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
PIK3CD	5293	hgsc.bcm.edu;bcgsc.ca	37	1	9779982	9779982	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	NM_005026	exon10	c.T1246C	p.C416R	CAGGACTGCCCCA		118	11	0.09	140	0	0				35	12	0.34			
.	0	bcgsc.ca	37	1	13171989	13171989	+	RNA	SNP	G	G	A	rs201114138		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TTGGCCGCTCACG		124	10	0.08	110	0	0				0	0				
PRAMEF19	391003	bcgsc.ca;mdanderson.org	37	1	13474974	13474974	+	Silent	SNP	G	G	A	rs4462137	bycluster	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	PRAMEF19	NM_001099790	exon3	c.C1155T	p.H385H	ATTGCCGTGAAAG		670	24	0.04	700	0	0		6		0	0				
TMEM51-AS1	200197	hgsc.bcm.edu	37	1	15439098	15439098	+	RNA	SNP	C	C	T	rs114844404	bycluster	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TTTTCTCCTCCCG		75	27	0.36	72	0	0				9	0	0.00			
FAM46B	115572	bcgsc.ca	37	1	27332465	27332466	+	Missense_Mutation	DNP	GT	GT	AC	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	GT	GT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	FAM46B	NM_052943	exon2	c.A1247G	p.H416R	ATAGGCGTGAGCC		218	9	0.04	226	0	0		44		582	0	0.00			
.	440585	broad.mit.edu;ucsc.edu	37	1	43610910	43610910	+	Translation_Start_Site	SNP	T	T	G	rs626842	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GGGCCATTGACAG		44	9	0.20	60	0	0				0	0				
BTBD19	149478	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	45275921	45275921	+	Silent	SNP	G	G	A	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	NM_001136537	exon2	c.G123A	p.E41E	GCAGGAGGTATTT		62	6	0.10	57	0	0				0	0				
JAK1	3716	hgsc.bcm.edu	37	1	65330611	65330611	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.,1	JAK1	NM_002227	exon8	c.1036delC	p.L346fs	TTCCAGTTTTTTC		141	10	0.07	146	0	0		209		38	0	0.00			
.	0	bcgsc.ca	37	1	79215138	79215138	+	RNA	SNP	G	G	T	rs12135932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GCAAAGGCCCGAT		44	6	0.14	48	0	0				1	0	0.00			
.	729779	bcgsc.ca	37	1	79520923	79520923	+	RNA	SNP	T	T	C	rs17131734	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GAGATTTGATGGA		59	6	0.10	31	0	0				0	0				
.	0	bcgsc.ca	37	1	157679691	157679691	+	RNA	SNP	C	C	T	rs17676303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TGATGCCTGGGCT		163	15	0.09	181	0	0				45	0	0.00			
.	0	bcgsc.ca	37	1	157679783	157679783	+	RNA	SNP	A	A	G	rs17727309	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GTGCCCAACCTGG		171	11	0.06	195	0	0				6	1	0.17			
.	0	bcgsc.ca	37	1	157680114	157680114	+	RNA	SNP	T	T	C	rs17727339	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GATCATTGCAAAC		60	6	0.10	65	0	0				85	85	1.00			
.	0	bcgsc.ca	37	1	158493554	158493554	+	RNA	SNP	A	A	G	rs6656837	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GATGTCACTGATC		58	5	0.09	49	0	0				0	0				
.	0	bcgsc.ca	37	1	160865612	160865612	+	RNA	SNP	A	A	C	rs112211905	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GTTCCAATCTCCA		136	11	0.08	141	0	0				196	0	0.00			
.	646891	bcgsc.ca	37	1	175013936	175013936	+	RNA	SNP	T	T	A	rs3737935	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CACCACTGTCAGG		92	6	0.07	82	0	0				0	0				
.	0	bcgsc.ca	37	1	240136251	240136251	+	RNA	SNP	C	C	G	rs4659558	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CACTGGCCGACTG		28	4	0.14	27	0	0				0	0				
C10orf105	414152	ucsc.edu	37	10	73497499	73497499	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	C10orf105	.	.	.	.	CCAGCCGCAGTGG		45	4	0.09	48	0	0		11		0	0				
PAPSS2	9060	bcgsc.ca	37	10	89473069	89473069	+	Splice_Site	SNP	T	T	A	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	PAPSS2,NS,lymphoid_neoplasm,0,2	PAPSS2	NM_004670	exon3	c.381+2T>A	.	CAAAGGTAAAAAA		88	19	0.22	90	8	0.0888888889		46	2	0	0				
PIK3C2A	5286	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	17170258	17170258	+	Silent	SNP	G	G	A	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	NM_002645	exon4	c.C1404T	p.G468G	ATAGCTGCCAACA		77	8	0.10	59	0	0				6	1	0.17			
.	0	bcgsc.ca	37	11	49329521	49329521	+	RNA	SNP	T	T	C	rs1164671	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TGGTCATAAGTCA		119	5	0.04	132	0	0				0	0				
.	0	broad.mit.edu	37	11	96514998	96514999	+	RNA	INS	-	-	A	rs149392521	bycluster;alternate_allele	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	AGTTATTAAAAAA		9	3	0.33	11	0	0				1	0	0.00			
.	387815	bcgsc.ca	37	11	124086175	124086175	+	RNA	SNP	T	T	C	rs2508890	bycluster;byfrequency;by2hit2allele	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	AGCCTTTAGCACT		79	6	0.08	90	0	0				2	0	0.00			
SCNN1A	6337	bcgsc.ca	37	12	6472752	6472753	+	Missense_Mutation	DNP	GC	GC	AA	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	GC	GC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	SCNN1A	NM_001159576	exon2	c.G717T	p.R240W	TCCCCCGCAGGTC		81	8	0.10	33	0	0		54		3	0	0.00			
.	283463	bcgsc.ca;mdanderson.org	37	12	40834376	40834376	+	Missense_Mutation	SNP	C	C	G	rs10878592	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TTCCAGCGTCTGT		351	27	0.08	319	0	0				0	0				
.	283463	bcgsc.ca	37	12	40835734	40835734	+	Missense_Mutation	SNP	C	C	G	rs7966110	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CCACATCTATGGG		193	10	0.05	171	0	0				0	0				
.	283463	bcgsc.ca	37	12	40951596	40951596	+	Silent	SNP	A	A	G	rs3751167	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TTTTCCACTTTTC		134	10	0.07	129	0	0				0	0				
.	283463	bcgsc.ca	37	12	40951605	40951605	+	Silent	SNP	G	G	A	rs3751168	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TTTCTTGATTTGC		137	10	0.07	140	0	0				0	0				
.	0	bcgsc.ca	37	12	43965108	43965108	+	RNA	SNP	T	T	A	rs11611126	bycluster;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CTCCAATACAGTT		126	7	0.06	84	0	0				0	0				
.	144453	bcgsc.ca	37	12	70037520	70037520	+	Missense_Mutation	SNP	G	G	A	rs61747221	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GGGAGTGGGATTT		167	7	0.04	137	0	0				0	0				
HSP90B1	7184	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	104336993	104336993	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	NM_003299	exon13	c.G1786C	p.V596L	GAAGGAGTGAAGT		97	11	0.11	80	0	0				2786	635	0.23			
VPS33A	65082	bcgsc.ca	37	12	122723203	122723203	+	Silent	SNP	G	G	A	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	VPS33A	NM_022916	exon10	c.C1233T	p.C411C	TTGGAGGCAAACT		154	7	0.05	119	0	0		61		177	0	0.00			
.	374491	bcgsc.ca	37	13	25144717	25144717	+	RNA	SNP	C	C	A	rs3742168	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CACAGCCCCTGCT		127	6	0.05	105	1	0.0095238095				0	0				
.	81993	bcgsc.ca	37	13	47065127	47065127	+	RNA	SNP	G	G	A	rs200135094		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GCTGAAGCCCTGC		203	9	0.04	228	0	0				1	0	0.00			
.	440142	bcgsc.ca	37	13	60849048	60849048	+	RNA	SNP	C	C	T	rs9528094	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GAAATCCAGTGTC		40	4	0.10	46	0	0				0	0				
.	0	broad.mit.edu	37	14	19114215	19114215	+	RNA	DEL	T	T	-	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CTCAAGTTGAACT		7	3	0.43	5	0	0				0	0				
.	0	bcgsc.ca	37	14	45329860	45329860	+	RNA	SNP	C	C	T	rs17115657	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CATATGCTAATGG		169	7	0.04	138	0	0				0	0				
.	0	bcgsc.ca	37	14	45329930	45329930	+	RNA	SNP	A	A	G	rs8016855	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GTCCACATAAACA		157	12	0.08	113	0	0				0	0				
.	0	bcgsc.ca	37	14	45330315	45330315	+	RNA	SNP	A	A	G	rs17633092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TTCGCCATACCAA		394	14	0.04	323	0	0				0	0				
.	0	bcgsc.ca	37	14	45330929	45330929	+	RNA	SNP	T	T	C	rs11846198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GCTACATTGGAGA		73	5	0.07	53	0	0				0	0				
.	0	bcgsc.ca	37	14	45331397	45331397	+	RNA	SNP	T	T	C	rs12323568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TTCAGATTGTCCA		270	11	0.04	198	0	0				0	0				
.	0	bcgsc.ca	37	14	45331633	45331633	+	RNA	SNP	T	T	G	rs12323575	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TAAGATTCTGAAG		323	14	0.04	256	0	0				0	0				
.	0	bcgsc.ca	37	14	45332387	45332387	+	RNA	SNP	C	C	G	rs7161626	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GAAGTACACCAAA		270	10	0.04	182	0	0				0	0				
.	0	bcgsc.ca	37	14	45332752	45332752	+	RNA	SNP	G	G	A	rs74700367	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GCCTTGGGAAATC		155	8	0.05	119	0	0				0	0				
.	0	bcgsc.ca	37	14	45334503	45334503	+	RNA	SNP	C	C	A	rs8014660	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TTACATCAAATAA		146	6	0.04	113	0	0				0	0				
.	28429	bcgsc.ca	37	14	106866565	106866565	+	RNA	SNP	C	C	A	rs58308167	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CTCCAGCCCCTTC		162	8	0.05	124	0	0				7	0	0.00			
.	28429	bcgsc.ca	37	14	106866588	106866588	+	RNA	SNP	T	T	C	rs73379082	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GGCGGATCCAGCT		144	8	0.06	122	0	0				1	0	0.00			
DNM1P46	196968	hgsc.bcm.edu	37	15	100331823	100331823	+	RNA	SNP	G	G	C	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	ENSG00000214394,NS,haematopoietic_neoplasm,-2,1	ENSG00000214394	.	.	.	.	CCAGAGGACCTGG		30	3	0.10	12	1	0.0833333333		-2	1	0	0				
RHBDF1	64285	ucsc.edu	37	16	108653	108653	+	Silent	SNP	G	G	A	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	RHBDF1	NM_022450	exon18	c.C2254T	p.L752L	CAGCCAGCAGCTT		53	5	0.09	51	0	0		54		22	6	0.27			
LUC7L	55692	bcgsc.ca	37	16	239209	239209	+	Silent	SNP	G	G	A	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	LUC7L	NM_201412	exon10	c.C1104T	p.A368A	CTCGCCGGCCTCC		66	5	0.08	43	0	0		46		218	1	0.00			
HERC2P4	0	broad.mit.edu;bcgsc.ca	37	16	32163525	32163525	+	RNA	SNP	G	G	A	rs461744	bycluster;byfrequency;by2hit2allele	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	AGTCACGGTGCCT		102	9	0.09	98	0	0				4	0	0.00			
.	0	bcgsc.ca	37	16	32617196	32617196	+	RNA	SNP	G	G	A	rs28503299	bycluster;byfrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TATAGAGGAAGGT		50	6	0.12	41	0	0				0	0				
CCDC102A	92922	ucsc.edu	37	16	57550226	57550226	+	Silent	SNP	C	C	T	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	CCDC102A	NM_033212	exon7	c.G1398A	p.E466E	GGCCAGCTCCTTC		27	2	0.07	34	0	0		22		57	15	0.26			
.	0	broad.mit.edu	37	17	20459719	20459719	+	RNA	DEL	A	A	-	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	ATATATATATATA		50	9	0.18	92	1	0.0108695652				0	0				
.	0	bcgsc.ca	37	17	44344738	44344749	+	RNA	DEL	GCTGGTGACCCT	GCTGGTGACCCT	-	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	GCTGGTGACCCT	GCTGGTGACCCT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CATCTGGCTGGTG		117	4	0.03	119	0	0				7	0	0.00			
.	0	bcgsc.ca	37	17	44344810	44344810	+	RNA	SNP	T	T	G	rs2732649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CCGACGTCTTCTT		169	8	0.05	149	0	0				2	0	0.00			
.	0	bcgsc.ca	37	17	44344822	44344822	+	RNA	SNP	G	G	A	rs76934998	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TCTTCCGAGTCCA		180	8	0.04	155	0	0				3	0	0.00			
.	0	bcgsc.ca	37	17	44344858	44344858	+	RNA	SNP	A	A	G	rs74358353	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GCTGCAATAAACC		156	9	0.06	145	0	0				4	0	0.00			
.	0	bcgsc.ca	37	17	60361652	60361652	+	RNA	SNP	C	C	G	rs139504127	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GTTGGACTAGAAG		235	15	0.06	228	0	0				0	0				
ANAPC11	51529	bcgsc.ca	37	17	79857807	79857807	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	ANAPC11	NM_001002244	exon4	c.G422T	p.R141L	GTGCCCGGCGACG		57	4	0.07	49	0	0		1		621	1	0.00			
NPC1	4864	hgsc.bcm.edu;bcgsc.ca	37	18	21134853	21134853	+	Silent	SNP	C	C	T	rs367900403		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	NM_000271	exon9	c.G1422A	p.P474P	GTTATACGGTGAA		139	6	0.04	178	0	0				17	0	0.00			
AZU1	566	broad.mit.edu	37	19	827874	827874	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	AZU1	NM_001700	exon1	c.28delC	p.L10fs	GCCCTGCTGGCTG		6	3	0.50	11	0	0		31		0	0				
PSPN	5623	broad.mit.edu	37	19	6375401	6375401	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	PSPN	NM_004158	exon2	c.G375T	p.R125R	AGTGGGCCGGCAG		20	6	0.30	14	1	0.0714285714		5		0	0				
.	126037	bcgsc.ca	37	19	14181974	14181974	+	RNA	SNP	T	T	A	rs13346822	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GGGGACTTACTTG		74	6	0.08	59	0	0				2	2	1.00			
BIRC8	112401	bcgsc.ca	37	19	53792954	53792955	+	Missense_Mutation	DNP	GC	GC	AT	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	GC	GC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	BIRC8	NM_033341	exon1	c.G673A	p.A225M	ATAACCGCGCTGC		155	8	0.05	125	0	0		54		0	0				
ZNF525	170958	broad.mit.edu	37	19	53879109	53879109	+	Silent	SNP	G	G	A	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	ZNF525	.	.	.	.	ATACAGGGACGTG		62	5	0.08	37	0	0		35		13	0	0.00			
.	0	bcgsc.ca	37	2	58688907	58688907	+	RNA	SNP	G	G	A	rs2075171	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TCCTTCGTGCAGC		142	6	0.04	166	2	0.0120481928				123	0	0.00			
PLGLA	0	broad.mit.edu	37	2	107007467	107007467	+	RNA	SNP	G	G	A	rs7575679	bycluster;byfrequency;byhapmap	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CTCCCCGCAGACC		61	6	0.10	61	0	0				0	0				
.	401018	bcgsc.ca	37	2	168570749	168570749	+	RNA	SNP	G	G	A	rs12987185	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TGTCCTGGTGGAG		130	7	0.05	151	1	0.0066225166				0	0				
MFF	56947	bcgsc.ca	37	2	228194480	228194481	+	Missense_Mutation	DNP	AG	AG	TT	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	MFF	NM_020194	exon3	c.G20T	p.S7F	ACAAGCAGTGACA		216	7	0.03	228	0	0		48		6	0	0.00			
.	339766	bcgsc.ca	37	2	234717839	234717839	+	Missense_Mutation	SNP	C	C	A	rs188948269	bycluster;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TGGCCTCCTACTG		137	7	0.05	129	0	0				0	0				
.	100037280	bcgsc.ca	37	20	5273253	5273253	+	RNA	SNP	G	G	A	rs7271296	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	ATTTGGGTGATAA		145	7	0.05	122	0	0				6	4	0.67			
.	600	bcgsc.ca	37	20	31277958	31277958	+	RNA	SNP	G	G	A	rs117063806	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	AACTGGGACCCCA		115	9	0.08	104	0	0				3	0	0.00			
RARB	5915	bcgsc.ca	37	3	25502825	25502825	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	RARB	NM_000965	exon2	c.G299A	p.G100E	GTGAGGGATGTAA		73	5	0.07	75	0	0		123		34	2	0.06			
WDR48	57599	hgsc.bcm.edu;bcgsc.ca	37	3	39130788	39130788	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	NM_020839	exon16	c.G1647T	p.W549C	ACAATGGGTAATT		109	5	0.05	105	0	0				56	0	0.00			
.	0	bcgsc.ca	37	3	53098775	53098775	+	RNA	SNP	A	A	G	rs1811351	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CAGTTAATTCATC		119	8	0.07	93	0	0				2	0	0.00			
.	100289640	bcgsc.ca	37	3	87100988	87100988	+	RNA	SNP	T	T	C	rs2256479	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CGGTATTTTATTG		60	5	0.08	80	0	0				0	0				
.	0	bcgsc.ca	37	3	88367906	88367906	+	RNA	SNP	C	C	T	rs1350410	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	AACCCCCACATGC		60	6	0.10	63	0	0				1	0	0.00			
.	0	bcgsc.ca	37	3	98378701	98378701	+	RNA	SNP	A	A	G	rs3796139	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	AAGCATATGTTAA		75	6	0.08	71	0	0				1	0	0.00			
LOC653712	0	bcgsc.ca	37	3	128580585	128580585	+	RNA	SNP	C	C	A	rs789247	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CCTCCACGGCAGA		96	6	0.06	88	0	0				1	0	0.00			
.	0	bcgsc.ca	37	3	132106634	132106634	+	RNA	SNP	G	G	A	rs10935006	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GCATACGTTATTG		78	7	0.09	83	0	0				0	0				
.	0	bcgsc.ca	37	3	180042256	180042256	+	RNA	SNP	A	A	G	rs9867767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	AAGATTACACAAA		94	8	0.09	111	0	0				0	0				
WDR19	57728	bcgsc.ca	37	4	39257506	39257506	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	WDR19	NM_025132	exon27	c.G3040T	p.A1014S	AGCATTGCCTTAT		69	5	0.07	86	0	0		96		21	0	0.00			
KIT	3815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	55593603	55593603	+	Missense_Mutation	SNP	T	T	C	rs121913235	bycluster	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	KIT,NS,germ_cell_tumour,0,64	KIT	NM_000222	exon11	c.T1669C	p.W557R	GTACAGTGGAAGG		95	11	0.12	87	0	0		0	64	97	8	0.08			
UGT2B7	7364	bcgsc.ca	37	4	69964337	69964338	+	Missense_Mutation	DNP	AT	AT	TC	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	AT	AT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	UGT2B7	NM_001074	exon2	c.T802C	p.Y268H	GTTTCCATATCCA		143	7	0.05	123	0	0		79		0	0				
.	344978	bcgsc.ca	37	4	117519499	117519499	+	RNA	SNP	T	T	C	rs4834570	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TTACTATGACTCC		86	5	0.06	71	0	0				0	0				
OTUD4	54726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	146085375	146085375	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	NM_017493	exon4	c.A150T	p.K50N	AAAATCTTTCCTG		136	16	0.12	174	0	0				16	3	0.19			
.	0	bcgsc.ca	37	5	119016414	119016414	+	RNA	SNP	C	C	G	rs330203	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	AAATCTCCTGCCC		80	7	0.09	78	0	0				0	0				
CDKAL1	54901	bcgsc.ca	37	6	21065449	21065450	+	Missense_Mutation	DNP	CA	CA	TG	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	CDKAL1,NS,carcinoma,0,1	CDKAL1	NM_017774	exon12	c.A1227G	p.P409L	AAGTTCCAGCACA		112	8	0.07	96	0	0		55	1	49	0	0.00			
GFRAL	389400	hgsc.bcm.edu;bcgsc.ca	37	6	55216242	55216242	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	NM_207410	exon5	c.T562C	p.F188L	TTGGCTTTTTGTG		149	8	0.05	131	0	0				1	0	0.00			
.	442237	bcgsc.ca	37	6	97096688	97096688	+	RNA	SNP	T	T	C	rs11759390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TCCCACTGAACTT		125	7	0.06	110	0	0				0	0				
LAMA2	3908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	129785566	129785566	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	NM_000426	exon50	c.C7124T	p.A2375V	CGAGTGCTCTTCT		148	19	0.13	114	0	0				9	3	0.33			
.	153932	bcgsc.ca	37	6	158658937	158658937	+	RNA	SNP	T	T	C	rs7753292	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TATCTTTTGGATT		55	4	0.07	52	0	0				1	0	0.00			
.	0	bcgsc.ca	37	7	35473	35473	+	RNA	SNP	T	T	C	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TGCTGCTGCCGCC		343	16	0.05	256	3	0.01171875				0	0				
.	0	bcgsc.ca	37	7	29757664	29757664	+	RNA	SNP	G	G	A	rs111261285	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TTAGGCGTTTCAG		220	10	0.05	182	0	0				0	0				
ANLN	54443	broad.mit.edu	37	7	36446171	36446171	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	ANLN	NM_018685	exon4	c.C869T	p.S290F	CCAGCTCTGTGGT		28	4	0.14	18	0	0		101		29	6	0.21			
.	0	bcgsc.ca	37	7	55002841	55002841	+	RNA	SNP	T	T	G	rs374147543	alternate_allele	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TGAAAATCCAAAG		59	5	0.08	55	1	0.0181818182				0	0				
.	0	bcgsc.ca	37	7	55005265	55005265	+	RNA	SNP	A	A	G	rs2192264	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GTTAGCAGGAACG		133	7	0.05	101	0	0				0	0				
LOC649395	0	bcgsc.ca	37	7	63894558	63894558	+	RNA	SNP	A	A	C	rs73125103	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CTGGACAAAAACC		189	6	0.03	135	0	0				2	0	0.00			
ZNF680	340252	ucsc.edu	37	7	63981631	63981631	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	ZNF680,NS,carcinoma,+1,1	ZNF680	NM_178558	exon4	c.C1501T	p.R501W	AGGACCGGTTAAA		120	2	0.02	97	0	0		58	1	44	25	0.57	rescued with RNA-seq		
.	0	bcgsc.ca	37	8	123782133	123782133	+	RNA	SNP	C	C	T	rs6992158	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CAATGACGTCGAT		32	5	0.16	39	0	0				0	0				
.	6960	bcgsc.ca	37	9	33662557	33662557	+	Missense_Mutation	SNP	G	G	C	rs41302224	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	ATCTTTGCTCTGA		50	4	0.08	51	0	0				0	0				
.	0	bcgsc.ca	37	9	40610136	40610136	+	RNA	SNP	G	G	A	rs76194885	bycluster;byfrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CAGTGGGGCATCA		255	10	0.04	225	0	0				2	0	0.00			
.	0	bcgsc.ca	37	9	71224796	71224796	+	RNA	SNP	G	G	C	rs10781073	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TGGATGGCTCCCT		44	4	0.09	40	0	0				0	0				
SPATA31D5P	0	broad.mit.edu	37	9	84532319	84532319	+	RNA	DEL	G	G	-	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TTCCATGGAGAAT		257	14	0.05	260	0	0				0	0				
.	0	broad.mit.edu	37	9	98180677	98180678	+	RNA	INS	-	-	GTGTGT	rs113946320	bycluster;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GGGTGTGGTGTGT		6	2	0.33	4	0	0				0	0				
.	347265	bcgsc.ca;mdanderson.org	37	9	102068058	102068058	+	Missense_Mutation	SNP	A	A	G	rs184437	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	ACATGAACAAGGC		81	7	0.09	81	0	0				5	0	0.00			
UBAC1	10422	ucsc.edu;bcgsc.ca	37	9	138830111	138830111	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	UBAC1	NM_016172	exon9	c.C1059A	p.N353K	CACCGGGTTATCC		32	4	0.13	41	0	0		40		211	0	0.00			
NHS	4810	hgsc.bcm.edu	37	X	17750309	17750309	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	NM_198270	exon8	c.G4618A	p.D1540N	AGCACCGATGATG		182	8	0.04	161	0	0				1	0	0.00			
PTCHD1	139411	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	23411681	23411681	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	NM_173495	exon3	c.C2046G	p.F682L	CGTCTTCAATCCG		96	11	0.11	55	0	0				1	0	0.00			
.	139163	bcgsc.ca	37	X	49432879	49432880	+	RNA	DNP	CA	CA	TG	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TGTGATCACTGAG		49	6	0.12	41	0	0				0	0				
.	139163	bcgsc.ca	37	X	49432943	49432943	+	RNA	SNP	T	T	C	rs6608907	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TGGCTGTGGCTGG		40	5	0.13	33	0	0				0	0				
.	0	bcgsc.ca	37	X	68003320	68003320	+	RNA	SNP	T	T	C	rs12012713	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CATGCCTGGGCAC		58	5	0.09	59	0	0				0	0				
.	0	bcgsc.ca	37	X	68004148	68004148	+	RNA	SNP	T	T	C	rs7061948	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CCACCTTGTGAAC		89	8	0.09	75	0	0				0	0				
.	0	bcgsc.ca	37	X	68004230	68004230	+	RNA	SNP	A	A	C	rs7058210	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	ACCGACATATTCG		187	16	0.09	172	0	0				0	0				
.	0	bcgsc.ca	37	X	68004333	68004333	+	RNA	SNP	G	G	T	rs111708563	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TGATAGGCATAGT		184	16	0.09	172	0	0				33	0	0.00			
.	0	bcgsc.ca	37	X	68004709	68004709	+	RNA	SNP	C	C	T	rs16990731	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	ATGGACCGTCATT		127	17	0.13	87	0	0				0	0				
.	0	bcgsc.ca	37	X	89294856	89294856	+	RNA	SNP	G	G	T	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TGGTCCGGCCTTG		40	11	0.28	24	0	0				0	0				
.	254700	bcgsc.ca	37	X	89368606	89368606	+	RNA	SNP	G	G	T	rs5941478	bycluster;byfrequency;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TATTGCGATAGTT		73	5	0.07	68	0	0				0	0				
.	84443	bcgsc.ca	37	X	106796084	106796084	+	Silent	SNP	T	T	C	rs12011630	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TGCTCTTGTCCTT		65	5	0.08	77	0	0				0	0				
.	392517	bcgsc.ca;mdanderson.org	37	X	107037795	107037795	+	Silent	SNP	C	C	A	rs5962885	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GGATGTCGGTTTT		88	7	0.08	71	0	0				0	0				
.	642812	bcgsc.ca	37	X	115239675	115239675	+	RNA	SNP	G	G	C	rs7057314	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	CTCTACGTTCGGC		72	8	0.11	90	0	0				0	0				
.	286423	bcgsc.ca	37	X	122250996	122250996	+	Missense_Mutation	SNP	G	G	T	rs6648942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	GAGTATGTGGCCT		199	10	0.05	147	0	0				0	0				
CXorf48	54967	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	134294393	134294393	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	NM_017863	exon3	c.G367A	p.E123K	TATCTTCATTTAT		291	45	0.15	278	0	0				5	1	0.20			
.	0	bcgsc.ca	37	X	134345975	134345975	+	RNA	SNP	G	G	A	rs147984738	bycluster;by1000genomes	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	.	.	.	.	.	.	TTAATTGGATGTG		230	13	0.06	214	0	0				0	0				
