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
NOL9	79707	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	6586826	6586826	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	NM_024654	exon11	c.A1889T	p.E630V	AGCTCTTCCGGGG		130	28	0.22	124	0	0				70	13	0.19			
PIK3CD	5293	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	9775907	9775907	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	NM_005026	exon5	c.G371A	p.G124D	CCGCAGGCCTCCA		82	12	0.15	77	0	0				86	9	0.10			
.	729779	bcgsc.ca	37	1	79521355	79521355	+	RNA	SNP	C	C	T	rs3795404	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	TAACTCCCAAGTT		89	7	0.08	83	0	0				1	0	0.00			
.	440595	bcgsc.ca	37	1	96913449	96913449	+	RNA	SNP	C	C	T	rs11165631	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GTTCATCGTGGCA		116	6	0.05	118	0	0				85	0	0.00			
.	0	bcgsc.ca	37	1	106435772	106435772	+	RNA	SNP	T	T	G	rs12066937	bycluster;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	TGAGAGTTCATTT		173	12	0.07	174	0	0				25	0	0.00			
NRAS	4893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	rs11554290	bycluster;byfrequency;byhapmap	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	NRAS,NS,haematopoietic_neoplasm,-1,2068	NRAS	NM_002524	exon3	c.A182G	p.Q61R	TCTTCTTGTCCAG		136	18	0.13	151	0	0		-1	2068	53	14	0.26			
.	0	bcgsc.ca	37	1	146523045	146523045	+	RNA	SNP	A	A	G	rs580852	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	TCACTAAGTAGAC		81	6	0.07	86	0	0				0	0				
.	0	bcgsc.ca	37	1	146791020	146791020	+	RNA	SNP	A	A	G	rs4950399	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GGCCAGATTTGTG		129	5	0.04	184	0	0				0	0				
.	0	bcgsc.ca	37	1	157679783	157679783	+	RNA	SNP	A	A	G	rs17727309	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GTGCCCAACCTGG		197	9	0.05	228	0	0				12	1	0.08			
OBSCN	84033	bcgsc.ca	37	1	228412227	228412228	+	Missense_Mutation	DNP	TG	TG	CA	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	TG	TG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	OBSCN	NM_001271223	exon10	c.G2998A	p.A908T	AGCCAGTGCCACA		98	8	0.08	104	0	0		2142		10	0	0.00			
OBSCN	84033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	228480321	228480321	+	Silent	SNP	G	G	T	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	NM_001271223	exon45	c.G11988T	p.V3996V	CCCTGTGGAGTGG		168	24	0.14	185	0	0				3	1	0.33			
.	388761	bcgsc.ca;mdanderson.org	37	1	247886949	247886949	+	Missense_Mutation	SNP	T	T	C	rs36075193	bycluster;byfrequency;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	TCATGATTACCTC		123	8	0.07	142	0	0				0	0				
.	0	bcgsc.ca	37	10	37626786	37626786	+	RNA	SNP	G	G	A	rs144068387	by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GCAATCGAAGTTC		189	8	0.04	219	0	0				0	0				
.	0	bcgsc.ca	37	10	52026055	52026055	+	RNA	SNP	C	C	T	rs138093924	bycluster;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GCAAAGCTGGAAT		169	6	0.04	197	0	0				82	0	0.00			
.	0	bcgsc.ca	37	11	4233016	4233016	+	RNA	SNP	A	A	C	rs75810507	bycluster;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	AAGAAGAGTCTCT		86	7	0.08	96	0	0				1	0	0.00			
.	401663	bcgsc.ca;mdanderson.org	37	11	4880892	4880892	+	Silent	SNP	T	T	C	rs11034368	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	TCAAATTTGCTTG		46	4	0.09	59	0	0				0	0				
C11orf48	79081	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	11	62434994	62434994	+	Splice_Site	DEL	C	C	-	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	C11orf48	NM_024099	exon5	c.538+2G>-	.	TACTTACCCTCAA		134	16	0.12	142	0	0		18		1	0	0.00			
.	0	bcgsc.ca	37	11	67524358	67524358	+	RNA	SNP	A	A	G	rs140614895	bycluster;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	AATGCCAAGGGCA		32	6	0.19	26	0	0				0	0				
.	0	bcgsc.ca	37	12	43030796	43030796	+	RNA	SNP	G	G	A	rs79463838	bycluster;byfrequency;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	CTTTCTGGATGTG		115	6	0.05	130	0	0				0	0				
OR8S1	341568	bcgsc.ca	37	12	48919659	48919660	+	Missense_Mutation	DNP	TG	TG	CA	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	TG	TG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	OR8S1	NM_001005203	exon1	c.G246A	p.L82P	AGATGCTGGAGAA		111	10	0.09	136	1	0.0073529412		47		0	0				
LOC100507377	0	bcgsc.ca	37	12	74565295	74565295	+	RNA	SNP	C	C	T	rs6582210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	AATCCTCAAGGCC		28	5	0.18	23	0	0				2	0	0.00			
HECTD4	283450	hgsc.bcm.edu	37	12	112628625	112628625	+	Missense_Mutation	SNP	G	G	T	rs151280588	by1000genomes;alternate_allele	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	NM_001109662	exon60	c.C9035A	p.P3012Q	GATGTCGGAATGG		115	5	0.04	123	0	0				39	0	0.00			
LRRC43	254050	ucsc.edu	37	12	122685163	122685164	+	Missense_Mutation	DNP	AA	AA	GG	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	AA	AA					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	LRRC43	NM_001098519	exon9	c.A1577G	p.K526G	AAAGGGAAGGAGA		64	22	0.34	52	0	0		105		2	0	0.00			
PGAM5	192111	hgsc.bcm.edu;mdanderson.org	37	12	133291445	133291445	+	Nonsense_Mutation	SNP	C	C	T	rs374915398		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	NM_138575	exon2	c.C193T	p.R65X	ATCAGGCGAGAAC		107	10	0.09	93	0	0				37	4	0.11			
.	0	bcgsc.ca	37	14	45330721	45330721	+	RNA	SNP	A	A	T	rs7149683	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	TCTTCAACTATAT		129	7	0.05	141	0	0				0	0				
.	0	bcgsc.ca	37	14	45331290	45331290	+	RNA	SNP	C	C	T	rs73345244	bycluster;byfrequency;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	ACCTCACAGCAAA		143	6	0.04	166	0	0				0	0				
.	0	bcgsc.ca	37	14	45331397	45331397	+	RNA	SNP	T	T	C	rs12323568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	TTCAGATTGTCCA		282	9	0.03	285	0	0				0	0				
.	0	bcgsc.ca	37	14	45331633	45331633	+	RNA	SNP	T	T	G	rs12323575	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	TAAGATTCTGAAG		293	10	0.03	332	1	0.0030120482				1	1	1.00	rescued with RNA-seq		
.	0	bcgsc.ca	37	14	45332387	45332387	+	RNA	SNP	C	C	G	rs7161626	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GAAGTACACCAAA		242	15	0.06	278	0	0				0	0				
.	28452	bcgsc.ca	37	14	106518415	106518415	+	RNA	SNP	C	C	A	rs188349361	bycluster;byfrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GTAATACACAGCC		224	25	0.11	242	5	0.020661157				2416	381	0.16			
LOC727924	0	bcgsc.ca	37	15	22298279	22298279	+	RNA	SNP	G	G	A	rs11856712	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GTCGCCGGTCACA		146	10	0.07	191	0	0				0	0				
.	0	bcgsc.ca	37	15	30297737	30297737	+	RNA	SNP	C	C	T	rs2015398	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	CTTATCCGGTGTT		144	7	0.05	121	0	0				0	0				
.	0	bcgsc.ca	37	15	78272318	78272318	+	RNA	SNP	C	C	G	rs12439777	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	CCAGGGCCCTCCC		489	31	0.06	551	0	0				0	0				
.	0	bcgsc.ca	37	15	85806001	85806001	+	RNA	SNP	C	C	T	rs2002507	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	TGTCCCCGCCAGG		37	4	0.11	41	0	0				1	0	0.00			
PKMYT1	9088	bcgsc.ca	37	16	3025413	3025413	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	PKMYT1	NM_182687	exon4	c.C779A	p.T260K	CCTGCTGTACCCA		117	6	0.05	111	0	0		23		135	0	0.00			
FUK	197258	mdanderson.org	37	16	70508475	70508475	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	NM_145059	exon17	c.G2033T	p.G678V	GGGCTGGTCAGAT		23	3	0.13	28	0	0				14	0	0.00			
HYDIN	54768	broad.mit.edu	37	16	70868034	70868034	+	Missense_Mutation	SNP	G	G	T	rs202145562	bycluster	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	HYDIN	NM_001270974	exon79	c.C13435A	p.L4479M	GCTTCAGTGTGAT		49	6	0.12	60	1	0.0166666667		788		0	0				
LOC100130015	0	broad.mit.edu;mdanderson.org	37	16	90110027	90110027	+	Missense_Mutation	SNP	G	G	A	rs3743824	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GTCGGCGGCACCT		26	4	0.15	35	0	0				8	0	0.00			
SENP3	26168	bcgsc.ca	37	17	7466636	7466636	+	Silent	SNP	G	G	A	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	SENP3	NM_015670	exon2	c.G243A	p.E81E	AGAAGAGGAGGAG		90	5	0.06	102	2	0.0196078431		18		131	1	0.01			
FLCN	201163	bcgsc.ca	37	17	17118366	17118366	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	FLCN	NM_144997	exon13	c.A1471G	p.T491A	GGTTGGTCAGAGC		64	5	0.08	88	0	0		87		80	0	0.00			
.	0	broad.mit.edu	37	17	20418724	20418728	+	RNA	DEL	TCAGC	TCAGC	-	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	TCAGC	TCAGC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	CCAGGGTCAGCTC		352	10	0.03	413	0	0				1	0	0.00			
.	0	bcgsc.ca	37	17	60324448	60324448	+	RNA	SNP	C	C	T	rs12325728	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GCCTTACTTCCTC		212	12	0.06	246	0	0				0	0				
NPC1	4864	ucsc.edu;bcgsc.ca	37	18	21114422	21114422	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	NPC1	NM_000271	exon23	c.C3579A	p.H1193Q	GCCCATGTGGGCA		53	5	0.09	57	0	0		114		94	0	0.00			
GPR108	56927	hgsc.bcm.edu	37	19	6737580	6737580	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	NM_001080452	exon1	c.T8G	p.V3G	TCGCTCACTGCCA		17	5	0.29	6	0	0				6	1	0.17			
.	100506916	bcgsc.ca	37	19	16091763	16091763	+	RNA	SNP	T	T	C	rs8103740	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	TCTCTCTTTGCTA		27	4	0.15	36	0	0				0	0				
FKBP8	23770	hgsc.bcm.edu;broad.mit.edu;mdanderson.org	37	19	18650505	18650505	+	Silent	SNP	C	C	A	rs370114965	alternate_allele	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	FKBP8,NS,carcinoma,0,1	FKBP8	NM_012181	exon3	c.G318T	p.T106T	GACCAGCGTCTTC		35	5	0.14	31	0	0		0	1	401	87	0.22			
CRIM1	51232	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	36623892	36623892	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	NM_016441	exon2	c.G467A	p.S156N	TTCCAAGTCAGGA		142	22	0.15	163	0	0				19	4	0.21			
.	0	broad.mit.edu	37	2	78019879	78019880	+	RNA	INS	-	-	T	rs369659281	bycluster	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	AAATTCCTTTTTT		7	3	0.43	4	0	0				1	0	0.00			
ANKRD36BP2	0	broad.mit.edu	37	2	89104503	89104504	+	RNA	INS	-	-	C	rs149625899	bycluster;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	ATTTTTTTCAGAT		23	14	0.61	17	5	0.2941176471				2	0	0.00			
GPR45	11250	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	2	105859305	105859305	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	NM_007227	exon1	c.A990T	p.K330N	CAAAAAATTCCGC		131	11	0.08	120	0	0				6	1	0.17			
.	0	bcgsc.ca;mdanderson.org	37	2	171649402	171649402	+	Silent	SNP	C	C	T	rs3764916	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	AGAGTACCAGCTG		262	11	0.04	258	1	0.003875969				14	0	0.00			
CDH22	64405	broad.mit.edu;mdanderson.org	37	20	44839036	44839036	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	CDH22	NM_021248	exon7	c.G1196A	p.G399D	AGGAGGCCGGAGG		36	5	0.14	39	0	0		112		1	0	0.00			
THOC5	8563	broad.mit.edu	37	22	29932681	29932681	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	THOC5,NS,carcinoma,0,2	THOC5	NM_001002878	exon8	c.646delC	p.L216fs	CCTTGAGAATCTT		105	9	0.09	124	0	0		58	2	92	12	0.13			
.	0	bcgsc.ca	37	3	11926467	11926467	+	RNA	SNP	A	A	G	rs2055282	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GACTTTATGTGGA		40	4	0.10	61	0	0				0	0				
.	0	bcgsc.ca	37	3	12926399	12926399	+	RNA	SNP	C	C	T	rs61739284	bycluster;byfrequency;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	CCCTGACCTCGGA		20	4	0.20	20	0	0				0	0				
.	79299	bcgsc.ca	37	3	97940932	97940932	+	RNA	SNP	A	A	G	rs35658290	bycluster;byfrequency;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	TCTCACAGGATTT		47	10	0.21	40	0	0				0	0				
.	79299	bcgsc.ca	37	3	97941104	97941104	+	RNA	SNP	A	A	G	rs13063850	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GTGGATACTTGGT		92	7	0.08	110	0	0				0	0				
.	79291	bcgsc.ca	37	3	97957490	97957490	+	RNA	SNP	G	G	A	rs6439724	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	TGCATGGTACAAT		117	9	0.08	123	0	0				0	0				
KIAA2018	205717	hgsc.bcm.edu	37	3	113376107	113376107	+	Silent	SNP	C	C	T	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	KIAA2018,colon,carcinoma,0,1	KIAA2018	NM_001009899	exon7	c.G4422A	p.Q1474Q	TTGTTGCTGTTGC		59	6	0.10	53	0	0		0	1	1	0	0.00			
.	285329	bcgsc.ca	37	3	148703787	148703787	+	RNA	SNP	T	T	G	rs3732559	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	CTCACTTCTGACG		107	9	0.08	118	1	0.0084745763				4	0	0.00			
.	200958	bcgsc.ca	37	3	195345872	195345872	+	Missense_Mutation	SNP	A	A	C	rs199805117		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	CTCTGAAGAGGCA		593	16	0.03	772	0	0				1	0	0.00			
ZNF721	170960	ucsc.edu	37	4	437132	437132	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	ZNF721	NM_133474	exon3	c.T1124A	p.F375Y	TTCAGGGCTGTGT		86	4	0.05	93	0	0		205		28	8	0.29			
.	644548	bcgsc.ca	37	4	63682706	63682706	+	RNA	SNP	A	A	T	rs11946403	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	CTCCAGATAATGG		125	7	0.06	156	0	0				0	0				
.	644548	bcgsc.ca	37	4	63683038	63683038	+	RNA	SNP	C	C	T	rs6852768	bycluster;byfrequency;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GTTGCACCTAATT		183	7	0.04	214	0	0				3	0	0.00			
.	0	bcgsc.ca	37	4	189659777	189659777	+	RNA	SNP	G	G	A	rs6553227	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	ATGAAGGTTTAAG		170	7	0.04	167	0	0				5	5	1.00			
.	0	bcgsc.ca	37	4	189660025	189660025	+	RNA	SNP	G	G	C	rs72553033	bycluster	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	AGTGAAGTAGGTG		90	5	0.06	120	0	0				0	0				
DHX29	54505	hgsc.bcm.edu;bcgsc.ca	37	5	54581236	54581236	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	NM_019030	exon10	c.T1241C	p.V414A	TTGATTACCCTAA		124	7	0.06	151	0	0				20	5	0.25			
ANKHD1	54882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	139907915	139907915	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	NM_017747	exon29	c.G5384A	p.G1795E	CATCTGGAGTAGG		91	13	0.14	128	0	0				67	24	0.36			
PCDHA3	56145	ucsc.edu	37	5	140182571	140182571	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	PCDHA3	NM_031497	exon1	c.G1789T	p.V597L	CGCGCAGTGGATG		43	4	0.09	54	0	0		396		0	0				
ERVFRD-1	405754	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	6	11105023	11105023	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	NM_207582	exon2	c.A521T	p.K174I	GGAGGTTTGGGGA		116	9	0.08	133	0	0				1	0	0.00			
HLA-C	3107	ucsc.edu	37	6	31238898	31238898	+	Missense_Mutation	SNP	A	A	C	rs201707949	byfrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	HLA-C_ENST00000383329,NS,carcinoma,0,4	HLA-C	NM_002117	exon3	c.T571G	p.W191G	GGAGCCACTCCAC		50	1	0.02	57	2	0.0350877193		92	4	2926	507	0.17			
HLA-DRB6	0	broad.mit.edu	37	6	32523273	32523274	+	RNA	DEL	GA	GA	-	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	GA	GA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	CACTGTGAGAGGG		10	4	0.40	12	0	0				16	0	0.00			
SEPT7P2	0	broad.mit.edu	37	7	45787002	45787002	+	RNA	DEL	A	A	-	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	TTAGCCAAAAAAA		6	3	0.50	13	0	0				0	0				
.	653175	bcgsc.ca	37	7	53255471	53255471	+	RNA	SNP	A	A	G	rs6943510	bycluster;byfrequency;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	AAGCAGATACGAA		247	13	0.05	198	0	0				0	0				
.	653175	bcgsc.ca	37	7	53256265	53256265	+	RNA	SNP	G	G	A	rs11972016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	CTTGTCGCAGTCA		262	8	0.03	244	1	0.0040983607				12	0	0.00			
.	135942	bcgsc.ca	37	7	143815744	143815744	+	RNA	SNP	T	T	C	rs10263904	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	AAGAACTCCACCA		74	6	0.08	75	1	0.0133333333				0	0				
.	135942	bcgsc.ca	37	7	143815780	143815780	+	RNA	SNP	G	G	T	rs10274340	bycluster;byfrequency;by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GAGAAGGCCTTTC		68	5	0.07	60	0	0				0	0				
LINC00583	0	broad.mit.edu	37	9	13928081	13928084	+	RNA	DEL	ATTC	ATTC	-	rs35583621	alternate_allele	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	ATTC	ATTC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	LINC00583	.	.	.	.	AAACATATTCAAT		541	12	0.02	566	0	0		1		0	0				
LOC642236	0	bcgsc.ca	37	9	68433564	68433564	+	RNA	SNP	C	C	A	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	CATTTTCCCCTAA		167	9	0.05	167	3	0.0179640719				11	0	0.00			
NUP188	23511	ucsc.edu	37	9	131735464	131735464	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	NUP188	NM_015354	exon12	c.G1139T	p.C380F	GCATGTGTGTCTA		37	4	0.11	46	0	0		140		68	0	0.00			
ND5	4540	broad.mit.edu;bcgsc.ca	37	MT	13812	13812	+	Silent	SNP	T	T	C	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	ENST00000361567	exon1	c.T1476C	p.A492A	CCTCGCTGTCACT		12	7	0.58	22	0	0				0	0				
KDM6A	7403	broad.mit.edu	37	X	44918601	44918602	+	Frame_Shift_Del	DEL	TA	TA	-	novel		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	TA	TA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	KDM6A	NM_021140	exon12	c.1084_1085del	p.362_362del	ACTCTCTATGAAT		208	7	0.03	205	0	0		274		30	0	0.00			
FAM104B	90736	ucsc.edu	37	X	55172630	55172630	+	Nonsense_Mutation	SNP	G	G	A	rs113263757	bycluster	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	FAM104B	NM_001166699	exon3	c.C238T	p.Q80X	AGAACTGGGGAAA		37	7	0.19	38	2	0.0526315789		28		66	0	0.00			
FAM104B	90736	ucsc.edu;mdanderson.org	37	X	55172645	55172645	+	Missense_Mutation	SNP	C	C	G	rs1047042	bycluster;byfrequency;alternate_allele	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	FAM104B	NM_001166699	exon3	c.G223C	p.D75H	TTGCATCGGGTTC		39	8	0.21	38	1	0.0263157895		28		77	0	0.00			
MAGEA10-MAGEA5	0	broad.mit.edu	37	X	151290002	151290003	+	RNA	INS	-	-	T	rs200557971	by1000genomes	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	.	.	.	.	.	.	GATATTGTTTTTT		12	4	0.33	8	0	0				2	0	0.00			
