTG		167	10	0.06	233	0	0				0	0				
.	0	bcgsc.ca	37	1	12898445	12898445	+	RNA	SNP	C	C	A	rs11121996	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAGGATCCATGTC		184	20	0.11	276	0	0				0	0				
PRAMEF8	441871	bcgsc.ca;mdanderson.org	37	1	12980150	12980150	+	Missense_Mutation	SNP	A	A	G	rs141480481	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_001012276	exon4	c.A1342G	p.I448V	CCCAAGATCATTG		318	24	0.08	366	0	0				0	0				
LOC440563	0	bcgsc.ca	37	1	13183615	13183615	+	RNA	SNP	T	T	C	rs200176197		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_001136561	exon2	c.A258G	p.A86A	TGGCTCTGCAGCC		174	16	0.09	201	9	0.0447761194				1	0	0.00			
.	0	bcgsc.ca	37	1	45457681	45457681	+	RNA	SNP	G	G	A	rs12126314	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTTCGCGGAACAG		57	4	0.07	54	0	0				5	0	0.00			
.	729779	bcgsc.ca	37	1	79520923	79520923	+	RNA	SNP	T	T	C	rs17131734	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GAGATTTGATGGA		36	6	0.17	55	0	0				1	0	0.00			
LOC100129138	0	bcgsc.ca	37	1	104615959	104615959	+	RNA	SNP	A	A	G	rs3811506	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACAAGCAGCCATC		105	13	0.12	111	0	0				7	0	0.00			
.	0	bcgsc.ca	37	1	111391513	111391513	+	RNA	SNP	C	C	T	rs12750061	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTGCTCGTCTGC		24	4	0.17	35	0	0				0	0				
.	100132332	bcgsc.ca	37	1	116107337	116107337	+	RNA	SNP	T	T	A	rs55771787	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTATGGTCACCGA		51	5	0.10	58	0	0				1	1	1.00			
.	0	bcgsc.ca	37	1	146522606	146522606	+	RNA	SNP	T	T	C	rs521687	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGTCTCTAAAAAG		158	22	0.14	168	1	0.005952381				8	0	0.00			
.	0	bcgsc.ca	37	1	146522686	146522686	+	RNA	SNP	C	C	T	rs522558	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTTTGGCTCAATA		109	18	0.17	93	1	0.0107526882				27	0	0.00			
.	0	bcgsc.ca	37	1	146523670	146523670	+	RNA	SNP	T	T	C	rs594716	byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GGATGGTCATCAT		61	9	0.15	45	0	0				0	0				
.	0	bcgsc.ca	37	1	147313509	147313509	+	RNA	SNP	C	C	T	rs146788179	by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GACTGTCCAAGGA		156	11	0.07	153	0	0				0	0				
.	0	bcgsc.ca	37	1	148193730	148193730	+	RNA	SNP	G	G	A	rs61811779	bycluster	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGTCGGGAATTCC		261	17	0.07	226	0	0				110	0	0.00			
.	0	bcgsc.ca	37	1	157029199	157029199	+	RNA	SNP	A	A	G	rs11264607	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGATCCATTCACC		146	17	0.12	119	0	0				41	0	0.00			
.	0	bcgsc.ca	37	1	158424637	158424637	+	RNA	SNP	A	A	C	rs1844787	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTTGTAGGTCAG		60	11	0.18	82	0	0				0	0				
.	0	bcgsc.ca	37	1	158493554	158493554	+	RNA	SNP	A	A	G	rs6656837	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GATGTCACTGATC		49	4	0.08	60	0	0				1	0	0.00			
.	0	bcgsc.ca	37	1	158493726	158493726	+	RNA	SNP	C	C	T	rs7548349	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAAACCCTCACTA		36	7	0.19	41	0	0				0	0				
.	0	bcgsc.ca	37	1	158493852	158493852	+	RNA	SNP	A	A	T	rs7514968	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTATGATTGGCC		73	10	0.14	70	0	0				0	0				
.	0	bcgsc.ca	37	1	158493890	158493890	+	RNA	SNP	G	G	C	rs7525362	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTATTTGGTTGCC		67	8	0.12	61	0	0				0	0				
.	0	bcgsc.ca	37	1	158494110	158494110	+	RNA	SNP	A	A	G	rs7515245	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TATCCCATTACTC		44	5	0.11	51	0	0				36	1	0.03			
.	0	bcgsc.ca	37	1	158494693	158494693	+	RNA	SNP	A	A	G	rs12145401	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAGGAAAAATTTG		68	13	0.19	41	0	0				0	0				
.	0	bcgsc.ca	37	1	158495209	158495209	+	RNA	SNP	C	C	T	rs6699473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTTGTGCCAAACT		69	10	0.14	62	0	0				29	29	1.00			
.	0	bcgsc.ca	37	1	158495431	158495431	+	RNA	SNP	G	G	A	rs6674656	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTGGTCGTCTTGC		57	6	0.11	59	0	0				0	0				
OR10X1	128367	bcgsc.ca	37	1	158549420	158549421	+	Missense_Mutation	DNP	CG	CG	TA	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CG	CG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	OR10X1,face,carcinoma,-1,1	OR10X1	NM_001004477	exon1	c.C269T	p.T90I	GGTCAGCGTATAG		151	7	0.05	126	1	0.0079365079		96	1	0	0				
UAP1	6675	ucsc.edu	37	1	162549362	162549362	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	UAP1	NM_003115	exon4	c.G630T	p.L210F	TATTTTGGAAGAG		43	4	0.09	51	0	0		47		98	0	0.00			
.	677790	broad.mit.edu;bcgsc.ca	37	1	229385670	229385671	+	Frame_Shift_Del	DEL	TC	TC	-	rs140311590	bycluster;alternate_allele	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	TC	TC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTCTTTCTCTCT		12	6	0.50	29	0	0				0	0				
.	0	bcgsc.ca	37	1	236274147	236274147	+	RNA	SNP	G	G	A	rs7516388	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCTGGCGTAGACT		42	5	0.12	38	0	0				1	0	0.00			
.	0	bcgsc.ca	37	1	240136252	240136252	+	RNA	SNP	C	C	T	rs72762530	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACTGGCCGACTGG		50	6	0.12	34	0	0				0	0				
.	388761	bcgsc.ca;mdanderson.org	37	1	247886493	247886493	+	Missense_Mutation	SNP	G	G	A	rs62619787	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTACAGGGTTAAA		171	12	0.07	220	0	0				0	0				
.	388761	bcgsc.ca	37	1	247886949	247886949	+	Missense_Mutation	SNP	T	T	C	rs36075193	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCATGATTACCTC		122	8	0.07	134	0	0				0	0				
.	148818	bcgsc.ca	37	1	247991516	247991516	+	RNA	SNP	C	C	G	rs6698863	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATGCCACTAATAT		58	5	0.09	72	0	0				0	0				
.	0	bcgsc.ca	37	10	8203302	8203302	+	RNA	SNP	T	T	C	rs2664906	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTCGAATGCGAAT		40	4	0.10	55	0	0				0	0				
MYO3A	53904	ucsc.edu;bcgsc.ca	37	10	26357747	26357748	+	Missense_Mutation	DNP	CG	CG	TA	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CG	CG					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	MYO3A	NM_017433	exon12	c.G1105A	p.V369I	GATCTACGTCTAT		86	9	0.10	84	0	0		371		6	0	0.00			
.	0	bcgsc.ca	37	10	37284272	37284272	+	RNA	SNP	A	A	G	rs10764117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GGGTTGATGGAAA		50	9	0.18	61	0	0				1	1	1.00			
.	653365	bcgsc.ca;mdanderson.org	37	10	48003992	48003992	+	Missense_Mutation	SNP	C	C	T	rs3739968	bycluster;byfrequency;byhapmap	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCATTACACACTA		936	57	0.06	1430	2	0.0013986014				12	0	0.00			
.	653045	bcgsc.ca;mdanderson.org	37	10	49313245	49313245	+	Missense_Mutation	SNP	C	C	T	rs71242628	bycluster;byfrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	PTPN20C_ENST00000455582,bladder,carcinoma,0,9	.	.	.	.	.	CCTCCTCATCCTC		264	27	0.10	347	0	0			9	0	0				
.	0	bcgsc.ca	37	10	52443585	52443585	+	RNA	SNP	T	T	C	rs11006622	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACTGGATGCCCCC		144	9	0.06	179	0	0				0	0				
.	0	bcgsc.ca	37	10	69510905	69510905	+	RNA	SNP	C	C	T	rs10997795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAACCACACTCAG		40	5	0.13	64	0	0				0	0				
ZSWIM8	23053	bcgsc.ca	37	10	75551642	75551642	+	Missense_Mutation	SNP	C	C	T	rs201390871	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_015037	exon10	c.C1345T	p.R449W	CAGCTGCGGCAGT		74	5	0.07	96	0	0				28	0	0.00			
LOC653486	147199	bcgsc.ca	37	11	194441	194441	+	Silent	SNP	C	C	T	rs61997072	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_001097610	exon3	c.C279T	p.D93D	TCAGGACGGTGCC		86	6	0.07	124	0	0				1	0	0.00			
.	387745	bcgsc.ca	37	11	3437850	3437850	+	RNA	SNP	G	G	A	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCAAAAGCTCTGT		76	5	0.07	99	0	0				2	0	0.00			
.	387745	bcgsc.ca	37	11	3439455	3439455	+	RNA	SNP	A	A	C	rs12421377	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GAAAGCACCGGGC		71	5	0.07	75	0	0				0	0				
.	340990	bcgsc.ca	37	11	17579783	17579783	+	Missense_Mutation	SNP	C	C	A	rs61611064	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGCAGGCCCCTAA		96	8	0.08	100	0	0				0	0				
.	340990	bcgsc.ca;mdanderson.org	37	11	17593709	17593709	+	Missense_Mutation	SNP	T	T	C	rs7106548	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTGGTCTCTGGCT		129	9	0.07	205	0	0				0	0				
.	340990	bcgsc.ca;mdanderson.org	37	11	17596313	17596313	+	Silent	SNP	G	G	A	rs4757548	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GGCCCCGTGTGGA		55	8	0.15	61	0	0				0	0				
.	340990	ucsc.edu;mdanderson.org	37	11	17600033	17600033	+	Missense_Mutation	SNP	G	G	A	rs2355466	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTGTCAGCCCGTG		21	6	0.29	17	0	0				0	0				
.	340990	bcgsc.ca	37	11	17656686	17656686	+	Silent	SNP	C	C	T	rs11024350	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAGATCCTGATCA		62	5	0.08	63	0	0				2	0	0.00			
FIBP	9158	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	65651461	65651461	+	Missense_Mutation	SNP	C	C	T	rs140853801	bycluster	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	FIBP,colon,carcinoma,0,1	FIBP	NM_198897	exon10	c.G1079A	p.R360H	TACAGGCGCAGGA		75	10	0.13	89	0	0	0	0	1	219	42	0.19			
PIWIL4	143689	bcgsc.ca	37	11	94322352	94322353	+	Missense_Mutation	DNP	AG	AG	TA	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	PIWIL4	NM_152431	exon8	c.G981A	p.Q327L	CCTTTCAGAAGCG		47	5	0.11	88	0	0		70		15	0	0.00			
.	401708	bcgsc.ca	37	11	122484722	122484722	+	RNA	SNP	C	C	T	rs61910452	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGCTTACAAGCAG		54	10	0.19	111	0	0				0	0				
SLC6A13	6540	ucsc.edu	37	12	351879	351879	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	SLC6A13,caecum,carcinoma,0,2	SLC6A13	NM_016615	exon4	c.G379T	p.V127F	AGTAGACGTTGAG		159	22	0.14	98	2	0.0204081633		62	2	0	0				
.	0	bcgsc.ca	37	12	6588445	6588445	+	RNA	SNP	A	A	G	rs2008134	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCCCTGATAGGAG		70	6	0.09	34	0	0				3	0	0.00			
PEX5	5830	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	7354887	7354887	+	Silent	SNP	C	C	T	rs140332077	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_001131023	exon8	c.C738T	p.S246S	GGAGTCCGGTGCA		218	33	0.15	122	0	0	0			311	18	0.06			
.	0	bcgsc.ca	37	12	10659228	10659228	+	Missense_Mutation	SNP	A	A	T	rs61738398	byfrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	Q5I0X0_HUMAN,NS,carcinoma,-1,2	.	.	.	.	.	AAGAAAATTCCAG		893	42	0.05	541	0	0			2	239	0	0.00			
TAS2R19	259294	ucsc.edu	37	12	11174765	11174765	+	Missense_Mutation	SNP	G	G	A	rs199722277	bycluster	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	TAS2R19	NM_176888	exon1	c.C406T	p.P136S	CCAAGGGCCCCAA		169	1	0.01	99	0	0		30		30	13	0.43			
HTR7P1	0	broad.mit.edu	37	12	13154583	13154583	+	RNA	DEL	G	G	-	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTGAGCGGGGGCC		10	5	0.50	4	0	0				0	0				
KRAS	3845	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	25378562	25378562	+	Missense_Mutation	SNP	C	C	T	rs121913527		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	KRAS_ENST00000256078,colon,carcinoma,+1,137	KRAS_ENST00000256078	NM_004985	exon4	c.G436A	p.A146T	TCTTTGCTGATGT		134	26	0.19	74	1	0.0135135135		1	137	262	49	0.19			
.	0	bcgsc.ca	37	12	27292934	27292934	+	RNA	SNP	G	G	C	rs41512649		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCAGAAGTTGGAT		240	13	0.05	143	0	0				10	0	0.00			
.	283463	bcgsc.ca;mdanderson.org	37	12	40823354	40823354	+	Missense_Mutation	SNP	G	G	C	rs11564245	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGCCAAGATGCAA		93	7	0.08	91	0	0				0	0				
.	283463	bcgsc.ca;mdanderson.org	37	12	40826514	40826514	+	Silent	SNP	T	T	C	rs10506162	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGTTCCTGTGATG		168	20	0.12	149	0	0				0	0				
.	283463	bcgsc.ca;mdanderson.org	37	12	40834918	40834918	+	Missense_Mutation	SNP	C	C	T	rs4768261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GAAATTCTAAAGG		179	29	0.16	142	0	0				0	0				
.	283463	bcgsc.ca;mdanderson.org	37	12	40837898	40837898	+	Missense_Mutation	SNP	G	G	A	rs11564109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTCTTTGTGGAAA		112	11	0.10	83	0	0				0	0				
.	283463	ucsc.edu	37	12	40921902	40921902	+	Silent	SNP	C	C	T	rs4768287	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGGAAGCTTCAGC		35	6	0.17	17	0	0				0	0				
.	0	bcgsc.ca	37	12	43964281	43964281	+	RNA	SNP	T	T	G	rs11831774	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTTGAGTGAATGC		112	5	0.04	94	0	0				0	0				
.	0	bcgsc.ca	37	12	43965011	43965011	+	RNA	SNP	A	A	T	rs66501365	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCACCAACACAGG		131	11	0.08	94	0	0				0	0				
PLEKHA8P1	0	broad.mit.edu;bcgsc.ca	37	12	45566862	45566867	+	RNA	DEL	TTTATT	TTTATT	-	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	TTTATT	TTTATT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	PLEKHA8P1	.	.	.	.	TATTTATTTATTT		45	13	0.29	43	0	0		38		0	0				
.	85349	bcgsc.ca	37	12	52646139	52646139	+	RNA	SNP	G	G	A	rs146544749	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGATCAGGCAGGC		104	8	0.08	94	0	0				0	0				
.	0	bcgsc.ca	37	12	55197244	55197244	+	RNA	SNP	C	C	T	rs11171086	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTGAGCTTGTAA		42	7	0.17	29	0	0				2	0	0.00			
.	653441	bcgsc.ca	37	12	55805647	55805647	+	RNA	SNP	A	A	G	rs12825123	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTCTGCAATCTCT		369	14	0.04	335	1	0.0029850746				3798	1	0.00			
.	0	bcgsc.ca	37	12	64118558	64118558	+	Splice_Site	SNP	A	A	G	rs3864455	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCAGTTAATTCTG		128	10	0.08	94	0	0				1	0	0.00			
SLC5A8	160728	hgsc.bcm.edu	37	12	101603313	101603313	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	SLC5A8,colon,carcinoma,0,1	SLC5A8	NM_145913	exon1	c.C314A	p.P105Q	AACACCGGGAGGA		95	5	0.05	79	1	0.0126582278		0	1	0	0				
.	0	bcgsc.ca	37	12	106566174	106566174	+	RNA	SNP	A	A	C	rs3853777	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCTGACAACAGCG		85	5	0.06	79	0	0				0	0				
.	171222	bcgsc.ca	37	13	31002373	31002373	+	RNA	SNP	G	G	A	rs2892546	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CGAAAAGGGGCAG		127	6	0.05	190	0	0				0	0				
.	100128626	bcgsc.ca	37	13	64385632	64385632	+	RNA	SNP	C	C	T	rs78786519	byfrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCTCCTCGACACT		51	6	0.12	65	0	0				12	0	0.00			
.	122199	bcgsc.ca	37	13	65532930	65532930	+	RNA	SNP	A	A	G	rs9598891	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCAGGCAGGTGGT		33	6	0.18	61	0	0				1	0	0.00			
.	100288130	bcgsc.ca	37	13	71498338	71498338	+	RNA	SNP	C	C	T	rs7335663	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CATTGGCGTGGGC		74	6	0.08	78	0	0				0	0				
.	100288130	bcgsc.ca	37	13	71498360	71498360	+	RNA	SNP	G	G	C	rs7336024	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGCAGGGAGGAAG		72	4	0.06	81	0	0				0	0				
.	150928	bcgsc.ca;mdanderson.org	37	13	82264343	82264343	+	RNA	SNP	A	A	G	rs7326041	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCAGGAAGCTGAC		108	13	0.12	136	0	0				38	34	0.89			
.	150928	bcgsc.ca	37	13	82264468	82264468	+	RNA	SNP	G	G	A	rs9574945	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCAAGCGGGCAGC		35	4	0.11	56	0	0				605	0	0.00			
.	121727	bcgsc.ca	37	13	90644911	90644911	+	RNA	SNP	G	G	A	rs9588829	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CGCCCCGCCTACT		60	5	0.08	87	0	0				0	0				
MYO16	23026	broad.mit.edu	37	13	109793111	109793111	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	MYO16	NM_001198950	exon32	c.4551delC	p.F1517fs	GGTGTTCCCCCCG		2242	13	0.01	101	0	0		285		7	0	0.00			
POTEG	404785	bcgsc.ca;mdanderson.org	37	14	19566036	19566036	+	Silent	SNP	C	C	T	rs8142076	bycluster;byfrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	POTEG	NM_001005356	exon6	c.C1080T	p.Y360Y	TGACTACAAAGAA		227	23	0.10	360	0	0		118		0	0				
.	440153	bcgsc.ca	37	14	19806717	19806717	+	RNA	SNP	A	A	C	rs1575832	bycluster;byfrequency;byhapmap	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AATAGTATAGGAT		379	40	0.11	476	2	0.0042016807				0	0				
.	0	bcgsc.ca	37	14	22070355	22070355	+	RNA	SNP	T	T	C	rs199637760	bycluster	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCCCGATGTCCAC		128	11	0.09	154	0	0				0	0				
.	319089	bcgsc.ca;mdanderson.org	37	14	38277999	38277999	+	Missense_Mutation	SNP	C	C	T	rs4901284	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTTATACAGCATT		388	18	0.05	503	0	0				0	0				
.	0	bcgsc.ca	37	14	69335445	69335445	+	RNA	SNP	G	G	A	rs75789840	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACATACGTTCTGT		16	4	0.25	19	0	0				0	0				
.	0	broad.mit.edu	37	14	92040590	92040590	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCGCCTCCGCCCC		40	7	0.18	57	0	0				0	0				
.	3503	bcgsc.ca	37	14	106091329	106091329	+	RNA	SNP	G	G	C	rs8015545	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GGTGCAGGACGGT		172	9	0.05	252	0	0				1483	1	0.00			
.	3503	bcgsc.ca	37	14	106092152	106092152	+	RNA	SNP	G	G	A	rs41493549		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATCTACGTTGCAG		92	6	0.07	137	0	0				592	0	0.00			
.	3501	bcgsc.ca	37	14	106110137	106110137	+	RNA	SNP	C	C	T	rs8009156	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCTCCACGCCGTC		150	10	0.07	259	0	0				11907	9	0.00			
.	3505	bcgsc.ca	37	14	106134806	106134806	+	RNA	SNP	G	G	A	rs10144746	bycluster;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCGCTGGGGTAGA		266	11	0.04	359	0	0				6195	2	0.00			
.	28388	bcgsc.ca;mdanderson.org	37	14	107035142	107035142	+	RNA	SNP	G	G	A	rs61732461	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GAGGGCGAGGATG		91	8	0.09	103	0	0				1397	0	0.00			
.	28461	bcgsc.ca;mdanderson.org	37	14	107170207	107170207	+	RNA	SNP	C	C	T	rs11845287	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCCAGACTGCACC		86	7	0.08	116	0	0				1341	8	0.01			
.	28454	bcgsc.ca	37	14	107178941	107178941	+	RNA	SNP	T	T	A	rs10133751	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTGTAGTATTTAT		261	12	0.05	334	2	0.005988024				393	5	0.01			
.	28454	bcgsc.ca	37	14	107179013	107179013	+	RNA	SNP	A	A	G	rs61732216	bycluster;byfrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAGCTCACACACA		200	10	0.05	251	0	0				440	0	0.00			
.	28454	bcgsc.ca	37	14	107179017	107179017	+	RNA	SNP	A	A	G	rs61732209	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCACACACATTCC		196	8	0.04	248	0	0				468	0	0.00			
.	28454	bcgsc.ca	37	14	107179106	107179106	+	RNA	SNP	C	C	T	rs10144703	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GACTCCCTCAAGG		134	7	0.05	175	0	0				385	0	0.00			
.	0	bcgsc.ca	37	15	20445987	20445987	+	RNA	SNP	C	C	T	rs4931804	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	ENSG00000215407,NS,carcinoma,0,1	.	.	.	.	.	CCTCAACGGGGGC		227	8	0.04	202	1	0.004950495			1	2	0	0.00			
.	0	bcgsc.ca	37	15	20453913	20453913	+	RNA	SNP	C	C	T	rs2601516	bycluster;byfrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GGGACACACACCC		169	10	0.06	166	1	0.0060240964				0	0				
.	606	bcgsc.ca	37	15	20867370	20867370	+	RNA	SNP	T	T	C	rs7402675	bycluster;byfrequency;by2hit2allele	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGCACATCATGAA		121	15	0.12	142	0	0				2	0	0.00			
.	606	bcgsc.ca	37	15	20868281	20868281	+	RNA	SNP	T	T	C	rs11248797	bycluster;byfrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCTGTTTCAGAAA		638	46	0.07	627	1	0.0015948963				0	0				
LOC727924	0	bcgsc.ca	37	15	22298230	22298230	+	RNA	SNP	A	A	T	rs8036276	bycluster;byfrequency;by2hit2allele	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATCTCTAAAAAGG		207	9	0.04	192	0	0				0	0				
LOC727924	0	bcgsc.ca	37	15	22298333	22298333	+	RNA	SNP	A	A	T	rs1816290	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTGCATATGTTGT		167	18	0.11	172	0	0				0	0				
.	0	bcgsc.ca	37	15	23500403	23500403	+	RNA	SNP	G	G	A	rs199579714	bycluster	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAGCACGGAAGTG		146	10	0.07	155	0	0				0	0				
.	0	bcgsc.ca	37	15	30297821	30297821	+	RNA	SNP	G	G	C	rs1004818	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGAGATGAGATGC		59	5	0.08	70	0	0				0	0				
C15orf55	256646	hgsc.bcm.edu	37	15	34640735	34640735	+	Silent	SNP	T	T	C	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_175741	exon2	c.T582C	p.T194T	GGCCACTCTATCC		64	4	0.06	72	0	0				15	0	0.00			
.	0	bcgsc.ca	37	15	35385338	35385338	+	RNA	SNP	T	T	C	rs12901760	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGGCGGTGGCCCA		49	7	0.14	47	0	0				4	0	0.00			
.	0	bcgsc.ca	37	15	62654429	62654429	+	RNA	SNP	C	C	T	rs2089322	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGGCTGCGCTTCC		221	14	0.06	211	0	0				2	0	0.00			
CCDC33	80125	ucsc.edu;bcgsc.ca	37	15	74623054	74623054	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	CCDC33	NM_025055	exon13	c.A1507G	p.R503G	AAACTGAGGGACA		33	4	0.12	28	0	0		160		0	0				
.	0	bcgsc.ca	37	15	78187053	78187053	+	RNA	SNP	G	G	C	rs144204249	by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CACCTGGTCGGTC		159	13	0.08	187	0	0				0	0				
.	0	bcgsc.ca	37	15	78272318	78272318	+	RNA	SNP	C	C	G	rs12439777	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCAGGGCCCTCCC		717	70	0.10	759	5	0.0065876153				0	0				
.	0	bcgsc.ca	37	15	79852289	79852289	+	RNA	SNP	A	A	G	rs1685164	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAGCACATTTAAG		88	8	0.09	96	0	0				0	0				
LOC390660	0	bcgsc.ca	37	15	82620272	82620272	+	RNA	SNP	A	A	T	rs141755317	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACTCCCACCTTCC		64	10	0.16	52	0	0				1	0	0.00			
.	0	bcgsc.ca	37	15	84722797	84722798	+	RNA	DNP	TT	TT	GC	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	TT	TT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCAAGCTTTATAA		67	6	0.09	62	0	0				0	0				
.	0	bcgsc.ca	37	16	16463250	16463250	+	RNA	SNP	A	A	G	rs56194511	bycluster	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CACTGCAAAGAGT		83	6	0.07	101	0	0				0	0				
ITPRIPL2	162073	ucsc.edu	37	16	19126254	19126254	+	Silent	SNP	C	C	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	ITPRIPL2	NM_001034841	exon1	c.C471T	p.I157I	CTTCATCCAGGTG		25	3	0.12	39	0	0		40		29	5	0.17			
.	400555	bcgsc.ca	37	16	88620195	88620195	+	Missense_Mutation	SNP	T	T	G	rs2879897	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	C16orf85,NS,carcinoma,0,1	.	.	.	.	.	TACACTTTCCATT		53	5	0.09	85	0	0			1	0	0				
.	400555	bcgsc.ca;mdanderson.org	37	16	88633052	88633052	+	Missense_Mutation	SNP	G	G	C	rs56983565	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AACGCTGGCAGGC		80	7	0.09	93	0	0				0	0				
RAP1GAP2	23108	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	2921439	2921439	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_015085	exon18	c.C1579T	p.L527F	GGCAGCCTCAGCG		79	16	0.20	106	0	0				47	27	0.57			
FLII	2314	bcgsc.ca	37	17	18151320	18151320	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	FLII	NM_002018	exon19	c.C2218A	p.L740M	GTGGCAGCTCCAG		53	5	0.09	69	0	0		79		202	0	0.00			
.	284167	bcgsc.ca	37	17	60214681	60214681	+	RNA	SNP	G	G	A	rs12937135	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTTCTGCTTTCG		80	6	0.08	87	0	0				65	0	0.00			
.	732538	bcgsc.ca	37	17	66091753	66091753	+	RNA	SNP	C	C	T	rs35320230	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCCAGTCGATCTG		129	9	0.07	125	0	0				0	0				
.	0	bcgsc.ca	37	17	74591725	74591725	+	RNA	SNP	T	T	A	rs72867697	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTTAGTTTTCAT		40	5	0.13	47	0	0				0	0				
SMCHD1	23347	ucsc.edu	37	18	2666989	2666989	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	SMCHD1	NM_015295	exon3	c.G383T	p.G128V	AAAGTGGCATGTA		95	2	0.02	124	0	0		88		68	8	0.12	rescued with RNA-seq		
SMCHD1	23347	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	18	2688481	2688483	+	In_Frame_Del	DEL	TCT	TCT	-	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	TCT	TCT					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	SMCHD1	NM_015295	exon6	c.727_729del	p.243_243del	AAGCTGTCTTCTT		89	10	0.11	116	0	0		88		104	0	0.00			
.	100129556	bcgsc.ca	37	18	21252592	21252592	+	RNA	SNP	A	A	G	rs12962228	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GGTTGGACACATT		9	3	0.33	17	0	0				0	0				
AQP4-AS1	0	broad.mit.edu	37	18	24445878	24445878	+	RNA	DEL	T	T	-	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACTTAATTTTTTT		9	3	0.33	5	0	0				0	0				
.	390844	bcgsc.ca	37	18	26232188	26232188	+	RNA	SNP	T	T	G	rs2655356	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCTGCTTGGAGCA		33	4	0.12	55	0	0				0	0				
.	0	bcgsc.ca	37	18	33422218	33422218	+	RNA	SNP	A	A	T	rs61740693	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATGACAAAACAAT		53	9	0.17	51	0	0				0	0				
.	0	bcgsc.ca	37	18	45157181	45157181	+	RNA	SNP	T	T	C	rs3813071	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATTGACTATCTTT		64	8	0.13	93	0	0				1	0	0.00			
.	140623	bcgsc.ca	37	18	72057474	72057474	+	RNA	SNP	A	A	G	rs11553061	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCGACCATTTCCT		20	4	0.20	26	0	0				24	20	0.83			
KCNG2	26251	bcgsc.ca	37	18	77623903	77623903	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	KCNG2	NM_012283	exon1	c.G236T	p.R79L	CCTTCCGCGCCAT		27	4	0.15	26	0	0		48		0	0				
.	0	bcgsc.ca	37	19	22869030	22869030	+	Silent	SNP	G	G	A	rs78524936	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	ENSG00000198153,NS,carcinoma,0,1	.	.	.	.	.	AGAGAAGCCCTAC		415	24	0.06	436	0	0			1	2	0	0.00			
.	0	bcgsc.ca	37	19	22869372	22869372	+	Silent	SNP	C	C	T	rs35689937	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACCCTACAAGTGT		132	8	0.06	154	0	0				3	0	0.00			
.	440519	ucsc.edu;bcgsc.ca	37	19	23405580	23405580	+	Silent	SNP	T	T	C	rs10412126	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	ZNF724P_ENST00000418100,NS,carcinoma,0,2	.	.	.	.	.	TGAGGATAGGTTA		29	4	0.14	25	0	0			2	70	0	0.00			
.	0	bcgsc.ca	37	19	29282028	29282028	+	RNA	SNP	T	T	C	rs7351076	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATGACATGTATAT		27	4	0.15	31	0	0				0	0				
CAPNS1	826	bcgsc.ca	37	19	36640664	36640669	+	In_Frame_Del	DEL	GCTGGT	GCTGGT	-	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	GCTGGT	GCTGGT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	CAPNS1	.	.	.	.	AAAGGGGCTGGTG		102	6	0.06	115	0	0		19		1	0	0.00			
RUVBL2	10856	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	49502588	49502588	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_006666	exon2	c.A25G	p.K9E	ACAACCAAAGTCC		204	34	0.17	206	0	0				384	133	0.35			
.	0	bcgsc.ca	37	19	50222914	50222914	+	RNA	SNP	G	G	A	rs3810261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATGTTCGCCACCT		42	5	0.12	35	0	0				3	1	0.33			
.	10130	bcgsc.ca	37	2	10959407	10959407	+	Missense_Mutation	SNP	A	A	C	rs72779451	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GGGTGCATTAGCC		96	5	0.05	86	0	0				0	0				
.	10130	bcgsc.ca	37	2	10959461	10959461	+	Silent	SNP	G	G	T	rs72779452	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GGAGTGGGCAGGA		70	5	0.07	62	0	0				0	0				
.	10130	bcgsc.ca	37	2	10959475	10959475	+	Missense_Mutation	SNP	G	G	C	rs72779453	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AAGTTGGTGAGCC		66	5	0.08	57	0	0				0	0				
.	0	bcgsc.ca	37	2	38044830	38044830	+	RNA	SNP	C	C	G	rs4670218	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCGAATCCTACAA		51	5	0.10	55	0	0				1	0	0.00			
.	0	bcgsc.ca	37	2	43053772	43053772	+	RNA	SNP	C	C	T	rs13013413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTCTACGTGGAA		72	13	0.18	81	0	0				0	0				
.	0	bcgsc.ca	37	2	58688907	58688907	+	RNA	SNP	G	G	A	rs2075171	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCCTTCGTGCAGC		211	11	0.05	214	1	0.0046728972				153	0	0.00			
.	0	bcgsc.ca	37	2	65432857	65432857	+	RNA	SNP	T	T	C	rs11887325	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AATTTATCAGAAA		263	12	0.05	271	0	0				446	0	0.00			
.	0	bcgsc.ca	37	2	65432952	65432952	+	RNA	SNP	T	T	C	rs35295972	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATCAGTTGGATCC		264	10	0.04	267	0	0				547	0	0.00			
.	0	bcgsc.ca	37	2	81421951	81421951	+	RNA	SNP	A	A	G	rs13430688	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GACTCCACCAGCG		55	9	0.16	58	0	0				0	0				
.	0	bcgsc.ca	37	2	81422135	81422135	+	RNA	SNP	G	G	T	rs6722134	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGTAGGGGTTGGC		71	11	0.15	55	0	0				0	0				
LOC1720	0	bcgsc.ca	37	2	83084350	83084350	+	RNA	SNP	A	A	T	rs11126880	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TAAACTATTTGTC		46	6	0.13	63	0	0				0	0				
.	28902	bcgsc.ca	37	2	90193417	90193417	+	RNA	SNP	A	A	G	rs1724244	bycluster;byfrequency;bysubmitter	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTAATAATTACCC		312	14	0.04	356	1	0.0028089888				0	0				
.	28892	bcgsc.ca;mdanderson.org	37	2	90229260	90229260	+	RNA	SNP	T	T	C	rs842173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGATGATCCAGTC		112	8	0.07	137	0	0				0	0				
.	28904	bcgsc.ca	37	2	90259965	90259965	+	RNA	SNP	T	T	C	rs842156	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GATGTGTCATCTG		216	8	0.04	197	2	0.0101522843				3	0	0.00			
ANKRD20A8P	0	broad.mit.edu	37	2	95490959	95490960	+	RNA	INS	-	-	TGC	rs372560034		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTGTTGTTGCTGC		10	4	0.40	5	0	0				1	0	0.00			
.	649489	bcgsc.ca	37	2	107557712	107557712	+	RNA	SNP	G	G	A	rs12993155	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCACCCGTTATAC		32	4	0.13	37	0	0				0	0				
.	100130549	bcgsc.ca	37	2	129276720	129276720	+	RNA	SNP	T	T	C	rs841094	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACAGCCTGGACAG		221	17	0.08	186	1	0.0053763441				1	1	1.00			
.	284988	bcgsc.ca	37	2	130970911	130970911	+	RNA	SNP	A	A	G	rs12471586	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCCCACAGTGACG		162	17	0.10	154	2	0.012987013				0	0				
.	0	bcgsc.ca	37	2	130987792	130987792	+	RNA	SNP	G	G	A	rs12992461	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATCAGCGTGCTGG		95	6	0.06	80	1	0.0125				14	0	0.00			
.	2777	bcgsc.ca	37	2	132181483	132181483	+	RNA	SNP	G	G	T	rs1059524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TAATTTGGTCACT		65	6	0.09	66	0	0				2	2	1.00			
.	2777	bcgsc.ca	37	2	132182138	132182138	+	RNA	SNP	G	G	T	rs3730150	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATACTTGTATGGG		77	6	0.08	76	0	0				11	0	0.00			
.	2777	bcgsc.ca	37	2	132182159	132182159	+	RNA	SNP	T	T	C	rs3730148	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGAGTCTATGGCT		78	6	0.08	75	0	0				44	41	0.93			
LOC150776	0	broad.mit.edu	37	2	132250656	132250656	+	RNA	SNP	C	C	G	rs2272360	bycluster;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTTTGGCGCGGTG		21	5	0.24	32	0	0				7	0	0.00			
LOC150776	0	bcgsc.ca	37	2	132257830	132257830	+	RNA	SNP	C	C	T	rs13035779	bycluster;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCTAGACGGTGTC		172	11	0.06	197	1	0.0050761421				47	0	0.00			
.	646915	bcgsc.ca	37	2	133075301	133075301	+	RNA	SNP	A	A	G	rs17394868	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCATCTAGGAGAA		126	9	0.07	121	0	0				4	0	0.00			
.	0	bcgsc.ca	37	2	139045855	139045855	+	RNA	SNP	C	C	T	rs35998722	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCTAAGCGAATAG		129	11	0.09	87	0	0				4	0	0.00			
.	0	bcgsc.ca	37	2	139045987	139045987	+	RNA	SNP	C	C	T	rs13033503	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TAGTACCATTTCG		141	8	0.06	126	0	0				1	0	0.00			
.	0	bcgsc.ca	37	2	139065003	139065003	+	RNA	SNP	G	G	C	rs7570952	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GAGAAAGGGTTAT		78	12	0.15	95	0	0				0	0				
.	729399	bcgsc.ca	37	2	200525076	200525076	+	RNA	SNP	A	A	G	rs77443884	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GACATCAAGGGCT		69	6	0.09	70	0	0				0	0				
LOC100507443	1419	bcgsc.ca	37	2	209010891	209010891	+	Missense_Mutation	SNP	G	G	A	rs2289917	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GACTGCGGGAACG		118	13	0.11	116	1	0.0086206897				1	0	0.00			
MFF	56947	hgsc.bcm.edu	37	2	228194321	228194321	+	Splice_Site	SNP	G	G	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTTACAGCTGGAA		129	8	0.06	109	0	0				4	0	0.00			
MFF	56947	bcgsc.ca	37	2	228194480	228194481	+	Missense_Mutation	DNP	AG	AG	TT	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	MFF	NM_020194	exon3	c.G20T	p.S7F	ACAAGCAGTGACA		339	29	0.09	285	2	0.0070175439		48		28	0	0.00			
.	0	bcgsc.ca	37	2	241865211	241865211	+	Missense_Mutation	SNP	G	G	A	rs56199645		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AATGACGCGCTGG		149	9	0.06	165	1	0.0060606061				0	0				
.	0	bcgsc.ca	37	20	6194421	6194421	+	RNA	SNP	A	A	C	rs6076962	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCAGAAAATTTTC		96	13	0.14	91	0	0				17	0	0.00			
.	400836	bcgsc.ca	37	20	10366898	10366898	+	RNA	SNP	T	T	C	rs2223654	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTTCTGTGAAAGA		32	7	0.22	43	0	0				31	0	0.00			
.	400836	bcgsc.ca	37	20	10367323	10367323	+	RNA	SNP	C	C	G	rs6039900	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGTGAACTAAGGA		25	7	0.28	18	0	0				5	0	0.00			
.	400836	bcgsc.ca	37	20	10367909	10367909	+	RNA	SNP	A	A	C	rs6108519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGTCTCAGTGAGG		186	24	0.13	209	1	0.004784689				4	0	0.00			
FRG1B	284802	bcgsc.ca	37	20	29628233	29628233	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	FRG1B	.	.	.	.	GGGAAAATGGCTT		475	14	0.03	536	10	0.0186567164		181		277	0	0.00			
.	391242	bcgsc.ca	37	20	31635384	31635384	+	RNA	SNP	G	G	A	rs743172	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGCAACGGGGAGG		24	5	0.21	36	0	0				0	0				
BAGE	85319	broad.mit.edu	37	21	11058613	11058614	+	RNA	INS	-	-	A	rs377480117	bycluster	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTTTTTTAAAGCA		6	2	0.33	8	0	0				0	0				
.	642460	bcgsc.ca	37	21	14795475	14795475	+	RNA	SNP	G	G	A	rs459504	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTCATCGTCCTAT		126	9	0.07	114	0	0				0	0				
.	378810	bcgsc.ca	37	21	14899553	14899553	+	RNA	SNP	A	A	G	rs2257395	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAGCCCAAGAGCT		28	7	0.25	22	0	0				0	0				
.	100631381	bcgsc.ca	37	21	15384535	15384535	+	RNA	SNP	G	G	C	rs1297100	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CATGATGCGCCTG		26	4	0.15	28	0	0				0	0				
.	391269	bcgsc.ca	37	21	15436681	15436681	+	RNA	SNP	G	G	C	rs11908695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GGGCCAGATGGTC		257	33	0.13	187	1	0.0053475936				2	0	0.00			
.	0	broad.mit.edu	37	21	15461077	15461078	+	RNA	INS	-	-	A	rs200906842	bycluster;alternate_allele	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCTACTTAAAAAA		6	2	0.33	5	0	0				0	0				
.	54019	bcgsc.ca	37	21	20617291	20617291	+	RNA	SNP	G	G	T	rs9980261	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCTACAGACTACC		42	6	0.14	44	0	0				0	0				
.	391276	bcgsc.ca	37	21	30275638	30275638	+	RNA	SNP	C	C	T	rs2248470	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGAAGGCGACGTT		83	7	0.08	45	0	0				0	0				
.	7339	bcgsc.ca	37	21	32434300	32434300	+	RNA	SNP	T	T	C	rs41456545	bycluster	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AACTGCTGTCCTT		105	10	0.10	60	0	0				0	0				
.	7339	bcgsc.ca	37	21	32435334	32435334	+	RNA	SNP	T	T	C	rs11088156	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTGTGTTGTTTAG		42	8	0.19	41	0	0				0	0				
TIAM1	7074	bcgsc.ca	37	21	32638549	32638550	+	Missense_Mutation	DNP	CC	CC	AT	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	TIAM1	NM_003253	exon5	c.G739A	p.G247M	GGCCCCCCGTTTG		193	9	0.05	170	0	0		522		152	0	0.00			
ITSN1	6453	hgsc.bcm.edu;bcgsc.ca	37	21	35144472	35144491	+	Frame_Shift_Del	DEL	GCCCAGCTGGAGCGGGCGGA	GCCCAGCTGGAGCGGGCGGA	-	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	GCCCAGCTGGAGCGGGCGGA	GCCCAGCTGGAGCGGGCGGA					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	ITSN1	NM_001001132	exon12	c.1149_1168del	p.383_390del	CGCCTGGCCCAGC		150	18	0.12	124	0	0		166		62	0	0.00			
ITSN1	6453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	21	35147283	35147283	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_001001132	exon14	c.G1467C	p.K489N	TAAAAAGCATCAA		183	37	0.20	164	0	0				46	5	0.11			
OR11H1	81061	bcgsc.ca;mdanderson.org	37	22	16449050	16449050	+	Missense_Mutation	SNP	G	G	A	rs78804300		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	OR11H1	NM_001005239	exon1	c.C755T	p.A252V	GAGAAGGCCTTAT		309	21	0.07	337	0	0		44		0	0				
CLDN5	7122	mdanderson.org	37	22	19511442	19511442	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_001130861	exon1	c.G592A	p.A198T	CCTTGGCCGGGCC		30	5	0.17	24	0	0				10	0	0.00			
RIMBP3	85376	bcgsc.ca	37	22	20457060	20457060	+	Silent	SNP	C	C	G	rs200551182	bycluster	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	RIMBP3	NM_015672	exon1	c.G4242C	p.V1414V	TCTCTTCACCCCC		307	25	0.08	239	1	0.0041841004		42		5	0	0.00			
RIMBP3	85376	bcgsc.ca;mdanderson.org	37	22	20457204	20457204	+	Silent	SNP	G	G	A	rs364215	bycluster	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	RIMBP3	NM_015672	exon1	c.C4098T	p.G1366G	GCTGGCGCCCAGC		375	23	0.06	289	1	0.0034602076		42		5	0	0.00			
RIMBP3	85376	bcgsc.ca	37	22	20457841	20457841	+	Missense_Mutation	SNP	T	T	C	rs202034782	bycluster;byfrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	RIMBP3	NM_015672	exon1	c.A3461G	p.Q1154R	GGCACCTGTAGCT		837	30	0.04	783	0	0		42		1	0	0.00			
LOC400891	0	bcgsc.ca	37	22	21400282	21400282	+	Missense_Mutation	SNP	G	G	C	rs12170538	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATGAGGGGTTCCT		174	7	0.04	115	1	0.0086956522				0	0				
LOC400891	0	bcgsc.ca;mdanderson.org	37	22	21407656	21407656	+	Missense_Mutation	SNP	T	T	C	rs59837066	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAAACATCTTCCT		149	9	0.06	121	0	0				0	0				
.	0	broad.mit.edu	37	22	22516884	22516884	+	RNA	DEL	C	C	-	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGGCATCAGCAGC		205	10	0.05	188	0	0				26	0	0.00			
.	28785	bcgsc.ca;mdanderson.org	37	22	22516998	22516998	+	RNA	SNP	C	C	T	rs2073453	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCTGACCGCTACC		130	10	0.08	122	0	0				15	0	0.00			
.	28770	bcgsc.ca;mdanderson.org	37	22	22556270	22556270	+	RNA	SNP	T	T	C	rs5995639	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCCCTCTCTGTCT		57	6	0.11	62	0	0				0	0				
.	23751	bcgsc.ca	37	22	22577869	22577869	+	RNA	SNP	A	A	G	rs743515	bycluster;byfrequency;by2hit2allele	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CGGCGGACACCCG		382	28	0.07	304	1	0.0032894737				0	0				
.	28775	bcgsc.ca;mdanderson.org	37	22	22724341	22724341	+	RNA	SNP	A	A	C	rs9607803	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTGGACACCTGCC		101	10	0.10	94	0	0				62	0	0.00			
.	28810	bcgsc.ca	37	22	22922640	22922640	+	RNA	SNP	C	C	G	rs464317	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATGTCGCTAATTG		52	6	0.12	42	0	0				5	0	0.00			
.	641379	bcgsc.ca	37	22	25082586	25082586	+	RNA	SNP	T	T	G	rs5751933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATGCTGTGCTCTA		69	6	0.09	58	0	0				0	0				
.	641379	bcgsc.ca	37	22	25082635	25082635	+	RNA	SNP	C	C	T	rs5760578	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATGTCACGACTTT		79	6	0.08	71	0	0				0	0				
.	0	bcgsc.ca	37	22	41470522	41470522	+	RNA	SNP	G	G	A	rs8136923	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTCGGGGCAGTGG		37	5	0.14	37	0	0				6	0	0.00			
.	0	bcgsc.ca	37	22	47857537	47857537	+	Missense_Mutation	SNP	T	T	C	rs130877	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTCCCTTAGTTGC		188	10	0.05	162	0	0				0	0				
.	0	bcgsc.ca	37	22	47857551	47857551	+	Missense_Mutation	SNP	T	T	G	rs130878	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCTCTGTTCTTGA		193	9	0.05	169	0	0				0	0				
.	0	bcgsc.ca	37	22	47857576	47857576	+	Silent	SNP	A	A	G	rs130879	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTGCAAAACTAA		189	8	0.04	162	0	0				0	0				
.	0	bcgsc.ca	37	22	51193572	51193572	+	RNA	SNP	A	A	G	rs138661035	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCTATTATTGGTG		157	11	0.07	149	0	0				18	0	0.00			
.	0	bcgsc.ca	37	22	51193629	51193629	+	RNA	SNP	A	A	G	rs142680588	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACCTATACGGCAT		236	15	0.06	230	3	0.0130434783				26	0	0.00			
.	0	bcgsc.ca	37	3	14614889	14614889	+	RNA	SNP	T	T	C	rs11707648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCGGGATGGTCAT		30	4	0.13	50	0	0				6	0	0.00			
.	0	bcgsc.ca	37	3	14615601	14615601	+	RNA	SNP	A	A	C	rs9840720	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCACAGAATCGAG		116	9	0.08	109	0	0				1	0	0.00			
.	0	bcgsc.ca	37	3	14615612	14615612	+	RNA	SNP	T	T	C	rs9823227	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGTCCATCGTTTC		105	8	0.08	95	0	0				1	0	0.00			
.	391524	bcgsc.ca	37	3	31496295	31496295	+	RNA	SNP	T	T	G	rs724607	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGAGACTAACTGA		93	8	0.09	134	1	0.0074626866				1	1	1.00			
.	645548	bcgsc.ca	37	3	36809119	36809119	+	RNA	SNP	G	G	A	rs9311135	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACCTTTGGCATAG		96	6	0.06	119	0	0				2	0	0.00			
GOLGA4	2803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	37340359	37340359	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_001172713	exon9	c.C916G	p.L306V	GAAACACTCCAGC		253	50	0.20	285	0	0				134	41	0.31			
ITIH4	3700	hgsc.bcm.edu	37	3	52852482	52852482	+	Silent	SNP	G	G	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_002218	exon18	c.C2148A	p.I716I	ACCTTCGATTTTC		119	5	0.04	96	0	0				26	0	0.00			
.	0	bcgsc.ca	37	3	82855676	82855676	+	RNA	SNP	G	G	A	rs12636791	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATCTTCGTTTGTA		37	7	0.19	35	0	0				0	0				
.	0	bcgsc.ca	37	3	82856698	82856698	+	RNA	SNP	G	G	A	rs6782717	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTTAACGTTTTCT		175	13	0.07	178	1	0.0056179775				0	0				
.	0	bcgsc.ca	37	3	109635659	109635659	+	RNA	SNP	C	C	T	rs605795	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGTGTCCTCTTGA		31	4	0.13	40	0	0				0	0				
.	100130335	bcgsc.ca	37	3	120525556	120525556	+	RNA	SNP	G	G	C	rs115209237	byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACCAAAGAAAGAT		45	6	0.13	47	0	0				4	0	0.00			
.	646085	bcgsc.ca	37	3	161047583	161047583	+	RNA	SNP	T	T	C	rs115806772	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACCTTGTGGCTGA		19	4	0.21	24	0	0				0	0				
.	200958	bcgsc.ca	37	3	195346477	195346477	+	Missense_Mutation	SNP	C	C	T	rs7631117	bycluster;byfrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCCCCACGGAAGG		322	39	0.12	294	1	0.0034013605				2	0	0.00			
.	0	bcgsc.ca;mdanderson.org	37	4	9486098	9486098	+	RNA	SNP	C	C	G	rs114281488	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GGATTTCATCTTC		133	12	0.09	195	0	0				0	0				
.	0	bcgsc.ca	37	4	43900983	43900983	+	RNA	SNP	T	T	C	rs6830030	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGATGTTGTTCCC		62	6	0.10	101	0	0				0	0				
.	0	bcgsc.ca	37	4	43900995	43900995	+	RNA	SNP	A	A	G	rs10019693	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CATAGTATAAGCC		62	6	0.10	105	0	0				0	0				
.	0	bcgsc.ca	37	4	57627276	57627276	+	RNA	SNP	G	G	A	rs6844407	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CATTCAGCTTCAA		84	11	0.13	107	0	0				8	0	0.00			
.	644548	bcgsc.ca	37	4	63682913	63682913	+	RNA	SNP	T	T	C	rs6551720	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGACAATGGGCAG		83	8	0.10	109	0	0				0	0				
.	644548	bcgsc.ca	37	4	63682934	63682934	+	RNA	SNP	C	C	T	rs6551721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAGAAACTGATGA		88	11	0.13	117	0	0				0	0				
.	644548	bcgsc.ca	37	4	63683038	63683038	+	RNA	SNP	C	C	T	rs6852768	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTTGCACCTAATT		153	11	0.07	238	0	0				2	0	0.00			
.	0	bcgsc.ca	37	4	70212704	70212704	+	RNA	SNP	G	G	A	rs6851810	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTTTGAGAGCATT		78	6	0.08	97	1	0.0103092784				0	0				
.	391672	bcgsc.ca	37	4	83323062	83323062	+	RNA	SNP	T	T	C	rs7695741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TAGAAGTTGATGC		99	6	0.06	122	0	0				0	0				
.	100129714	bcgsc.ca	37	4	109710728	109710728	+	RNA	SNP	C	C	T	rs13137797	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TATCTGCGCGGGG		76	9	0.12	107	0	0				1	0	0.00			
.	285412	bcgsc.ca	37	4	113377127	113377127	+	RNA	SNP	G	G	T	rs231266	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGGGCCGTCACAC		41	6	0.15	42	0	0				0	0				
.	285412	bcgsc.ca	37	4	113377710	113377710	+	RNA	SNP	T	T	G	rs231267	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAGAAGTTCCCAA		73	7	0.10	90	0	0				0	0				
.	0	bcgsc.ca	37	4	120315906	120315906	+	RNA	SNP	C	C	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGTTTTCGCTATA		121	13	0.11	172	2	0.011627907				0	0				
.	0	bcgsc.ca	37	4	139402514	139402514	+	RNA	SNP	T	T	C	rs13101897	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTTCATTTGTGGG		24	6	0.25	29	0	0				0	0				
.	0	bcgsc.ca	37	4	189660460	189660460	+	RNA	SNP	G	G	C	rs60608362	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGTAAAGGAAGAT		133	11	0.08	189	1	0.0052910053				45	0	0.00			
.	0	bcgsc.ca	37	5	10664632	10664632	+	RNA	SNP	A	A	G	rs12523340	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGGTCAACTTCAC		110	10	0.09	152	0	0				0	0				
.	0	bcgsc.ca	37	5	10664999	10664999	+	RNA	SNP	C	C	G	rs111384023	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GGGGCCCGTGGCG		86	11	0.13	120	0	0				0	0				
.	0	bcgsc.ca	37	5	97361783	97361783	+	RNA	SNP	G	G	A	rs4355547	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATCATCGAGGTCG		33	4	0.12	69	0	0				0	0				
PCDHB4	56131	ucsc.edu;bcgsc.ca	37	5	140502343	140502344	+	Missense_Mutation	DNP	CC	CC	TT	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	PCDHB4	NM_018938	exon1	c.C764T	p.P255F	AACAGCCCCCTAG		75	8	0.11	125	1	0.008		177		0	0				
FLT4	2324	hgsc.bcm.edu	37	5	180048756	180048756	+	Silent	SNP	G	G	A	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_182925	exon13	c.C1806T	p.H602H	GTTCCCGTGCGCA		73	4	0.05	85	0	0				6	0	0.00			
.	9425	bcgsc.ca	37	6	4735035	4735035	+	Missense_Mutation	SNP	T	T	C	rs13196069	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	CDYL,NS,carcinoma,0,1	.	.	.	.	.	TCTCCGTGAGCAG		79	5	0.06	75	0	0			1	0	0				
.	0	bcgsc.ca	37	6	7517131	7517131	+	RNA	SNP	A	A	T	rs2798162	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATGCAGAAGTGAC		41	6	0.15	56	0	0				1	1	1.00			
DEK	7913	bcgsc.ca	37	6	18264096	18264096	+	Missense_Mutation	SNP	C	C	G	rs147127829	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	DEK	NM_003472	exon2	c.G123C	p.E41D	CTCCTCCTCGTCG		157	8	0.05	130	1	0.0076923077		31		79	0	0.00			
.	0	bcgsc.ca	37	6	23972696	23972696	+	RNA	SNP	G	G	T	rs34725714	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATGTTAGTTTCTT		87	8	0.09	110	0	0				0	0				
.	0	bcgsc.ca	37	6	23972870	23972870	+	RNA	SNP	T	T	A	rs35353646	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGATACTCACAGG		57	5	0.09	57	0	0				3	0	0.00			
ZNF322	79692	bcgsc.ca	37	6	26637724	26637724	+	Missense_Mutation	SNP	T	T	C	rs71557344	bycluster;byfrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_001242797	exon5	c.A1058G	p.Y353C	ACAGTGTATTTAT		465	16	0.03	506	2	0.0039525692				67	0	0.00			
ZKSCAN3	80317	bcgsc.ca	37	6	28331127	28331128	+	Missense_Mutation	DNP	AA	AA	GC	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	AA	AA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	ZKSCAN3,NS,other,-1,1	ZKSCAN3	NM_024493	exon4	c.A599C	p.K200A	GAAGATAAAGTGG		71	5	0.07	88	0	0		50	1	34	0	0.00			
.	729583	bcgsc.ca;mdanderson.org	37	6	28911802	28911802	+	Missense_Mutation	SNP	G	G	A	rs2071790	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCCAGGGAGTAAG		91	10	0.11	120	1	0.0083333333				0	0				
.	352965	bcgsc.ca	37	6	29901899	29901899	+	RNA	SNP	C	C	G	rs2524004	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTAAACCAGGACC		29	7	0.24	21	0	0				0	0				
.	352965	bcgsc.ca	37	6	29901919	29901919	+	RNA	SNP	T	T	C	rs1611304	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTGGACTGCGGCG		33	7	0.21	24	0	0				1	0	0.00			
HLA-C	3107	bcgsc.ca	37	6	31236853	31236854	+	Missense_Mutation	DNP	GT	GT	AC	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	GT	GT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	HLA-C	.	.	.	p.T397V	ATTCAGGTGCCTT		174	17	0.10	176	0	0		92		3197	0	0.00			
HLA-DQA1	3117	bcgsc.ca	37	6	32610008	32610009	+	Missense_Mutation	DNP	CC	CC	TG	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	HLA-DQA1	NM_002122	exon3	c.C592G	p.Q198E	CCTGGACCAGCCT		468	15	0.03	511	0	0		52		669	0	0.00			
.	642443	bcgsc.ca	37	6	66546941	66546941	+	RNA	SNP	A	A	G	rs61732140	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTGGACATATATT		234	13	0.06	267	0	0				8	0	0.00			
.	642443	bcgsc.ca	37	6	66547178	66547178	+	RNA	SNP	G	G	A	rs4392709	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCAGTCGTCTCAA		139	6	0.04	181	1	0.0055248619				0	0				
.	89761	bcgsc.ca	37	6	66803535	66803535	+	RNA	SNP	C	C	A	rs2881644	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCAAAACTTTTCT		123	11	0.09	162	0	0				1	0	0.00			
.	0	bcgsc.ca	37	6	80775738	80775738	+	RNA	SNP	C	C	G	rs3812151	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACATCTCCTGGGG		106	7	0.07	89	0	0				56	0	0.00			
.	0	bcgsc.ca	37	6	85996401	85996401	+	RNA	SNP	C	C	T	rs313229	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGCAAGCAGTGTG		224	12	0.05	222	0	0				8	0	0.00			
.	442237	bcgsc.ca	37	6	97096688	97096688	+	RNA	SNP	T	T	C	rs11759390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCCCACTGAACTT		148	14	0.09	133	0	0				0	0				
MICAL1	64780	bcgsc.ca	37	6	109767930	109767931	+	Missense_Mutation	DNP	GC	GC	TT	rs35260632		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	GC	GC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	MICAL1	NM_022765	exon18	c.G2272A	p.A777K	CCTTCCGCTTTGT		187	8	0.04	230	0	0		79		457	0	0.00			
.	0	bcgsc.ca	37	6	111244963	111244963	+	RNA	SNP	A	A	G	rs781496	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GAGTGAAGATGAA		49	5	0.10	55	0	0				0	0				
.	0	bcgsc.ca	37	6	111245074	111245074	+	RNA	SNP	T	T	C	rs781495	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTGGATGGGCCA		70	6	0.09	85	0	0				0	0				
.	387074	bcgsc.ca;mdanderson.org	37	6	137295352	137295352	+	RNA	SNP	C	C	T	rs2876354	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCCAGACGTATTT		51	7	0.14	54	0	0				0	0				
.	391040	bcgsc.ca	37	6	137865140	137865140	+	RNA	SNP	A	A	G	rs9484059	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCCAAGACTTGCC		84	7	0.08	87	1	0.0114942529				3	0	0.00			
.	153932	bcgsc.ca	37	6	158658857	158658857	+	RNA	SNP	A	A	C	rs112542076	byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGGCAAATGTTTA		47	4	0.09	45	0	0				3	0	0.00			
.	153932	bcgsc.ca	37	6	158658937	158658937	+	RNA	SNP	T	T	C	rs7753292	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TATCTTTTGGATT		66	5	0.08	60	0	0				2	0	0.00			
.	2789	bcgsc.ca	37	6	166653792	166653792	+	RNA	SNP	A	A	C	rs6931334	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGGAATAGAATTT		49	11	0.22	56	0	0				0	0				
.	0	bcgsc.ca;mdanderson.org	37	7	1733102	1733102	+	Missense_Mutation	SNP	G	G	T	rs4720922	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CACCCAGACAGGT		241	24	0.10	191	0	0				0	0				
.	0	bcgsc.ca	37	7	9767725	9767725	+	RNA	SNP	G	G	T	rs72583761	bycluster	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GGTTCCGGCTGAC		219	18	0.08	168	0	0				2	0	0.00			
.	0	bcgsc.ca	37	7	9767811	9767811	+	RNA	SNP	T	T	G	rs112406696	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCTTTTTGGTGGG		134	11	0.08	126	0	0				2	0	0.00			
.	0	bcgsc.ca	37	7	23603318	23603318	+	RNA	SNP	A	A	G	rs227944	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTCCAAAATAGAT		401	18	0.04	310	2	0.0064516129				2	0	0.00			
LOC646762	0	bcgsc.ca	37	7	29700039	29700039	+	RNA	SNP	C	C	T	rs1728603	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTAAAACGCTTCC		184	20	0.11	142	0	0				1	0	0.00			
.	653175	bcgsc.ca	37	7	53255471	53255471	+	RNA	SNP	A	A	G	rs6943510	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AAGCAGATACGAA		265	26	0.10	232	0	0				0	0				
.	653175	bcgsc.ca	37	7	53256265	53256265	+	RNA	SNP	G	G	A	rs11972016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTTGTCGCAGTCA		249	18	0.07	280	0	0				18	0	0.00			
.	653175	bcgsc.ca	37	7	53256324	53256324	+	RNA	SNP	T	T	C	rs35856447	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAAAGATGGGAAC		234	12	0.05	241	0	0				15	0	0.00			
.	804	bcgsc.ca	37	7	55327599	55327599	+	RNA	SNP	A	A	G	rs7787331	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCATCTATTAGTT		40	7	0.18	44	0	0				0	0				
.	360132	bcgsc.ca	37	7	55774888	55774888	+	RNA	SNP	C	C	T	rs12666519	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAGAAGCGTGCCA		338	22	0.07	302	0	0				2	0	0.00			
.	100128459	bcgsc.ca	37	7	56296553	56296553	+	RNA	SNP	G	G	T	rs10235373	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTTGGTGGTTCTG		78	10	0.13	62	0	0				0	0				
.	100128459	bcgsc.ca	37	7	56296598	56296598	+	RNA	SNP	A	A	G	rs1640564	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTGTCTAATGGAG		72	7	0.10	81	0	0				0	0				
.	100128459	bcgsc.ca	37	7	56296728	56296728	+	RNA	SNP	A	A	G	rs1640565	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATTATCATGAGCG		89	6	0.07	78	0	0				0	0				
.	100128459	bcgsc.ca	37	7	56296746	56296746	+	RNA	SNP	T	T	C	rs1621849	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TAGCTGTTCAATA		90	6	0.07	85	0	0				0	0				
.	100128459	bcgsc.ca	37	7	56296924	56296924	+	RNA	SNP	C	C	T	rs1622932	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTGCACATTTGG		64	11	0.17	59	0	0				1	0	0.00			
.	100128459	bcgsc.ca	37	7	56296984	56296984	+	RNA	SNP	C	C	T	rs1640566	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGAAGACCTGTTT		92	6	0.07	88	0	0				0	0				
.	100128459	bcgsc.ca	37	7	56297387	56297387	+	RNA	SNP	C	C	T	rs1640567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCTTTACAGGAGG		39	5	0.13	29	0	0				1	0	0.00			
LOC649395	0	bcgsc.ca	37	7	63894558	63894558	+	RNA	SNP	A	A	C	rs73125103	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTGGACAAAAACC		198	21	0.11	199	0	0				11	0	0.00			
.	0	bcgsc.ca	37	7	64030116	64030116	+	RNA	SNP	C	C	T	rs1446886	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGTAGGCGGCCCG		48	7	0.15	37	0	0				1	0	0.00			
LOC493754	0	bcgsc.ca	37	7	66038472	66038472	+	RNA	SNP	G	G	A	rs13240501	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GAGAATGTGAGGG		168	14	0.08	136	0	0				203	0	0.00			
.	641808	bcgsc.ca	37	7	76728248	76728248	+	RNA	SNP	C	C	T	rs75210105	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCATCTCGCTTTG		214	14	0.07	151	0	0				0	0				
ZNF804B	219578	bcgsc.ca	37	7	88964226	88964227	+	Missense_Mutation	DNP	CC	CC	AG	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	ZNF804B,NS,carcinoma,0,1	ZNF804B	NM_181646	exon4	c.C1931G	p.P644S	TGCAGTCCTCATT		186	7	0.04	173	0	0		322	1	0	0				
DLX6-AS1	285987	hgsc.bcm.edu	37	7	96637151	96637151	+	RNA	SNP	C	C	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TAATTCCCGAGAA		47	9	0.19	55	0	0				0	0				
AZGP1P1	0	broad.mit.edu	37	7	99581179	99581179	+	RNA	DEL	C	C	-	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATCCCACCCCCCC		6	2	0.33	7	0	0				0	0				
.	100130972	bcgsc.ca	37	7	139992942	139992942	+	RNA	SNP	A	A	G	rs12703712	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAATTTAAAATGA		57	6	0.11	33	0	0				0	0				
.	0	bcgsc.ca	37	7	154989982	154989982	+	Missense_Mutation	SNP	G	G	A	rs28664023	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CACCCCGAATCAC		208	11	0.05	188	1	0.0053191489				0	0				
.	0	bcgsc.ca	37	8	13880562	13880562	+	RNA	SNP	G	G	T	rs7003822	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ACGTAAGACAATC		187	13	0.07	192	0	0				0	0				
.	0	bcgsc.ca	37	8	70042263	70042263	+	RNA	SNP	A	A	G	rs67905920	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCGTGCAGAGATG		55	6	0.11	48	0	0				3	1	0.33			
.	0	bcgsc.ca	37	8	123781617	123781617	+	RNA	SNP	G	G	A	rs8192652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	ATGGGTGAGGCTG		22	6	0.27	23	0	0				0	0				
.	0	bcgsc.ca	37	8	123782133	123782133	+	RNA	SNP	C	C	T	rs6992158	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAATGACGTCGAT		46	8	0.17	48	0	0				0	0				
.	0	bcgsc.ca	37	8	143719983	143719983	+	RNA	SNP	G	G	C	rs2280881	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CATGACGCCAGTG		177	9	0.05	157	1	0.0063694268				0	0				
.	100132467	bcgsc.ca	37	9	6669375	6669375	+	RNA	SNP	C	C	G	rs2297556	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TTGCTGCATTGTT		56	4	0.07	66	0	0				1	0	0.00			
.	0	bcgsc.ca	37	9	7477728	7477728	+	RNA	SNP	T	T	C	rs12683102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CGACGGTTTCTCA		49	4	0.08	62	0	0				877	1	0.00			
.	392298	bcgsc.ca	37	9	27608549	27608549	+	RNA	SNP	G	G	A	rs142836655	by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTCATTGCAAATG		59	7	0.12	75	0	0				0	0				
.	441391	bcgsc.ca	37	9	30689910	30689911	+	RNA	DNP	CA	CA	TG	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CGTGATCATGACT		110	9	0.08	146	0	0				0	0				
.	0	bcgsc.ca	37	9	35147963	35147963	+	RNA	SNP	C	C	T	rs79434358		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GAGAACCGGCTAA		452	25	0.06	657	2	0.00304414				0	0				
.	0	bcgsc.ca	37	9	35147983	35147983	+	RNA	SNP	T	T	C	rs75970816		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GCTACATACTTCA		455	23	0.05	668	1	0.001497006				0	0				
.	0	bcgsc.ca	37	9	35148203	35148203	+	RNA	SNP	C	C	G	rs10972348	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTAGTACTGAGGA		70	7	0.10	142	0	0				0	0				
FAM74A3	728495	bcgsc.ca;mdanderson.org	37	9	40716224	40716224	+	RNA	SNP	C	C	A	rs56989493	bycluster;byfrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	FAM74A3	.	.	.	.	CTGCTGCACTTGG		260	17	0.07	291	0	0		17		0	0				
.	100287333	bcgsc.ca	37	9	44998898	44998898	+	RNA	SNP	C	C	T	rs9411886	bycluster	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGAAACCGCTTGT		259	13	0.05	244	0	0				3	0	0.00			
.	0	bcgsc.ca	37	9	76264026	76264026	+	RNA	SNP	C	C	T	rs62540675	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AAGGGCCTGGAGA		39	5	0.13	31	0	0				0	0				
LOC286238	0	bcgsc.ca	37	9	91262387	91262387	+	RNA	SNP	G	G	A	rs28550932	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_001100111	exon2	c.C256T	p.R86W	TGTCCCGTGTCTG		92	7	0.08	101	0	0				0	0				
AUH	549	bcgsc.ca	37	9	94060353	94060353	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	AUH	NM_001698	exon5	c.C511A	p.L171I	CTGGAAGATTAGC		78	5	0.06	91	0	0		32		80	0	0.00			
.	414319	bcgsc.ca;mdanderson.org	37	9	105405434	105405434	+	RNA	SNP	T	T	C	rs10990214	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AACAACTCCATCT		60	8	0.13	51	0	0				0	0				
LAMC3	10319	bcgsc.ca	37	9	133901819	133901820	+	Missense_Mutation	DNP	CC	CC	AG	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	LAMC3	NM_006059	exon2	c.C522G	p.P174Q	GCCGGCCCGAGGG		163	9	0.06	193	0	0		167		12	0	0.00			
.	0	bcgsc.ca	37	9	138340462	138340462	+	RNA	SNP	A	A	G	rs10732637	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GAAGGGATAGATC		25	5	0.20	43	0	0				0	0				
LOC389906	0	bcgsc.ca	37	X	3736489	3736489	+	Missense_Mutation	SNP	C	C	T	rs1133336	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAACAGCGTATAA		103	8	0.08	96	1	0.0104166667				119	0	0.00			
.	10064	bcgsc.ca	37	X	49397627	49397627	+	RNA	SNP	T	T	C	rs7891756	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CATTTTTCCCCCC		34	7	0.21	40	0	0				0	0				
.	0	bcgsc.ca	37	X	61999396	61999396	+	RNA	SNP	A	A	C	rs60576970	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AGAGGGAATAATT		33	4	0.12	29	0	0				1	0	0.00			
.	0	bcgsc.ca	37	X	65176531	65176531	+	RNA	SNP	T	T	C	rs199968155		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	AACTGGTCCTGAA		282	9	0.03	211	1	0.0047393365				37	0	0.00			
.	0	bcgsc.ca	37	X	65176539	65176539	+	RNA	SNP	G	G	C	rs112831485	byfrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTGAAGGTGCAGA		291	9	0.03	208	0	0				27	0	0.00			
BCYRN1	618	hgsc.bcm.edu	37	X	70617455	70617455	+	RNA	SNP	C	C	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAACTTCCAGAGT		42	7	0.17	34	0	0				0	0				
.	728748	bcgsc.ca	37	X	73617109	73617109	+	RNA	SNP	C	C	T	rs34974916	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTATACGTGTCA		55	10	0.18	50	0	0				0	0				
.	347363	bcgsc.ca	37	X	78580025	78580025	+	RNA	SNP	A	A	C	rs115569657	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GAACAAACCTGTT		31	4	0.13	31	0	0				0	0				
.	642546	bcgsc.ca	37	X	79827607	79827607	+	RNA	SNP	A	A	G	rs1828209	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CACAGCAGCCATG		56	7	0.13	33	0	0				0	0				
.	254700	bcgsc.ca	37	X	89367831	89367831	+	RNA	SNP	C	C	T	rs111832781	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GTCGTCCGTTTCG		34	4	0.12	43	0	0				1	0	0.00			
.	0	bcgsc.ca	37	X	100212432	100212432	+	RNA	SNP	C	C	G	rs12842818	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGAGGCCTCTCGC		95	12	0.13	74	0	0				0	0				
.	84443	broad.mit.edu	37	X	106846478	106846480	+	In_Frame_Del	DEL	CAG	CAG	-	rs201186557	alternate_allele	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CAG	CAG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CAACAACAGCAGC		127	0	0.00	132	0	0				0	0				
.	642812	bcgsc.ca	37	X	115239568	115239568	+	RNA	SNP	G	G	A	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCCTTAGTACCAC		41	6	0.15	43	0	0				0	0				
.	286423	bcgsc.ca	37	X	122250996	122250996	+	Missense_Mutation	SNP	G	G	T	rs6648942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	GAGTATGTGGCCT		237	19	0.08	159	2	0.0125786164				0	0				
.	0	bcgsc.ca	37	X	134807372	134807372	+	RNA	SNP	A	A	G	rs7890081	bycluster;by2hit2allele;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTTCTCAAGTTGC		121	24	0.20	104	0	0				0	0				
.	0	bcgsc.ca	37	X	134814932	134814932	+	RNA	SNP	G	G	T	rs111943338	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TGGAACGTTTCTG		206	22	0.11	182	0	0				0	0				
.	0	bcgsc.ca	37	X	145701530	145701530	+	RNA	SNP	T	T	G	rs17273448	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTCCCTCTCGAT		44	8	0.18	38	0	0				3	3	1.00			
.	0	bcgsc.ca	37	X	145701579	145701579	+	RNA	SNP	C	C	T	rs112188715	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CTGCTGCCTGAAC		63	11	0.17	44	0	0				132	0	0.00			
.	0	bcgsc.ca	37	X	147279972	147279972	+	RNA	SNP	T	T	C	rs142596624	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCTGGATACTTAA		37	5	0.14	31	0	0				0	0				
.	0	bcgsc.ca;mdanderson.org	37	X	152751497	152751497	+	Missense_Mutation	SNP	G	G	A	rs56165949	bycluster;by1000genomes	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	TCCCACGCGGCCT		49	7	0.14	53	0	0				0	0				
TAZ	6901	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	153648387	153648387	+	Silent	SNP	T	T	C	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	NM_000116	exon8	c.T600C	p.I200I	CCTGATTGCTGAG		223	22	0.10	149	0	0				38	3	0.08			
.	286544	bcgsc.ca	37	Y	14107272	14107272	+	RNA	SNP	C	C	T	novel		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	.	.	.	.	.	.	CCATGGCGGGCCA		82	16	0.20	103	0	0				2	0	0.00			
