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	bcgsc.ca;mdanderson.org	37	1	1855319	1855319	+	Silent	SNP	C	C	T	rs2295362	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GACGCCCTTGACG		110	11	0.10	123	0	0				0	0				
.	339457	bcgsc.ca;mdanderson.org	37	1	1858161	1858161	+	Silent	SNP	C	C	T	rs78807865	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGCCACCGTCGGG		212	17	0.08	257	0	0				0	0				
.	284498	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	11835556	11835556	+	Missense_Mutation	SNP	C	C	T	rs41275456	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCTGACCGCCGGA		183	24	0.13	222	0	0				0	0				
.	284498	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	11836670	11836670	+	Missense_Mutation	SNP	C	C	A	rs41275458	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AAGATGCGGCTTT		214	26	0.12	257	0	0				0	0				
.	284498	bcgsc.ca;mdanderson.org	37	1	11838762	11838762	+	Silent	SNP	G	G	A	rs72640211	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGCCTGAGATGG		173	11	0.06	257	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-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCACTGAGCAGCA		267	20	0.07	321	1	0.0031152648				0	0				
.	284498	bcgsc.ca;mdanderson.org	37	1	11839009	11839009	+	Silent	SNP	C	C	T	rs55685198	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCCGGACACTCTC		165	13	0.08	215	0	0				0	0				
.	284498	bcgsc.ca	37	1	11839034	11839034	+	Missense_Mutation	SNP	G	G	A	rs55967531	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTGTGGGCAGCTG		135	8	0.06	192	0	0				0	0				
.	0	bcgsc.ca	37	1	12898045	12898045	+	RNA	SNP	G	G	A	rs10158988	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGGACCGAAGAAG		63	18	0.29	82	0	0				0	0				
.	0	bcgsc.ca	37	1	12898647	12898647	+	RNA	SNP	C	C	T	rs149631941	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTTCTCCAGCAGA		72	8	0.11	99	1	0.0101010101				0	0				
PRAMEF8	441871	bcgsc.ca;mdanderson.org	37	1	12979729	12979729	+	Silent	SNP	G	G	A	rs1890766	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_001012276	exon4	c.G921A	p.S307S	AGAGTCGGACTTG		298	17	0.06	331	0	0				0	0				
PRAMEF8	441871	bcgsc.ca;mdanderson.org	37	1	12979845	12979845	+	Missense_Mutation	SNP	T	T	C	rs1890765	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_001012276	exon4	c.T1037C	p.V346A	AGCAAGTTGTGGC		587	58	0.10	653	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-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_001012276	exon4	c.A1342G	p.I448V	CCCAAGATCATTG		192	34	0.18	305	0	0				0	0				
TMEM51-AS1	200197	hgsc.bcm.edu	37	1	15439098	15439098	+	RNA	SNP	C	C	T	rs114844404	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTTTCTCCTCCCG		103	20	0.19	104	0	0				1	0	0.00			
ESPNP	0	broad.mit.edu	37	1	17030903	17030905	+	RNA	DEL	GAG	GAG	-	rs55663095	alternate_allele	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GAG	GAG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ATCGACGAGGAGG		6	3	0.50	8	0	0				0	0				
PADI6	353238	broad.mit.edu	37	1	17723476	17723477	+	RNA	INS	-	-	CA	rs61476146	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	PADI6	.	.	.	.	ATGCACCCAGGTG		95	7	0.07	108	0	0		51		0	0				
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808340	18808340	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_152375	exon1	c.G865T	p.V289L	GGCAAGGTGTACG		122	6	0.05	139	0	0				0	0				
.	0	bcgsc.ca	37	1	21738259	21738259	+	RNA	SNP	C	C	T	rs35836191	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AATGACCTTGTTG		35	4	0.11	48	0	0				0	0				
HSPG2	3339	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	1	22202476	22202476	+	Silent	SNP	G	G	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_005529	exon24	c.C3063T	p.S1021S	GGGTGTGGAGCCC		107	8	0.07	94	0	0				142	10	0.07			
CSMD2	114784	bcgsc.ca	37	1	33999430	33999430	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	CSMD2	NM_052896	exon62	c.C9525A	p.N3175K	GGTCAGGTTTGGG		155	6	0.04	154	0	0		946		0	0				
.	343296	bcgsc.ca	37	1	79987731	79987731	+	RNA	SNP	G	G	A	rs140314886	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTGGAGGATGGAA		150	11	0.07	149	0	0				0	0				
.	0	bcgsc.ca	37	1	100797449	100797449	+	RNA	SNP	A	A	T	rs614766	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AAGGCCATCACGC		185	7	0.04	258	0	0				0	0				
LOC100129138	0	bcgsc.ca	37	1	104615959	104615959	+	RNA	SNP	A	A	G	rs3811506	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACAAGCAGCCATC		124	7	0.06	168	0	0				5	0	0.00			
.	100132332	bcgsc.ca	37	1	116107337	116107337	+	RNA	SNP	T	T	A	rs55771787	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTATGGTCACCGA		58	8	0.14	73	0	0				0	0				
.	0	bcgsc.ca	37	1	116400426	116400426	+	RNA	SNP	T	T	C	rs7512945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGGAGATTCTGAC		23	4	0.17	40	0	0				0	0				
NBPF10	100132406	bcgsc.ca;mdanderson.org	37	1	145365372	145365372	+	Missense_Mutation	SNP	C	C	G	rs61813409		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	NBPF10	NM_001039703	exon80	c.C9997G	p.L3333V	GGTTGTCTTGAAC		97	11	0.11	108	0	0		221		14	0	0.00			
.	0	bcgsc.ca	37	1	146522606	146522606	+	RNA	SNP	T	T	C	rs521687	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGTCTCTAAAAAG		151	23	0.15	178	0	0				14	0	0.00			
.	0	bcgsc.ca	37	1	146522686	146522686	+	RNA	SNP	C	C	T	rs522558	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTTTGGCTCAATA		95	7	0.07	105	0	0				27	0	0.00			
.	0	bcgsc.ca	37	1	146522722	146522722	+	RNA	SNP	T	T	C	rs671205	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AACAAGTCAACAC		92	7	0.08	100	0	0				5	0	0.00			
.	0	bcgsc.ca	37	1	146523665	146523665	+	RNA	SNP	G	G	A	rs61997227	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CGAAAGGATGGTC		63	6	0.10	48	0	0				0	0				
.	0	bcgsc.ca	37	1	146523670	146523670	+	RNA	SNP	T	T	C	rs594716	byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGATGGTCATCAT		63	6	0.10	47	0	0				0	0				
.	0	bcgsc.ca	37	1	146523957	146523957	+	RNA	SNP	T	T	C	rs61734778	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACTGCATAGCACA		82	9	0.11	92	0	0				0	0				
.	0	bcgsc.ca	37	1	147313509	147313509	+	RNA	SNP	C	C	T	rs146788179	by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GACTGTCCAAGGA		189	9	0.05	188	0	0				0	0				
.	0	bcgsc.ca	37	1	148193730	148193730	+	RNA	SNP	G	G	A	rs61811779	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGTCGGGAATTCC		372	20	0.05	402	0	0				123	0	0.00			
HRNR	388697	bcgsc.ca;mdanderson.org	37	1	152188319	152188319	+	Missense_Mutation	SNP	C	C	T	rs201547528		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	HRNR	NM_001009931	exon3	c.G5786A	p.G1929D	CGGGAGCCAGACC		237	13	0.05	164	1	0.006097561		403		0	0				
.	0	bcgsc.ca	37	1	157029197	157029197	+	RNA	SNP	C	C	G	rs62640951	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTAGATCCATTCA		134	5	0.04	168	0	0				33	0	0.00			
.	0	bcgsc.ca	37	1	157030280	157030280	+	RNA	SNP	T	T	C	rs1706	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGTGACTTGGCAG		170	8	0.05	171	0	0				1	1	1.00			
PRRX1	5396	hgsc.bcm.edu;bcgsc.ca	37	1	170695392	170695392	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	PRRX1,colon,carcinoma,+1,1	PRRX1	NM_006902	exon3	c.G449A	p.R150H	AGTTCCGCAGGAA		194	8	0.04	209	2	0.009569378		1	1	34	0	0.00			
.	8497	bcgsc.ca	37	1	203015507	203015507	+	Silent	SNP	C	C	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTCACCAAGGCA		160	7	0.04	190	0	0				1	0	0.00			
.	0	bcgsc.ca	37	1	220490435	220490435	+	RNA	SNP	T	T	C	rs7553951	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTTCGCTGGCTCC		44	5	0.11	44	0	0				50	0	0.00			
.	100288517	bcgsc.ca	37	1	229178058	229178058	+	RNA	SNP	C	C	T	rs4654640	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ATAAAACAACTTC		65	9	0.14	69	1	0.0144927536				2	0	0.00			
.	645980	bcgsc.ca	37	1	242156734	242156734	+	RNA	SNP	C	C	T	rs28613024	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGTGCCCTCTACG		32	8	0.25	32	0	0				0	0				
.	388761	bcgsc.ca	37	1	247886493	247886493	+	Missense_Mutation	SNP	G	G	A	rs62619787	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTACAGGGTTAAA		215	12	0.06	238	0	0				0	0				
.	388761	bcgsc.ca;mdanderson.org	37	1	247886615	247886615	+	Missense_Mutation	SNP	G	G	A	rs11809582	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AAAACAGTGAGAT		95	11	0.12	136	0	0				0	0				
.	148818	bcgsc.ca	37	1	247990905	247990905	+	RNA	SNP	T	T	C	rs6703747	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ATGAAGTAAGACA		35	4	0.11	27	0	0				0	0				
.	148818	bcgsc.ca	37	1	247991718	247991718	+	RNA	SNP	C	C	A	rs4925725	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AATTTTCTCAAAA		75	17	0.23	117	0	0				0	0				
OR2T8	343172	bcgsc.ca	37	1	248084825	248084825	+	Missense_Mutation	SNP	C	C	T	rs61857492	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	OR2T8	NM_001005522	exon1	c.C506T	p.A169V	GCGGTGCACACGA		181	32	0.18	164	2	0.012195122		67		0	0				
.	0	bcgsc.ca	37	10	30669367	30669367	+	RNA	SNP	G	G	A	rs2149628	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCAAAGGCTATGC		18	4	0.22	28	0	0				0	0				
.	653365	bcgsc.ca;mdanderson.org	37	10	48003992	48003992	+	Missense_Mutation	SNP	C	C	T	rs3739968	bycluster;byfrequency;byhapmap	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCATTACACACTA		982	52	0.05	1587	3	0.0018903592				3	0	0.00			
.	399774	bcgsc.ca	37	10	54172174	54172174	+	RNA	SNP	G	G	A	rs7897513	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCGATCGCCACAA		106	7	0.07	163	0	0				0	0				
.	729262	bcgsc.ca	37	10	81471458	81471458	+	Silent	SNP	A	A	C	rs201762104	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCAGCTAGTGGAG		218	8	0.04	284	0	0				7	0	0.00			
.	0	bcgsc.ca	37	10	81651906	81651906	+	RNA	SNP	A	A	G	rs1972481	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCAGTCATGTAGA		65	5	0.08	111	0	0				0	0				
.	642538	bcgsc.ca	37	10	81791970	81791970	+	RNA	SNP	T	T	C	rs10887394	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGTGTATGCAGAA		171	13	0.08	230	0	0				0	0				
.	0	bcgsc.ca	37	10	120632048	120632048	+	RNA	SNP	A	A	G	rs9787461	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAACACAAAGATT		40	4	0.10	78	0	0				0	0				
MUC2	4583	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	1090890	1090890	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_002457	exon28	c.C3785T	p.P1262L	CACGCCCGTCCAC		130	16	0.12	134	0	0				0	0				
.	4586	bcgsc.ca	37	11	1156646	1156646	+	Missense_Mutation	SNP	C	C	G	rs35783651	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	ENSG00000196292,NS,carcinoma,0,2	.	.	.	.	.	GGTCAGCGAGCTC		187	8	0.04	169	0	0			2	0	0				
.	390035	bcgsc.ca	37	11	4496613	4496613	+	RNA	SNP	C	C	A	rs9633905	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGGGAACACTAGC		107	6	0.06	111	0	0				0	0				
.	340990	bcgsc.ca;mdanderson.org	37	11	17631751	17631751	+	Missense_Mutation	SNP	C	C	T	rs2041028	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CACCCCCACAGCC		88	7	0.08	109	0	0				1	0	0.00			
.	340990	ucsc.edu;bcgsc.ca;mdanderson.org	37	11	17632651	17632651	+	Missense_Mutation	SNP	C	C	T	rs7111528	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGCTCACGCCTGC		88	9	0.10	91	0	0				0	0				
DGKZ	8525	broad.mit.edu	37	11	46393272	46393274	+	In_Frame_Del	DEL	AAG	AAG	-	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AAG	AAG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	DGKZ	NM_001105540	exon10	c.1342_1344del	p.448_448del	GCAAGCAAGAAGA		167	7	0.04	195	0	0		199		48	0	0.00			
LOC440040	0	broad.mit.edu;ucsc.edu	37	11	49831483	49831483	+	RNA	SNP	C	C	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGGACTCTTGGAA		114	25	0.22	133	0	0				4	1	0.25			
.	256190	bcgsc.ca	37	11	51527482	51527482	+	RNA	SNP	C	C	T	rs35049610	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGTAGCACCAAA		57	5	0.09	62	0	0				0	0				
.	0	bcgsc.ca	37	11	61936839	61936839	+	RNA	SNP	G	G	C	rs17156910	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAGATTGTACGAG		41	4	0.10	40	0	0				0	0				
.	120126	bcgsc.ca	37	11	89486848	89486848	+	RNA	SNP	C	C	G	rs11018769	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCTGGACAGTTCC		245	11	0.04	234	0	0				0	0				
.	79515	bcgsc.ca	37	11	123880482	123880482	+	RNA	SNP	T	T	G	rs11601573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACCTCCTCATCCT		127	5	0.04	147	0	0				0	0				
.	79515	bcgsc.ca	37	11	123880685	123880685	+	RNA	SNP	G	G	A	rs55700020	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGCACCGAGTGTT		99	7	0.07	129	0	0				0	0				
.	0	bcgsc.ca	37	11	133734907	133734907	+	RNA	SNP	T	T	G	rs10894754	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAGCCGTCGTGCC		42	5	0.12	47	0	0				3	0	0.00			
WNK1	65125	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	994115	994115	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_001184985	exon19	c.G4925A	p.G1642E	AAGAGGGGATTGC		264	28	0.11	187	0	0				117	7	0.06			
.	0	bcgsc.ca	37	12	6588445	6588445	+	RNA	SNP	A	A	G	rs2008134	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCCCTGATAGGAG		108	8	0.07	60	0	0				0	0				
.	0	bcgsc.ca	37	12	8786982	8786982	+	RNA	SNP	T	T	C	rs12308718	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGGCGATTGGCAT		106	8	0.08	86	0	0				0	0				
GABARAPL1	23710	bcgsc.ca	37	12	10370734	10370734	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	GABARAPL1	NM_031412	exon2	c.C163G	p.L55V	TCTGACCTTACTG		324	11	0.03	195	0	0		10		211	9	0.04	rescued with RNA-seq		
HEBP1	50865	bcgsc.ca	37	12	13140216	13140216	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	HEBP1	NM_015987	exon3	c.G268A	p.E90K	CATCTTCATTGGG		376	13	0.03	150	1	0.0066666667		16		287	13	0.05	rescued with RNA-seq		
.	390352	bcgsc.ca	37	12	17144587	17144587	+	RNA	SNP	C	C	T	rs61265963	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAAAAACGACCCA		62	5	0.08	32	0	0				6	4	0.67			
.	0	bcgsc.ca	37	12	20094524	20094524	+	RNA	SNP	G	G	T	rs1844950	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCTAATGTTCTTT		312	10	0.03	208	0	0				0	0				
ITPR2	3709	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	26811025	26811025	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_002223	exon17	c.C1925T	p.T642I	GCAGTGGTATTAG		403	42	0.10	231	0	0				14	2	0.14			
ERGIC2	51290	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	12	29521221	29521221	+	Splice_Site	SNP	C	C	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_016570	exon5	c.216-1G>T	.	AATTTGCTGAAAG		706	54	0.08	422	0	0				12	0	0.00			
.	283463	bcgsc.ca	37	12	40826514	40826514	+	Silent	SNP	T	T	C	rs10506162	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGTTCCTGTGATG		143	16	0.11	167	2	0.0119760479				0	0				
.	283463	bcgsc.ca;mdanderson.org	37	12	40834918	40834918	+	Missense_Mutation	SNP	C	C	T	rs4768261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAAATTCTAAAGG		153	20	0.13	207	0	0				0	0				
.	283463	bcgsc.ca	37	12	40835749	40835749	+	Silent	SNP	T	T	C	rs11176655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGGTCATGTTAGA		189	7	0.04	203	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-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTCTTTGTGGAAA		99	14	0.14	93	0	0				0	0				
.	283463	bcgsc.ca	37	12	40843504	40843504	+	Silent	SNP	A	A	C	rs12581232	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TACAACAGCTACC		683	29	0.04	827	3	0.0036275695				0	0				
.	0	bcgsc.ca	37	12	43963769	43963769	+	RNA	SNP	A	A	G	rs75198585	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTTCATACTGCTC		39	5	0.13	58	0	0				0	0				
.	0	bcgsc.ca	37	12	43964280	43964281	+	RNA	DNP	GT	GT	TG	rs34593988		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GT	GT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CGTTGAGTGAATG		73	6	0.08	85	0	0				0	0				
.	0	bcgsc.ca	37	12	43965011	43965011	+	RNA	SNP	A	A	T	rs66501365	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCACCAACACAGG		92	10	0.11	111	0	0				0	0				
.	0	bcgsc.ca	37	12	43965468	43965468	+	RNA	SNP	G	G	T	rs67397305	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTTCCTGCTCAGA		62	5	0.08	74	0	0				1	0	0.00			
.	85349	bcgsc.ca	37	12	52646139	52646139	+	RNA	SNP	G	G	A	rs146544749	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGATCAGGCAGGC		127	11	0.09	130	0	0				2	0	0.00			
EIF4B	1975	ucsc.edu;mdanderson.org	37	12	53431298	53431298	+	Missense_Mutation	SNP	T	T	A	rs146008363	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	EIF4B	NM_001417	exon11	c.T1412A	p.L471Q	AGCCCCTAAAGGT		244	24	0.10	279	0	0		38		672	1	0.00			
.	653441	bcgsc.ca	37	12	55805647	55805647	+	RNA	SNP	A	A	G	rs12825123	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTCTGCAATCTCT		333	20	0.06	405	0	0				394	0	0.00			
.	0	bcgsc.ca	37	12	75057687	75057687	+	RNA	SNP	G	G	A	rs7311420	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACAGGAGGAAGGC		45	4	0.09	53	0	0				0	0				
.	144535	bcgsc.ca	37	12	97098549	97098549	+	Missense_Mutation	SNP	T	T	C	rs11108643	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAAAACTTCTTAC		547	71	0.13	528	4	0.0075757576				0	0				
.	0	bcgsc.ca	37	12	106566174	106566174	+	RNA	SNP	A	A	C	rs3853777	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTGACAACAGCG		69	12	0.17	64	0	0				0	0				
RNF34	80196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	121855684	121855684	+	Silent	SNP	C	C	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_194271	exon4	c.C606T	p.D202D	TGGAGACCAAACA		143	30	0.21	151	0	0				124	38	0.31			
CDK2AP1	8099	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	123746287	123746287	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_004642	exon4	c.C344A	p.S115Y	AGCTAGGATCTGG		61	8	0.13	77	0	0				466	131	0.28			
.	642395	bcgsc.ca	37	13	19801534	19801534	+	RNA	SNP	G	G	A	rs139266746	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCATACGTCCCAG		67	5	0.07	136	0	0				0	0				
.	646208	bcgsc.ca	37	13	23490250	23490250	+	RNA	SNP	C	C	A	rs3825451		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTAAAACAACAGC		146	10	0.07	233	4	0.017167382				2	0	0.00			
RFC3	5983	bcgsc.ca	37	13	34540232	34540232	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	RFC3_ENST00000434425,NS,carcinoma,0,1	RFC3	NM_181558	exon9	c.G888T	p.K296N	ATGTAAGGAGGAA		46	4	0.09	63	0	0		40	1	0	0				
.	730174	bcgsc.ca	37	13	48337965	48337965	+	RNA	SNP	T	T	C	rs9534813	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAATTATGAACCT		55	5	0.09	119	0	0				0	0				
.	100287887	bcgsc.ca	37	13	55015252	55015252	+	RNA	SNP	A	A	C	rs9591591	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTCTGGAAGGGCT		142	6	0.04	200	2	0.01				3	0	0.00			
.	122199	bcgsc.ca	37	13	65532930	65532930	+	RNA	SNP	A	A	G	rs9598891	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCAGGCAGGTGGT		33	5	0.15	75	0	0				0	0				
.	100288130	bcgsc.ca	37	13	71498338	71498338	+	RNA	SNP	C	C	T	rs7335663	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CATTGGCGTGGGC		68	8	0.12	105	0	0				0	0				
.	100288130	bcgsc.ca	37	13	71498360	71498360	+	RNA	SNP	G	G	C	rs7336024	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGCAGGGAGGAAG		67	7	0.10	106	0	0				0	0				
.	100288130	bcgsc.ca	37	13	71498385	71498385	+	RNA	SNP	C	C	T	rs7335686	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CGCCAGCGAGGCA		62	7	0.11	95	0	0				0	0				
.	100874450	bcgsc.ca	37	13	81847284	81847284	+	RNA	SNP	C	C	A	rs1287528	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGAATTCTGGGAA		27	4	0.15	35	0	0				0	0				
.	121727	bcgsc.ca	37	13	90644911	90644911	+	RNA	SNP	G	G	A	rs9588829	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CGCCCCGCCTACT		45	6	0.13	100	0	0				0	0				
.	100128011	bcgsc.ca	37	13	90823825	90823825	+	RNA	SNP	G	G	T	rs9560569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAATACGGACAAT		37	6	0.16	59	0	0				0	0				
.	100128011	bcgsc.ca	37	13	90823859	90823859	+	RNA	SNP	C	C	T	rs9555981	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTAAACCTTGAAG		36	5	0.14	59	0	0				1	0	0.00			
.	100129259	bcgsc.ca	37	13	95411309	95411309	+	RNA	SNP	T	T	A	rs1924075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTGGATCCTGCT		36	5	0.14	52	0	0				0	0				
.	100129259	bcgsc.ca	37	13	95411450	95411450	+	RNA	SNP	A	A	G	rs9516470	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTGAGGACCAGCC		25	5	0.20	43	0	0				0	0				
CLYBL	171425	mdanderson.org	37	13	100258996	100258996	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_206808	exon1	c.C47T	p.A16V	CGGCGGCGGCGCT		15	3	0.20	10	0	0				0	0				
.	144	bcgsc.ca	37	13	111591265	111591265	+	RNA	SNP	G	G	A	rs2239661	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGCAGCGACTCTC		32	5	0.16	66	0	0				0	0				
.	0	bcgsc.ca	37	14	21190932	21190932	+	RNA	SNP	C	C	T	rs60729716	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCCTGACGTCCAA		65	5	0.08	72	0	0				0	0				
.	0	bcgsc.ca	37	14	22070355	22070355	+	RNA	SNP	T	T	C	rs199637760	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCCCGATGTCCAC		152	19	0.13	167	1	0.005988024				0	0				
.	100288948	bcgsc.ca	37	14	24219529	24219529	+	RNA	SNP	G	G	A	rs35845573	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAGACTGGGAATG		53	5	0.09	79	0	0				0	0				
FSCB	84075	bcgsc.ca;mdanderson.org	37	14	44975510	44975511	+	Missense_Mutation	DNP	CG	CG	TA	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	CG	CG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	FSCB	NM_032135	exon1	c.C680T	p.P227L	AAGTACCGGGGGA		97	7	0.07	123	1	0.0081300813		173		0	0				
.	0	bcgsc.ca	37	14	45334034	45334034	+	RNA	SNP	T	T	C	rs115079816	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTTCATTTGAAAG		148	7	0.05	208	0	0				0	0				
.	319123	bcgsc.ca	37	14	51171922	51171922	+	RNA	SNP	G	G	A	rs72681673	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CACACAGGTAACA		32	4	0.13	48	0	0				0	0				
.	246720	bcgsc.ca	37	14	81712844	81712844	+	RNA	SNP	C	C	G	rs12891586	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACTCCACTGAGTT		58	4	0.07	90	0	0				0	0				
.	317775	bcgsc.ca	37	14	90204548	90204548	+	RNA	SNP	A	A	G	rs10484019	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ATCGTGAAAGACT		59	11	0.19	87	0	0				0	0				
ATXN3	4287	hgsc.bcm.edu	37	14	92537354	92537355	+	In_Frame_Ins	INS	-	-	CTGCTGCTGCTGCTGCTGCTG	rs76478261	alternate_allele	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	ATXN3,NS,carcinoma,0,7	ATXN3	NM_004993	exon10	c.916_917insCAGCAGCAGCAGCAGCAGCAG	p.G306delinsQQQQQQQG	GGTCCCCCTGCTG		50	25	0.50	70	0	0		46		38	0	0.00			
.	3494	bcgsc.ca	37	14	106054108	106054108	+	RNA	SNP	G	G	A	rs12105	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGGCCGGTCAGT		139	11	0.08	173	1	0.0057803468				489	0	0.00			
.	3501	bcgsc.ca	37	14	106110057	106110057	+	RNA	SNP	G	G	A	rs11160859	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTGCACGACGGTG		154	9	0.06	186	1	0.0053763441				3663	7	0.00			
.	3501	bcgsc.ca	37	14	106110060	106110060	+	RNA	SNP	G	G	A	rs7146603	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CACGACGGTGAGG		159	9	0.06	185	0	0				3703	2	0.00			
.	3493	bcgsc.ca	37	14	106174123	106174123	+	RNA	SNP	G	G	A	rs141644948	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCCACCGGATTTT		107	5	0.05	144	0	0				4409	6	0.00			
.	28474	bcgsc.ca	37	14	106452817	106452817	+	RNA	SNP	A	A	G	rs1065059	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGATCCATCCCAT		466	21	0.05	685	6	0.0087591241				520	2	0.00			
.	28452	bcgsc.ca	37	14	106518565	106518565	+	RNA	SNP	C	C	T	rs113460079	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGCCCCTTCCCT		562	29	0.05	808	4	0.004950495				923	0	0.00			
.	28452	bcgsc.ca	37	14	106518848	106518848	+	RNA	SNP	T	T	C	rs2073679	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCCCAATTCCATG		190	20	0.11	248	2	0.0080645161				587	4	0.01			
.	28451	bcgsc.ca	37	14	106552310	106552310	+	RNA	SNP	G	G	A	rs8020204	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AAGGCCGTGTCCT		143	7	0.05	220	0	0				1000	0	0.00			
.	28449	bcgsc.ca	37	14	106586354	106586354	+	RNA	SNP	G	G	C	rs10131161	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AATCCAGAGGCTG		66	5	0.08	93	0	0				534	0	0.00			
.	28445	bcgsc.ca;mdanderson.org	37	14	106667810	106667810	+	RNA	SNP	C	C	A	rs112170273	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCTGCACAGGAGA		86	15	0.17	163	0	0				34	0	0.00			
.	28426	bcgsc.ca	37	14	106926311	106926311	+	RNA	SNP	T	T	G	rs4977158	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ATAGTATGTGCTA		121	5	0.04	159	0	0				995	1	0.00			
.	28388	bcgsc.ca	37	14	107035142	107035142	+	RNA	SNP	G	G	A	rs61732461	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAGGGCGAGGATG		79	6	0.08	111	0	0				1700	2	0.00			
.	28420	bcgsc.ca	37	14	107048767	107048767	+	RNA	SNP	G	G	T	rs200617568	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGAATCGGCCCTT		129	6	0.05	154	0	0				454	0	0.00			
.	28414	bcgsc.ca;mdanderson.org	37	14	107113851	107113851	+	RNA	SNP	C	C	T	rs2072045	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGAGTCTGCATA		87	13	0.15	119	0	0				10	0	0.00			
.	28414	bcgsc.ca	37	14	107114193	107114193	+	RNA	SNP	A	A	G	rs2073670	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AACTCCATCATGA		159	36	0.23	205	3	0.0146341463				6	0	0.00			
.	28461	bcgsc.ca;mdanderson.org	37	14	107170055	107170055	+	RNA	SNP	G	G	A	rs8009570	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTTGCTGTACCAA		223	12	0.05	273	0	0				6970	6	0.00			
.	28461	bcgsc.ca;mdanderson.org	37	14	107170062	107170062	+	RNA	SNP	A	A	G	rs55891010	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TACCAAAGATAGG		222	13	0.06	275	0	0				6793	21	0.00			
.	28461	bcgsc.ca	37	14	107170077	107170077	+	RNA	SNP	C	C	T	rs11845244	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGATCCCTCCCAT		227	12	0.05	293	1	0.0034129693				7113	37	0.01			
.	28461	bcgsc.ca;mdanderson.org	37	14	107170207	107170207	+	RNA	SNP	C	C	T	rs11845287	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCCAGACTGCACC		168	11	0.07	246	0	0				9139	14	0.00			
.	28461	bcgsc.ca	37	14	107170219	107170219	+	RNA	SNP	C	C	G	rs2187989	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGCTGCACCTGG		163	20	0.12	255	2	0.0078431373				7831	4	0.00			
.	28454	bcgsc.ca	37	14	107179013	107179013	+	RNA	SNP	A	A	G	rs61732216	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGCTCACACACA		347	11	0.03	551	0	0				151	0	0.00			
.	28409	bcgsc.ca	37	14	107211211	107211211	+	RNA	SNP	G	G	A	rs2073668	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCCCCCGGACTCC		88	15	0.17	118	1	0.0084745763				400	0	0.00			
.	0	bcgsc.ca	37	15	20450317	20450317	+	RNA	SNP	G	G	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTCCTCGTGATGA		189	8	0.04	154	0	0				5	0	0.00			
.	0	bcgsc.ca	37	15	20453913	20453913	+	RNA	SNP	C	C	T	rs2601516	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGGACACACACCC		208	27	0.13	249	3	0.0120481928				0	0				
.	0	bcgsc.ca	37	15	20467151	20467151	+	RNA	SNP	C	C	T	rs4983660	bycluster;by2hit2allele;byhapmap	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTGCCGCGTGGGT		109	7	0.06	99	1	0.0101010101				1	0	0.00			
.	646379	bcgsc.ca	37	15	22482858	22482858	+	RNA	SNP	A	A	G	rs1807224	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACGGCCATGTCCT		71	6	0.08	72	0	0				1	1	1.00			
.	56476	bcgsc.ca	37	15	22691462	22691462	+	RNA	SNP	A	A	G	rs76627098		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGCACCATAAGCA		136	8	0.06	157	0	0				0	0				
.	56476	bcgsc.ca	37	15	22691729	22691729	+	RNA	SNP	G	G	C	rs71469079	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AAGCGGGATCGGC		94	7	0.07	119	0	0				2	0	0.00			
NUSAP1	51203	bcgsc.ca	37	15	41634587	41634588	+	Missense_Mutation	DNP	AC	AC	GA	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AC	AC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	NUSAP1,NS,carcinoma,+1,2	NUSAP1	NM_018454	exon2	c.C98A	p.T33D	CAGGCAACCAAGT		104	7	0.07	84	0	0		32	2	208	0	0.00			
.	440278	bcgsc.ca	37	15	44020902	44020902	+	RNA	SNP	C	C	T	rs72489216	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGGTTACACTGAA		89	6	0.07	111	0	0				0	0				
.	0	bcgsc.ca	37	15	57848320	57848320	+	RNA	SNP	G	G	A	rs1690317	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AATTAAGTGGTAG		16	4	0.25	22	0	0				0	0				
.	0	bcgsc.ca	37	15	62654429	62654429	+	RNA	SNP	C	C	T	rs2089322	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGGCTGCGCTTCC		192	11	0.06	223	2	0.0089686099				0	0				
.	0	bcgsc.ca	37	15	79019546	79019546	+	RNA	SNP	C	C	A	rs66615064	alternate_allele	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTCCCCACCCCA		98	12	0.12	74	0	0				0	0				
.	0	bcgsc.ca	37	15	79852090	79852090	+	RNA	SNP	C	C	A	rs1765254	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCGTGCCGGTTTC		93	13	0.14	92	0	0				9	0	0.00			
.	0	bcgsc.ca	37	15	79852517	79852517	+	RNA	SNP	T	T	C	rs138410408	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCAAGGTGAGGAG		97	9	0.09	158	1	0.0063291139				5	0	0.00			
.	0	bcgsc.ca	37	15	85806810	85806810	+	RNA	SNP	G	G	A	rs62021386	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGGGCCGGGGAAG		53	11	0.21	64	0	0				0	0				
.	0	bcgsc.ca	37	15	89532954	89532954	+	RNA	SNP	A	A	G	rs57920986	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTCATTAGACACT		161	7	0.04	169	0	0				12	0	0.00			
LRRK1	79705	bcgsc.ca	37	15	101606889	101606890	+	Missense_Mutation	DNP	GC	GC	AA	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GC	GC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	LRRK1	NM_024652	exon33	c.C5814A	p.G1938E	ATTCTGGCGCCCA		131	6	0.05	152	0	0		310		32	0	0.00			
.	729486	bcgsc.ca	37	16	85561	85561	+	RNA	SNP	C	C	T	rs3930589	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTACTCCGGGTCC		44	8	0.18	52	0	0				6	0	0.00			
.	647187	bcgsc.ca	37	16	32941279	32941279	+	RNA	SNP	G	G	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCAAGGGCATTTG		214	8	0.04	263	0	0				0	0				
.	0	bcgsc.ca	37	16	75226838	75226838	+	RNA	SNP	T	T	A	rs1991035	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTTGGGTCACAGA		51	5	0.10	69	1	0.0144927536				0	0				
.	8389	bcgsc.ca	37	17	3019881	3019881	+	RNA	SNP	C	C	T	rs7214748	bycluster;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTCCCACCTCCAC		106	6	0.06	111	0	0				0	0				
XAF1	54739	ucsc.edu;bcgsc.ca	37	17	6663894	6663895	+	Missense_Mutation	DNP	GC	GC	AG	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GC	GC					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	XAF1,colon,carcinoma,+2,1	XAF1	NM_017523	exon4	c.C396G	p.R132Q	TCTGTCGCAGTGA		286	32	0.11	298	2	0.0067114094		16	1	56	0	0.00			
.	100130110	bcgsc.ca	37	17	15672538	15672538	+	RNA	SNP	G	G	A	rs62072425	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAAGGCGTGGAGC		61	6	0.10	58	0	0				0	0				
.	0	bcgsc.ca	37	17	19658853	19658853	+	RNA	SNP	A	A	G	rs11204415	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGGGGCAGCCCGT		48	6	0.13	32	0	0				0	0				
.	0	bcgsc.ca	37	17	19659299	19659299	+	RNA	SNP	T	T	C	rs9898251	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCTGGTTGGGGGA		27	5	0.19	23	0	0				0	0				
.	0	broad.mit.edu	37	17	20459625	20459630	+	RNA	DEL	TGGCTG	TGGCTG	-	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	TGGCTG	TGGCTG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAGGGTTGGCTGT		413	7	0.02	469	0	0				0	0				
.	0	bcgsc.ca	37	17	20657648	20657648	+	RNA	SNP	T	T	C	rs8064233	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGGACATCTGACC		47	5	0.11	52	0	0				0	0				
.	729490	bcgsc.ca	37	17	21544599	21544599	+	RNA	SNP	A	A	G	rs9912297	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACAAGTAAAAGTC		228	10	0.04	257	0	0				0	0				
.	23666	ucsc.edu;bcgsc.ca	37	17	21731041	21731041	+	Missense_Mutation	SNP	G	G	A	rs145087783	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCCCCCGACCAGC		127	16	0.13	162	0	0				140	0	0.00			
.	645668	bcgsc.ca	37	17	25409812	25409812	+	RNA	SNP	G	G	A	rs2061899	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGTGAAGCACTGG		89	5	0.06	107	0	0				0	0				
NARR	83871	bcgsc.ca	37	17	27043933	27043933	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_001256281	exon2	c.C576A	p.D192E	GTGCCTGTCCGGT		74	5	0.07	65	0	0				195	0	0.00			
.	619519	bcgsc.ca	37	17	27530666	27530666	+	RNA	SNP	C	C	T	rs28419601	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGGGCTCTTGCAG		170	13	0.08	203	1	0.0049261084				13	0	0.00			
.	0	bcgsc.ca	37	17	30415954	30415954	+	RNA	SNP	A	A	G	rs41290974	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTCAATATATCGT		391	24	0.06	409	1	0.0024449878				0	0				
LRRC37A11P	342666	bcgsc.ca	37	17	37188445	37188446	+	RNA	DEL	TG	TG	-	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	TG	TG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTGACTGAAGTC		62	7	0.11	74	0	0				0	0				
TMEM99	147184	bcgsc.ca	37	17	38991052	38991053	+	Missense_Mutation	DNP	TT	TT	GA	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	TT	TT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	TMEM99	NM_001195386	exon3	c.T285A	p.L95R	AAGGACTTCTTCT		182	13	0.07	187	1	0.0053475936		21		82	0	0.00			
.	85354	bcgsc.ca;mdanderson.org	37	17	39258221	39258221	+	Missense_Mutation	SNP	G	G	A	rs141088836	by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGCTGGGGTGGCA		69	8	0.12	91	0	0				0	0				
LRRC37A	9884	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	17	44408722	44408722	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_014834	exon9	c.C4079T	p.S1360L	CTTTTTCATCCTT		106	33	0.31	80	0	0				33	3	0.09			
CDC27	996	hgsc.bcm.edu	37	17	45216115	45216115	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	CDC27_ENST00000531206,NS,carcinoma,0,2	CDC27_ENST00000531206	NM_001114091	exon13	c.A1712T	p.N571I	GGCGAATTTTTAT		57	3	0.05	73	1	0.0136986301		0	2	82	0	0.00			
.	0	bcgsc.ca	37	17	60361652	60361652	+	RNA	SNP	C	C	G	rs139504127	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTTGGACTAGAAG		327	43	0.13	361	1	0.0027700831				0	0				
.	0	bcgsc.ca	37	17	67703437	67703437	+	RNA	SNP	C	C	T	rs140678444	by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCCATACGGAATA		76	5	0.07	87	0	0				0	0				
.	388478	bcgsc.ca	37	18	57677294	57677294	+	RNA	SNP	A	A	G	rs2000746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTCAGTATCTCAG		62	4	0.06	65	0	0				0	0				
.	5273	bcgsc.ca	37	18	61575232	61575232	+	Missense_Mutation	SNP	A	A	G	rs1006961	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTTACTACAGGAG		417	16	0.04	522	0	0				0	0				
DOT1L	84444	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	2222030	2222030	+	Silent	SNP	C	C	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_032482	exon24	c.C2862T	p.A954A	CCCGGCCTCTCTC		97	12	0.12	86	0	0				45	8	0.18			
DENND1C	79958	bcgsc.ca	37	19	6470310	6470310	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	DENND1C	NM_024898	exon18	c.G1358A	p.R453H	ACCGAGCGGTACA		119	7	0.06	155	0	0		93		22	0	0.00			
AP1M2	10053	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	10694299	10694299	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_005498	exon3	c.C250G	p.L84V	TATACAGGAAGGA		124	10	0.08	142	0	0				126	28	0.22			
.	0	bcgsc.ca	37	19	22868096	22868096	+	Missense_Mutation	SNP	A	A	G	rs55716469	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	ENSG00000198153,NS,carcinoma,0,1	.	.	.	.	.	ATTTACAGTTAGG		159	8	0.05	164	0	0			1	0	0				
.	0	bcgsc.ca	37	19	22868205	22868205	+	Silent	SNP	T	T	C	rs597906	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	ENSG00000198153,NS,carcinoma,0,1	.	.	.	.	.	ATGTGATAAATAT		146	11	0.08	173	0	0			1	0	0				
.	0	bcgsc.ca	37	19	22868445	22868445	+	Silent	SNP	C	C	T	rs56224405	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	ENSG00000198153,NS,carcinoma,0,1	.	.	.	.	.	GAAACCCTACAAA		581	15	0.03	673	1	0.0014858841			1	0	0				
.	0	bcgsc.ca	37	19	22868541	22868541	+	Silent	SNP	G	G	A	rs71356000		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	ENSG00000198153,NS,carcinoma,0,1	.	.	.	.	.	ATGTGAGGACTGT		311	12	0.04	353	0	0			1	1	0	0.00			
.	0	bcgsc.ca	37	19	22869030	22869030	+	Silent	SNP	G	G	A	rs78524936	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	ENSG00000198153,NS,carcinoma,0,1	.	.	.	.	.	AGAGAAGCCCTAC		420	26	0.06	531	1	0.0018832392			1	0	0				
.	0	bcgsc.ca	37	19	22869372	22869372	+	Silent	SNP	C	C	T	rs35689937	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACCCTACAAGTGT		125	10	0.08	157	0	0				0	0				
ZNF91	7644	bcgsc.ca	37	19	23542290	23542291	+	Missense_Mutation	DNP	AG	AG	GC	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	ZNF91	NM_003430	exon4	c.C3490G	p.L1164A	CAAAGTAGTGGGA		57	6	0.11	46	0	0		349		20	0	0.00			
CAPNS1	826	bcgsc.ca	37	19	36640664	36640669	+	In_Frame_Del	DEL	GCTGGT	GCTGGT	-	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GCTGGT	GCTGGT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	CAPNS1	.	.	.	.	AAAGGGGCTGGTG		141	5	0.04	132	0	0		19		3	0	0.00			
MIA-RAB4B	0	hgsc.bcm.edu	37	19	41285813	41285813	+	RNA	SNP	C	C	T	rs61750952	alternate_allele	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTGTTTCTCTCCC		68	6	0.09	83	0	0				0	0				
TMEM91	641649	bcgsc.ca	37	19	41888851	41888861	+	Frame_Shift_Del	DEL	GGGGACTGGGC	GGGGACTGGGC	-	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GGGGACTGGGC	GGGGACTGGGC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	TMEM91	.	.	.	.	CTTGGAGGGGACT		82	6	0.07	133	0	0		22		6	0	0.00			
PSG3	5671	bcgsc.ca	37	19	43243217	43243218	+	Missense_Mutation	DNP	AA	AA	GG	rs34721205		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AA	AA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	PSG3,NS,carcinoma,0,1	PSG3	NM_021016	exon2	c.T88C	p.L30P	GTAGGCAAGTTCC		139	12	0.09	181	1	0.0055248619		82	1	0	0				
.	0	bcgsc.ca	37	19	43883273	43883273	+	Missense_Mutation	SNP	G	G	C	rs113172076	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ATCCTGGGTCTAG		48	5	0.10	60	0	0				1	0	0.00			
.	147711	bcgsc.ca	37	19	44977071	44977071	+	RNA	SNP	C	C	T	rs1897824	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ATTTTGCGTATAG		120	19	0.16	163	1	0.0061349693				0	0				
.	147711	bcgsc.ca	37	19	44977240	44977240	+	RNA	SNP	A	A	G	rs1897823	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCAGTCAGAATTC		67	8	0.12	62	0	0				0	0				
.	147711	bcgsc.ca	37	19	44977262	44977262	+	RNA	SNP	T	T	C	rs17714261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGTTCATCTCAGA		71	8	0.11	61	1	0.0163934426				0	0				
LMTK3	114783	bcgsc.ca	37	19	49012706	49012706	+	Silent	SNP	G	G	C	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	LMTK3	NM_001080434	exon5	c.C513G	p.G171G	AAACCAGCCACTC		197	13	0.07	310	1	0.0032258065		125		0	0				
.	0	bcgsc.ca	37	19	50222914	50222914	+	RNA	SNP	G	G	A	rs3810261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ATGTTCGCCACCT		44	9	0.20	38	0	0				2	2	1.00			
.	0	bcgsc.ca	37	19	50222955	50222955	+	RNA	SNP	T	T	C	rs1812666	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GATCAGTACGCCA		43	5	0.12	50	0	0				1	1	1.00			
MYH14	79784	hgsc.bcm.edu	37	19	50714016	50714016	+	Missense_Mutation	SNP	G	G	T	rs199910006	bycluster;alternate_allele	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_001077186	exon2	c.G394T	p.G132C	TACTCCGGCCTCA		67	4	0.06	75	0	0				15	0	0.00			
RFPL4A	342931	bcgsc.ca;mdanderson.org	37	19	56274424	56274424	+	Silent	SNP	C	C	A	rs150161449		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	RFPL4A	NM_001145014	exon3	c.C747A	p.P249P	CGAGCCCTGGCGT		153	13	0.08	234	0	0		8		2	0	0.00			
RFPL4A	342931	bcgsc.ca	37	19	56274460	56274460	+	Silent	SNP	A	A	G	rs4801626		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	RFPL4A	NM_001145014	exon3	c.A783G	p.Q261Q	AAGTCAAGATGAT		143	10	0.07	206	3	0.0145631068		8		0	0				
ZNF417	147687	bcgsc.ca;mdanderson.org	37	19	58421141	58421141	+	Missense_Mutation	SNP	G	G	A	rs142466487	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	ZNF417	NM_152475	exon3	c.C505T	p.P169S	CAAATGGCTCCTG		498	22	0.04	598	0	0		44		11	0	0.00			
.	728597	bcgsc.ca	37	2	3800383	3800383	+	Silent	SNP	C	C	T	rs357969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTTGGGCGACTCA		272	9	0.03	276	3	0.0108695652				0	0				
.	10130	bcgsc.ca;mdanderson.org	37	2	10959407	10959407	+	Missense_Mutation	SNP	A	A	C	rs72779451	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGGTGCATTAGCC		116	9	0.08	92	0	0				0	0				
.	10130	bcgsc.ca	37	2	10959461	10959461	+	Silent	SNP	G	G	T	rs72779452	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGAGTGGGCAGGA		98	7	0.07	83	0	0				0	0				
.	100420972	bcgsc.ca	37	2	17466075	17466075	+	RNA	SNP	A	A	G	rs10208884	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GACAGCACCTTGG		65	10	0.15	72	1	0.0138888889				0	0				
.	0	bcgsc.ca	37	2	21360583	21360583	+	Missense_Mutation	SNP	A	A	G	rs312966	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGAGTCATGGAAA		122	19	0.16	126	1	0.0079365079				0	0				
.	0	bcgsc.ca	37	2	27789861	27789861	+	Missense_Mutation	SNP	T	T	A	rs965813	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCTGTGTTCAGGA		220	10	0.05	261	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-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCTCTACGTGGAA		86	15	0.17	83	0	0				1	0	0.00			
LOC388948	0	bcgsc.ca;mdanderson.org	37	2	47045321	47045321	+	Missense_Mutation	SNP	A	A	G	rs17773492	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCAGGGAACTCTT		120	9	0.08	148	0	0				0	0				
.	0	bcgsc.ca	37	2	58688907	58688907	+	RNA	SNP	G	G	A	rs2075171	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCCTTCGTGCAGC		237	16	0.07	291	1	0.0034364261				66	0	0.00			
ZNF638	27332	ucsc.edu;mdanderson.org	37	2	71654529	71654529	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	ZNF638	NM_014497	exon24	c.G5530T	p.E1844X	ATGATTGAAAGAC		20	4	0.20	14	0	0		179		353	0	0.00			
.	0	bcgsc.ca	37	2	81421951	81421951	+	RNA	SNP	A	A	G	rs13430688	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GACTCCACCAGCG		53	9	0.17	54	1	0.0185185185				0	0				
.	0	bcgsc.ca	37	2	81422135	81422135	+	RNA	SNP	G	G	T	rs6722134	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGTAGGGGTTGGC		72	12	0.17	86	0	0				0	0				
.	0	bcgsc.ca	37	2	81427036	81427036	+	RNA	SNP	C	C	T	rs1809229	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTTTGACGGCCCG		20	4	0.20	25	0	0				0	0				
.	0	bcgsc.ca	37	2	81427187	81427187	+	RNA	SNP	C	C	T	rs2010447	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTCATGCCTTTGA		14	4	0.29	21	0	0				0	0				
LOC1720	0	bcgsc.ca	37	2	83084350	83084350	+	RNA	SNP	A	A	T	rs11126880	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TAAACTATTTGTC		57	8	0.14	74	0	0				0	0				
.	0	bcgsc.ca	37	2	87365531	87365531	+	RNA	SNP	G	G	A	rs3761695		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTCTACGTCTGTT		223	14	0.06	275	0	0				0	0				
.	28875	bcgsc.ca;mdanderson.org	37	2	90154131	90154131	+	RNA	SNP	C	C	T	rs77198710	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CATCCACCAGGGC		340	21	0.06	395	0	0				184	7	0.04			
.	28875	bcgsc.ca	37	2	90154203	90154203	+	RNA	SNP	G	G	T	rs190666649	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCAGCAGCCTGCA		517	22	0.04	571	0	0				191	0	0.00			
.	28902	bcgsc.ca	37	2	90193417	90193417	+	RNA	SNP	A	A	G	rs1724244	bycluster;byfrequency;bysubmitter	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTAATAATTACCC		342	16	0.05	412	1	0.0024271845				0	0				
.	28892	bcgsc.ca	37	2	90229260	90229260	+	RNA	SNP	T	T	C	rs842173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGATGATCCAGTC		122	7	0.06	147	0	0				0	0				
.	28904	bcgsc.ca	37	2	90259965	90259965	+	RNA	SNP	T	T	C	rs842156	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GATGTGTCATCTG		212	19	0.09	282	2	0.0070921986				1	0	0.00			
.	0	bcgsc.ca	37	2	91800282	91800282	+	RNA	SNP	A	A	G	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGGAAGAACATCG		281	8	0.03	283	0	0				0	0				
.	643126	bcgsc.ca	37	2	96241051	96241051	+	RNA	SNP	G	G	A	rs1974909	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCTGAGGAACACC		95	7	0.07	150	0	0				0	0				
IL1RL1	9173	ucsc.edu;bcgsc.ca	37	2	102968211	102968212	+	Missense_Mutation	DNP	CA	CA	AG	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	IL1RL1	NM_016232	exon11	c.A1502G	p.Q501R	TCCCTCCAGCATC		144	18	0.13	184	1	0.0054347826		114		0	0				
.	0	bcgsc.ca	37	2	124520286	124520286	+	RNA	SNP	G	G	C	rs12997146	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AAACAAGCCATCT		34	5	0.15	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-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACAGCCTGGACAG		217	20	0.09	196	0	0				0	0				
LOC401010	0	bcgsc.ca	37	2	132201466	132201466	+	RNA	SNP	G	G	A	rs66493058	alternate_allele	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGGACGGGGCCAA		179	11	0.06	242	0	0				4	0	0.00			
LOC401010	0	bcgsc.ca	37	2	132201468	132201468	+	RNA	SNP	G	G	A	rs4522649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GACGGGGCCAAGG		179	13	0.07	247	0	0				4	0	0.00			
LOC401010	0	bcgsc.ca	37	2	132201582	132201582	+	RNA	SNP	A	A	G	rs1806886	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGCATACGGCAC		101	9	0.09	116	0	0				16	16	1.00			
LOC401010	0	bcgsc.ca	37	2	132201736	132201736	+	RNA	SNP	C	C	G	rs2076798	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGAGCCGGCTGC		59	6	0.10	58	0	0				0	0				
LOC150776	0	bcgsc.ca	37	2	132257830	132257830	+	RNA	SNP	C	C	T	rs13035779	bycluster;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTAGACGGTGTC		192	13	0.07	220	0	0				13	0	0.00			
LOC150776	0	bcgsc.ca	37	2	132258593	132258593	+	RNA	SNP	A	A	G	rs76033185	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACCACAACAAGGT		145	6	0.04	164	0	0				31	0	0.00			
.	0	bcgsc.ca	37	2	139045855	139045855	+	RNA	SNP	C	C	T	rs35998722	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTAAGCGAATAG		118	8	0.07	136	0	0				2	0	0.00			
.	0	bcgsc.ca	37	2	139045987	139045987	+	RNA	SNP	C	C	T	rs13033503	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TAGTACCATTTCG		138	7	0.05	186	0	0				1	0	0.00			
.	401018	bcgsc.ca	37	2	168571044	168571044	+	RNA	SNP	T	T	C	rs7577934	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAAATGTTGTATT		121	14	0.12	122	0	0				0	0				
.	401018	bcgsc.ca	37	2	168571488	168571488	+	RNA	SNP	A	A	T	rs34125069	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCAAAGATGCTTG		58	6	0.10	78	0	0				0	0				
LRP2	4036	bcgsc.ca;mdanderson.org	37	2	170150695	170150695	+	Silent	SNP	G	G	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	LRP2	NM_004525	exon6	c.C615T	p.D205D	ATCATTGTCATGG		476	40	0.08	612	1	0.0016339869		751		1	1	1.00			
UBR3	130507	hgsc.bcm.edu	37	2	170783231	170783231	+	Nonsense_Mutation	SNP	T	T	G	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_172070	exon15	c.T2181G	p.Y727X	AGATTATTTTATT		190	10	0.05	205	0	0				15	1	0.07			
.	0	bcgsc.ca	37	2	194141586	194141586	+	RNA	SNP	A	A	T	rs55991515		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGGGTTATCCACC		137	9	0.07	182	0	0				0	0				
.	729399	bcgsc.ca	37	2	200525076	200525076	+	RNA	SNP	A	A	G	rs77443884	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GACATCAAGGGCT		52	6	0.12	75	0	0				0	0				
.	0	ucsc.edu;bcgsc.ca;mdanderson.org	37	2	202974360	202974360	+	Missense_Mutation	SNP	T	T	G	rs12615065	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACGATGTGGCCCC		80	12	0.15	91	0	0				9	0	0.00			
.	0	bcgsc.ca	37	2	203003085	203003085	+	RNA	SNP	T	T	C	rs16838883	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTATGGTATATAT		71	7	0.10	100	0	0				0	0				
.	645805	bcgsc.ca	37	2	203066419	203066419	+	RNA	SNP	C	C	T	rs10931992	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGAAAGCGGCCGA		60	5	0.08	80	0	0				0	0				
.	0	bcgsc.ca	37	2	207275255	207275256	+	RNA	INS	-	-	CTGGTCTTG	rs57664845	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GACCACCACCTTG		84	3	0.04	120	0	0				0	0				
.	200575	bcgsc.ca	37	2	208977135	208977135	+	RNA	SNP	A	A	G	rs35960349	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACGCGCACCGAGT		63	7	0.11	68	0	0				1	0	0.00			
LOC100507443	1419	bcgsc.ca	37	2	209010891	209010891	+	Missense_Mutation	SNP	G	G	A	rs2289917	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GACTGCGGGAACG		124	19	0.15	114	0	0				0	0				
CCDC108	255101	hgsc.bcm.edu	37	2	219870199	219870199	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	CCDC108,NS,carcinoma,+2,1	CCDC108	NM_194302	exon32	c.C5008A	p.Q1670K	TCTTCTGCTTGGA		120	5	0.04	140	0	0		2	1	0	0				
.	266724	bcgsc.ca	37	2	222828022	222828022	+	RNA	SNP	G	G	T	rs76862842	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GACATTGATGCCA		117	8	0.07	127	1	0.0078740157				1	0	0.00			
MFF	56947	ucsc.edu;bcgsc.ca	37	2	228194480	228194481	+	Missense_Mutation	DNP	AG	AG	TT	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	MFF	NM_020194	exon3	c.G20T	p.S7F	ACAAGCAGTGACA		310	37	0.12	327	1	0.003058104		48		17	0	0.00			
SLC16A14	151473	hgsc.bcm.edu;bcgsc.ca	37	2	230924017	230924017	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	SLC16A14,NS,carcinoma,0,1	SLC16A14	NM_152527	exon2	c.G52T	p.D18Y	TTTTGTCTTTGGG		204	10	0.05	256	0	0		0	1	8	0	0.00			
SAG	6295	bcgsc.ca;mdanderson.org	37	2	234255547	234255548	+	Missense_Mutation	DNP	GT	GT	AC	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GT	GT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	SAG	NM_000541	exon16	c.T1208C	p.V403T	AATGACGTTGATG		86	7	0.08	109	0	0		77		3	0	0.00			
.	339766	bcgsc.ca	37	2	234708428	234708428	+	Silent	SNP	G	G	A	rs13013882	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCAGGTGAGGATG		110	17	0.15	109	1	0.0091743119				0	0				
.	339766	bcgsc.ca;mdanderson.org	37	2	234710831	234710831	+	Silent	SNP	G	G	C	rs10929306	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAGGCTGCTGTGC		88	14	0.16	95	0	0				0	0				
.	339766	bcgsc.ca	37	2	234716426	234716426	+	Silent	SNP	G	G	A	rs11563241	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AAAAACGGTGCTG		122	7	0.06	209	2	0.009569378				0	0				
.	339766	bcgsc.ca	37	2	234727333	234727333	+	Missense_Mutation	SNP	C	C	G	rs719418	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCCAAGCAGAAGG		163	8	0.05	170	0	0				0	0				
.	0	bcgsc.ca	37	2	241865211	241865211	+	Missense_Mutation	SNP	G	G	A	rs56199645		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AATGACGCGCTGG		181	12	0.07	218	0	0				0	0				
.	643503	bcgsc.ca	37	20	6182755	6182755	+	RNA	SNP	C	C	T	rs3747924	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGTGGACAGCAGC		20	4	0.20	30	0	0				0	0				
.	0	broad.mit.edu	37	20	10869748	10869748	+	RNA	DEL	T	T	-	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTTTTATTTTTTT		6	2	0.33	8	0	0				0	0				
.	388795	bcgsc.ca	37	20	31481077	31481077	+	Missense_Mutation	SNP	C	C	T	rs73904069	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AACCCCCGTATCC		191	7	0.04	154	0	0				0	0				
.	391269	bcgsc.ca	37	21	15436681	15436681	+	RNA	SNP	G	G	C	rs11908695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGGCCAGATGGTC		249	25	0.10	256	1	0.00390625				4	0	0.00			
.	653214	bcgsc.ca	37	21	20230102	20230102	+	RNA	SNP	C	C	T	rs2825212	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CATGGTCAACCCC		271	15	0.06	265	3	0.0113207547				5048	6	0.00			
.	54019	bcgsc.ca	37	21	20617291	20617291	+	RNA	SNP	G	G	T	rs9980261	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCTACAGACTACC		46	8	0.17	48	0	0				0	0				
.	391276	bcgsc.ca	37	21	30274198	30274198	+	RNA	SNP	G	G	A	rs2248250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTAGACGTTCTTT		32	5	0.16	36	0	0				0	0				
.	391276	bcgsc.ca	37	21	30274205	30274205	+	RNA	SNP	T	T	C	rs2738935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTCTTTTCCGCCC		28	4	0.14	33	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-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGAAGGCGACGTT		77	5	0.06	65	0	0				1	0	0.00			
.	391276	bcgsc.ca	37	21	30275705	30275705	+	RNA	SNP	G	G	A	rs2705643	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTCAATGTCACCA		77	9	0.12	56	1	0.0178571429				0	0				
TIAM1	7074	bcgsc.ca	37	21	32638549	32638550	+	Missense_Mutation	DNP	CC	CC	AT	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	TIAM1	NM_003253	exon5	c.G739A	p.G247M	GGCCCCCCGTTTG		234	13	0.06	202	0	0		522		19	0	0.00			
PAXBP1	94104	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	21	34123334	34123336	+	In_Frame_Del	DEL	ACG	ACG	-	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	ACG	ACG					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_013329	exon10	c.1616_1618del	p.539_540del	TTGTCTACGACGA		172	26	0.15	158	0	0				87	0	0.00			
KRTAP12-2	353323	bcgsc.ca	37	21	46086718	46086719	+	Missense_Mutation	DNP	GA	GA	CG	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GA	GA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	KRTAP12-2	NM_181684	exon1	c.T85C	p.S29R	TGGCAGGAGCTGG		94	10	0.11	77	1	0.012987013		10		0	0				
.	644768	bcgsc.ca	37	22	16940793	16940793	+	RNA	SNP	C	C	T	rs150627359	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTCTTGCGACACC		153	12	0.08	144	0	0				0	0				
RIMBP3	85376	bcgsc.ca;mdanderson.org	37	22	20457841	20457841	+	Missense_Mutation	SNP	T	T	C	rs202034782	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	RIMBP3	NM_015672	exon1	c.A3461G	p.Q1154R	GGCACCTGTAGCT		972	31	0.03	1100	0	0		42		3	0	0.00			
LOC400891	0	ucsc.edu;bcgsc.ca;mdanderson.org	37	22	21407656	21407656	+	Missense_Mutation	SNP	T	T	C	rs59837066	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAAACATCTTCCT		138	15	0.11	137	0	0				0	0				
.	0	broad.mit.edu	37	22	22516884	22516884	+	RNA	DEL	C	C	-	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGGCATCAGCAGC		196	14	0.07	263	0	0				56	0	0.00			
.	28785	bcgsc.ca	37	22	22516998	22516998	+	RNA	SNP	C	C	T	rs2073453	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCTGACCGCTACC		121	8	0.07	140	0	0				62	0	0.00			
.	28770	bcgsc.ca	37	22	22556368	22556368	+	RNA	SNP	C	C	T	rs9306341	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGAAGCCAGGGAG		98	7	0.07	76	0	0				0	0				
.	23751	bcgsc.ca	37	22	22577869	22577869	+	RNA	SNP	A	A	G	rs743515	bycluster;byfrequency;by2hit2allele	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CGGCGGACACCCG		289	21	0.07	341	0	0				0	0				
.	28802	bcgsc.ca;mdanderson.org	37	22	23114327	23114327	+	RNA	SNP	T	T	C	rs6003299	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGCCATGGCCTG		102	17	0.17	133	0	0				2	0	0.00			
.	28802	bcgsc.ca;mdanderson.org	37	22	23114350	23114350	+	RNA	SNP	A	A	G	rs5996382	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTCCTCAGCCTCC		110	23	0.21	150	1	0.0066666667				1	0	0.00			
.	28802	bcgsc.ca;mdanderson.org	37	22	23114993	23114993	+	RNA	SNP	G	G	A	rs2073451	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AACACCGCCACCC		93	14	0.15	98	0	0				4	0	0.00			
GAS2L1	10634	bcgsc.ca;mdanderson.org	37	22	29707888	29707888	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	GAS2L1	.	.	.	.	CAGCACCCCGGCT		17	5	0.29	18	0	0		54		65	6	0.09			
LIMK2	3985	ucsc.edu	37	22	31655980	31655980	+	Silent	SNP	G	G	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	LIMK2,colon,carcinoma,0,1	LIMK2	NM_005569	exon5	c.G468A	p.P156P	CATGCCGGCCACC		43	4	0.09	52	1	0.0192307692		101	1	53	0	0.00			
.	0	bcgsc.ca	37	22	44761797	44761797	+	Missense_Mutation	SNP	T	T	A	rs5765809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ATGTGCTTAGACA		141	8	0.06	138	0	0				0	0				
.	0	bcgsc.ca	37	22	51193572	51193572	+	RNA	SNP	A	A	G	rs138661035	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTATTATTGGTG		137	16	0.12	143	0	0				3	0	0.00			
.	0	bcgsc.ca	37	22	51193629	51193629	+	RNA	SNP	A	A	G	rs142680588	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACCTATACGGCAT		232	24	0.10	253	0	0				9	0	0.00			
.	0	bcgsc.ca	37	3	11915154	11915154	+	RNA	SNP	A	A	G	rs3732701	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTCAGCAAATACG		69	10	0.14	83	0	0				0	0				
.	152110	bcgsc.ca;mdanderson.org	37	3	27204052	27204052	+	Silent	SNP	G	G	A	rs17854381	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	NEK10_ENST00000429845,NS,carcinoma,0,1	.	.	.	.	.	GAGCATGTGGGGT		127	10	0.08	145	1	0.0068965517			1	0	0				
.	152110	bcgsc.ca	37	3	27216197	27216197	+	Missense_Mutation	SNP	C	C	T	rs55780680	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	NEK10,NS,carcinoma,0,2	.	.	.	.	.	CAGGCCCTGTCTT		235	8	0.03	268	0	0			2	0	0				
.	152110	bcgsc.ca	37	3	27243045	27243045	+	Silent	SNP	G	G	C	rs17680166	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTCTGGGACTGGT		169	6	0.04	184	0	0				0	0				
.	391524	bcgsc.ca	37	3	31494587	31494587	+	RNA	SNP	G	G	A	rs17027714	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTGGGCGCAACAG		57	7	0.12	57	0	0				0	0				
.	391524	bcgsc.ca	37	3	31494993	31494993	+	RNA	SNP	C	C	T	rs9824199	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CACCTACGGCACT		51	6	0.12	68	0	0				0	0				
.	391524	bcgsc.ca	37	3	31496145	31496145	+	RNA	SNP	T	T	C	rs9849739	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCATTTTCCAGCA		138	6	0.04	185	0	0				0	0				
.	391526	bcgsc.ca	37	3	32662531	32662531	+	RNA	SNP	T	T	C	rs6550143	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGAATTTCTCTGG		60	7	0.12	108	0	0				0	0				
.	391526	bcgsc.ca	37	3	32662803	32662803	+	RNA	SNP	C	C	A	rs59067676	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAATCCCCCTTTG		132	15	0.11	176	1	0.0056818182				0	0				
.	391526	bcgsc.ca	37	3	32662807	32662807	+	RNA	SNP	T	T	C	rs58963522	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCCCCTTTGAAGG		139	15	0.11	186	1	0.0053763441				0	0				
.	391526	bcgsc.ca	37	3	32662919	32662919	+	RNA	SNP	C	C	T	rs34045705	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTGTATCTCTCTA		169	20	0.12	182	1	0.0054945055				0	0				
.	391526	bcgsc.ca	37	3	32662938	32662938	+	RNA	SNP	T	T	C	rs35370637	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTGCCTTTGAGA		168	12	0.07	164	0	0				0	0				
.	391526	bcgsc.ca	37	3	32662960	32662960	+	RNA	SNP	A	A	G	rs35066348	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AACGAGACTAGGA		161	23	0.14	162	0	0				1	0	0.00			
.	0	bcgsc.ca	37	3	39255730	39255730	+	RNA	SNP	G	G	A	rs7643880	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTTTTTGTGACAT		28	5	0.18	29	0	0				0	0				
.	0	bcgsc.ca	37	3	39686013	39686013	+	RNA	SNP	A	A	T	rs78908069	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TAATCTACAAAGG		117	9	0.08	90	0	0				0	0				
.	391530	bcgsc.ca	37	3	42363697	42363697	+	RNA	SNP	C	C	T	rs139639533	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCTCTTCGCATTC		28	5	0.18	28	0	0				0	0				
.	9430	bcgsc.ca	37	3	75377715	75377715	+	RNA	SNP	C	C	T	rs4677496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGAGGACGATGAA		60	5	0.08	56	0	0				0	0				
.	0	bcgsc.ca	37	3	103782249	103782249	+	RNA	SNP	G	G	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAAAGAGTTGTAG		31	4	0.13	38	0	0				0	0				
.	339881	bcgsc.ca	37	3	122380888	122380888	+	RNA	SNP	C	C	T	rs790117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTCCACCAAAGGA		89	8	0.09	77	0	0				0	0				
.	339881	bcgsc.ca	37	3	122380923	122380923	+	RNA	SNP	G	G	C	rs790116	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCTAACGCTCCTG		89	10	0.11	80	0	0				0	0				
LOC653712	0	bcgsc.ca	37	3	128580585	128580585	+	RNA	SNP	C	C	A	rs789247	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTCCACGGCAGA		158	8	0.05	151	0	0				7	0	0.00			
.	0	bcgsc.ca	37	3	132105901	132105901	+	RNA	SNP	A	A	G	rs2124506	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTGCTCAGAATTT		102	8	0.08	108	0	0				0	0				
.	0	bcgsc.ca	37	3	166579857	166579857	+	RNA	SNP	C	C	T	rs9832877	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCTGTACTTTTGT		131	16	0.12	131	2	0.0152671756				0	0				
.	280644	bcgsc.ca	37	3	186479009	186479009	+	RNA	SNP	A	A	G	rs866601	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AACAGCAGAACTG		139	9	0.06	103	0	0				1	0	0.00			
.	0	bcgsc.ca	37	4	3938121	3938121	+	RNA	SNP	C	C	T	rs7676401	bycluster;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCAGCCCTGCTGG		63	5	0.08	90	0	0				4	0	0.00			
.	728564	bcgsc.ca	37	4	8176480	8176480	+	RNA	SNP	G	G	A	rs11547949	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GATGCCGGTGATT		94	6	0.06	138	0	0				114	0	0.00			
.	0	bcgsc.ca	37	4	9486098	9486098	+	RNA	SNP	C	C	G	rs114281488	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGATTTCATCTTC		170	6	0.04	236	0	0				0	0				
.	0	bcgsc.ca	37	4	9711554	9711554	+	RNA	SNP	G	G	A	rs111695399	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCGACCGCTCCGT		126	6	0.05	159	1	0.0062893082				0	0				
.	645641	bcgsc.ca	37	4	28825584	28825584	+	RNA	SNP	G	G	A	rs12644777	bycluster;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCAATCGTAGCTG		31	5	0.16	46	0	0				6	0	0.00			
.	0	bcgsc.ca	37	4	33012957	33012957	+	RNA	SNP	A	A	G	rs6531315	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACTGCAATTTCTT		47	4	0.09	63	0	0				0	0				
.	0	bcgsc.ca	37	4	49244932	49244932	+	RNA	SNP	C	C	T	rs201474862	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCATTGCTATTTT		15	5	0.33	19	0	0				0	0				
.	0	bcgsc.ca	37	4	57627451	57627451	+	RNA	SNP	G	G	A	rs2016218	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCCTTTGGAAAGC		103	10	0.10	172	2	0.011627907				0	0				
.	644548	bcgsc.ca	37	4	63683674	63683674	+	RNA	SNP	G	G	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AAAGATGTCATAG		65	21	0.32	138	0	0				1	0	0.00			
.	0	bcgsc.ca	37	4	70212704	70212704	+	RNA	SNP	G	G	A	rs6851810	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTTTGAGAGCATT		57	7	0.12	98	0	0				0	0				
.	345258	bcgsc.ca	37	4	83196536	83196536	+	RNA	SNP	G	G	A	rs13119500	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGCCAAGAAAGAT		24	5	0.21	29	0	0				1	0	0.00			
.	391672	bcgsc.ca	37	4	83323062	83323062	+	RNA	SNP	T	T	C	rs7695741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TAGAAGTTGATGC		81	8	0.10	115	0	0				0	0				
SEC31A	22872	ucsc.edu	37	4	83778879	83778879	+	Silent	SNP	G	G	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	SEC31A	NM_001077206	exon15	c.C1665A	p.P555P	AGATGAGGGTAGA		43	4	0.09	53	0	0		227		181	0	0.00			
.	391686	bcgsc.ca	37	4	111866561	111866561	+	RNA	SNP	C	C	T	rs28696178	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTGCTACGTGGTA		36	4	0.11	62	0	0				0	0				
.	729249	bcgsc.ca	37	4	120275268	120275268	+	RNA	SNP	A	A	G	rs62320725	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TAGGTGAGATGAG		213	17	0.08	284	0	0				0	0				
.	0	bcgsc.ca	37	4	120314664	120314664	+	RNA	SNP	T	T	C	rs13127114	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTCCATTGTGACG		104	11	0.11	171	0	0				0	0				
.	0	bcgsc.ca	37	4	120314741	120314741	+	RNA	SNP	C	C	A	rs13151285	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGCACCCAATGC		98	8	0.08	184	0	0				0	0				
.	0	bcgsc.ca	37	4	120314881	120314881	+	RNA	SNP	A	A	G	rs4309825	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAATTCATGGCAT		240	16	0.07	343	0	0				0	0				
.	0	bcgsc.ca	37	4	120314921	120314921	+	RNA	SNP	C	C	T	rs4604043	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGCTTCTAATGC		258	18	0.07	359	0	0				1	0	0.00			
.	0	bcgsc.ca	37	4	120315906	120315906	+	RNA	SNP	C	C	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGTTTTCGCTATA		176	10	0.06	204	0	0				1	0	0.00			
.	0	bcgsc.ca	37	4	120316075	120316075	+	RNA	SNP	A	A	G	rs11098513	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCCCCCACCAATG		135	10	0.07	150	2	0.0133333333				0	0				
.	344988	bcgsc.ca	37	4	121263497	121263497	+	RNA	SNP	G	G	A	rs1160185	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AATGGGGTTATCT		16	5	0.31	22	0	0				0	0				
.	100128266	bcgsc.ca	37	4	174555444	174555444	+	RNA	SNP	C	C	T	rs60395447	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTTTCACGAAGGT		28	5	0.18	64	0	0				0	0				
.	0	bcgsc.ca	37	4	189660460	189660460	+	RNA	SNP	G	G	C	rs60608362	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGTAAAGGAAGAT		120	7	0.06	205	0	0				30	0	0.00			
.	3323	bcgsc.ca	37	4	190395259	190395259	+	RNA	SNP	C	C	G	rs13143685	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAGGAGCTAATCC		54	7	0.13	94	0	0				0	0				
.	653082	bcgsc.ca	37	5	766939	766939	+	Silent	SNP	G	G	A	rs4957103	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	ZDHHC11B,NS,carcinoma,0,1	.	.	.	.	.	CCAGCCGTTCACT		61	5	0.08	76	0	0			1	0	0				
ZDHHC11	79844	bcgsc.ca	37	5	843766	843766	+	Missense_Mutation	SNP	C	C	T	rs76685897	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	ZDHHC11	NM_024786	exon4	c.G577A	p.V193I	ACTGGACGAGGAC		341	15	0.04	511	0	0		97		7	0	0.00			
.	391739	bcgsc.ca	37	5	14639939	14639939	+	RNA	SNP	C	C	T	rs144306780	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGACAGCCCTCAA		31	4	0.13	58	0	0				0	0				
.	4479	bcgsc.ca	37	5	25909764	25909764	+	RNA	SNP	C	C	T	rs11739167	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCAGGACACCAAA		64	9	0.14	116	0	0				32	0	0.00			
.	4479	bcgsc.ca	37	5	25910566	25910566	+	RNA	SNP	A	A	G	rs12655221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGAAGCAGATGGA		102	26	0.25	191	0	0				23	0	0.00			
.	4479	bcgsc.ca	37	5	25911136	25911136	+	RNA	SNP	C	C	A	rs9293194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AATGTACCACTGA		163	26	0.16	237	1	0.0042194093				8	0	0.00			
.	0	bcgsc.ca	37	5	32523748	32523748	+	RNA	SNP	T	T	C	rs591985	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTCAATTTCATCT		162	8	0.05	222	1	0.0045045045				0	0				
.	285634	bcgsc.ca	37	5	39719446	39719446	+	RNA	SNP	A	A	G	rs10512714	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCCACCAACAGTG		53	8	0.15	72	0	0				0	0				
.	0	bcgsc.ca	37	5	41586211	41586211	+	RNA	SNP	T	T	G	rs634858	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTTTACTTTCTGG		16	4	0.25	24	0	0				0	0				
.	0	bcgsc.ca	37	5	41587666	41587666	+	RNA	SNP	C	C	T	rs661845	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAACTTCAGCTGC		57	8	0.14	75	0	0				0	0				
.	0	bcgsc.ca	37	5	41587802	41587802	+	RNA	SNP	T	T	C	rs79920342	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGGCAATTGAAGC		33	4	0.12	48	0	0				0	0				
FBXO4	26272	hgsc.bcm.edu;bcgsc.ca	37	5	41927269	41927269	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_033484	exon2	c.G344T	p.W115L	TTGACTGGAAGTC		120	6	0.05	191	0	0				28	0	0.00			
GLRX	2745	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	95152294	95152294	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	GLRX,NS,carcinoma,0,1	GLRX	NM_001243659	exon2	c.G244A	p.G82R	TGCATCCGCCTAT		83	10	0.12	123	0	0		0	1	100	7	0.07			
PCDHB4	56131	ucsc.edu;bcgsc.ca	37	5	140502343	140502344	+	Missense_Mutation	DNP	CC	CC	TT	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	PCDHB4	NM_018938	exon1	c.C764T	p.P255F	AACAGCCCCCTAG		102	15	0.15	187	0	0		177		1	0	0.00			
.	0	bcgsc.ca	37	6	1514247	1514247	+	RNA	SNP	G	G	A	rs12211247	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCAATGGAGCTCC		16	4	0.25	18	0	0				0	0				
.	0	bcgsc.ca	37	6	1514652	1514652	+	RNA	SNP	C	C	T	rs3902814	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CACACCCTTCTCT		31	4	0.13	51	0	0				0	0				
.	9425	bcgsc.ca;mdanderson.org	37	6	4716016	4716016	+	Missense_Mutation	SNP	A	A	G	rs3812179	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	CDYL,NS,carcinoma,0,2	.	.	.	.	.	TTTATGACATTTC		229	14	0.06	262	1	0.0038167939			2	0	0				
.	9425	bcgsc.ca	37	6	4716037	4716037	+	Missense_Mutation	SNP	T	T	C	rs3812178	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	CDYL,NS,carcinoma,0,2	.	.	.	.	.	CACAGGTCAGCCT		243	13	0.05	268	2	0.0074626866			2	0	0				
.	9425	bcgsc.ca	37	6	4735035	4735035	+	Missense_Mutation	SNP	T	T	C	rs13196069	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	CDYL,NS,carcinoma,0,1	.	.	.	.	.	TCTCCGTGAGCAG		75	5	0.07	89	1	0.0112359551			1	0	0				
.	9425	bcgsc.ca	37	6	4735071	4735071	+	Missense_Mutation	SNP	C	C	G	rs28360500	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	CDYL,NS,carcinoma,0,1	.	.	.	.	.	CTCCCGCTTTACA		75	5	0.07	91	1	0.010989011			1	0	0				
.	0	bcgsc.ca	37	6	23972696	23972696	+	RNA	SNP	G	G	T	rs34725714	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ATGTTAGTTTCTT		72	5	0.07	109	0	0				0	0				
HIST1H2AB	8335	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	6	26033614	26033614	+	Silent	SNP	G	G	A	rs199590202	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_003513	exon1	c.C183T	p.A61A	GATCTCGGCGGTC		102	17	0.17	140	0	0	0.001			1	1	1.00			
HIST1H4F	8361	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	26240904	26240904	+	Missense_Mutation	SNP	C	C	G	rs374666858	alternate_allele	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_003540	exon1	c.C251G	p.A84G	TCACTGCAATGGA		98	22	0.22	132	0	0				0	0				
ZNF322	79692	bcgsc.ca;mdanderson.org	37	6	26637724	26637724	+	Missense_Mutation	SNP	T	T	C	rs71557344	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_001242797	exon5	c.A1058G	p.Y353C	ACAGTGTATTTAT		633	24	0.04	748	2	0.0026737968				37	0	0.00			
ZKSCAN3	80317	ucsc.edu;bcgsc.ca	37	6	28331127	28331128	+	Missense_Mutation	DNP	AA	AA	GC	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AA	AA					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	ZKSCAN3,NS,other,-1,1	ZKSCAN3	NM_024493	exon4	c.A599C	p.K200A	GAAGATAAAGTGG		79	7	0.09	101	1	0.0099009901		50	1	9	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-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCCAGGGAGTAAG		98	17	0.17	119	0	0				0	0				
.	352963	bcgsc.ca	37	6	29769497	29769497	+	RNA	SNP	A	A	C	rs1610711	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCTTCTAGTTGCT		27	6	0.22	21	0	0				0	0				
HLA-G	3135	ucsc.edu	37	6	29797394	29797394	+	Silent	SNP	G	G	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	HLA-G	NM_002127	exon5	c.G819A	p.V273V	GGTGGTGCCTTCT		132	1	0.01	137	0	0		90		866	344	0.40			
TRIM39	56658	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	6	30309904	30309904	+	Silent	SNP	A	A	G	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_021253	exon9	c.A1425G	p.T475T	TGTCACAGACCGC		86	7	0.08	130	0	0				42	0	0.00			
.	116935	bcgsc.ca	37	6	31248785	31248785	+	RNA	SNP	G	G	A	rs2524061	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCAGTCGTTGGCA		57	5	0.09	48	0	0				9	0	0.00			
.	3132	bcgsc.ca	37	6	32441276	32441276	+	RNA	SNP	C	C	T	rs12215313	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAGCCTCCAGGGA		129	6	0.05	129	0	0				277	0	0.00			
HLA-DRB6	0	broad.mit.edu	37	6	32521925	32521926	+	RNA	INS	-	-	T	rs140249246	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CACACTGAACAGT		10	3	0.30	14	0	0				0	0				
.	0	bcgsc.ca	37	6	51275042	51275042	+	RNA	SNP	T	T	C	rs62458490	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	ENSG00000180518,NS,carcinoma,0,1	.	.	.	.	.	ACTTGCTTGAGGT		355	12	0.03	436	1	0.002293578			1	162	0	0.00			
.	1204	bcgsc.ca	37	6	54350048	54350048	+	RNA	SNP	G	G	A	rs807991	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TATTGAGTCTTCT		115	6	0.05	124	0	0				0	0				
.	642443	bcgsc.ca	37	6	66546941	66546941	+	RNA	SNP	A	A	G	rs61732140	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTGGACATATATT		269	12	0.04	313	1	0.0031948882				8	0	0.00			
.	642443	bcgsc.ca	37	6	66547178	66547178	+	RNA	SNP	G	G	A	rs4392709	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCAGTCGTCTCAA		154	14	0.09	237	1	0.0042194093				0	0				
.	642443	bcgsc.ca	37	6	66547322	66547322	+	RNA	SNP	T	T	G	rs9363455	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGCCCTTGATAA		107	12	0.11	156	0	0				0	0				
.	0	bcgsc.ca	37	6	73308220	73308220	+	RNA	SNP	G	G	C	rs79957120	byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTTTTGGTACTGA		106	5	0.05	148	0	0				0	0				
PHIP	55023	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	6	79725372	79725372	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_017934	exon14	c.C1364G	p.T455S	TGACCAGTGTAAG		118	10	0.08	130	0	0				7	0	0.00			
.	0	bcgsc.ca	37	6	85996401	85996401	+	RNA	SNP	C	C	T	rs313229	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGCAAGCAGTGTG		252	15	0.06	278	1	0.0035971223				5	0	0.00			
.	442237	bcgsc.ca	37	6	97096688	97096688	+	RNA	SNP	T	T	C	rs11759390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCCCACTGAACTT		132	15	0.11	182	0	0				0	0				
MED23	9439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	131923359	131923359	+	Silent	SNP	T	T	G	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_015979	exon18	c.A2112C	p.T704T	CGTACCTGTTACA		100	26	0.26	130	0	0				23	10	0.43			
.	391040	bcgsc.ca	37	6	137865140	137865140	+	RNA	SNP	A	A	G	rs9484059	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCCAAGACTTGCC		74	6	0.08	120	0	0				1	0	0.00			
.	391040	bcgsc.ca	37	6	137865147	137865147	+	RNA	SNP	A	A	G	rs9494809	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTTGCCATGGGAA		71	6	0.08	126	0	0				0	0				
.	153932	bcgsc.ca	37	6	158658759	158658759	+	RNA	SNP	C	C	G	rs113731832	byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTATCTCTAGTAA		37	4	0.11	57	0	0				3	0	0.00			
.	153932	bcgsc.ca	37	6	158658857	158658857	+	RNA	SNP	A	A	C	rs112542076	byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGGCAAATGTTTA		50	7	0.14	51	0	0				1	0	0.00			
TCP1	6950	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	160205000	160205000	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_030752	exon7	c.C770T	p.P257L	TTTTCAGGGTCTG		127	20	0.16	168	0	0				618	105	0.17			
.	0	bcgsc.ca	37	6	167622347	167622347	+	RNA	SNP	A	A	C	rs9459922	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAAGGCAGCTTCC		85	8	0.09	113	0	0				13	0	0.00			
.	100421638	bcgsc.ca	37	6	168688281	168688281	+	RNA	SNP	T	T	G	rs9456019	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTCTTTCCTTGG		127	17	0.13	159	1	0.0062893082				0	0				
LOC389458	57786	bcgsc.ca	37	7	5112853	5112853	+	RNA	SNP	G	G	C	rs73316654	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TAGCTAGAGGTGC		143	6	0.04	168	0	0				0	0				
.	0	bcgsc.ca	37	7	9767725	9767725	+	RNA	SNP	G	G	T	rs72583761	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGTTCCGGCTGAC		157	12	0.08	175	0	0				13	0	0.00			
.	0	bcgsc.ca	37	7	9767811	9767811	+	RNA	SNP	T	T	G	rs112406696	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTTTTTGGTGGG		156	14	0.09	162	0	0				8	0	0.00			
.	0	bcgsc.ca	37	7	12511173	12511173	+	RNA	SNP	C	C	T	rs12699379	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTTTAACGTAATT		27	4	0.15	46	0	0				0	0				
.	0	bcgsc.ca	37	7	12511312	12511312	+	RNA	SNP	G	G	A	rs11275	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGATCTGTTTATA		71	5	0.07	87	0	0				3	0	0.00			
.	0	bcgsc.ca	37	7	12511924	12511924	+	RNA	SNP	T	T	G	rs847956	bycluster;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGCACTTAAAAAA		51	7	0.14	58	0	0				0	0				
.	0	bcgsc.ca	37	7	23603318	23603318	+	RNA	SNP	A	A	G	rs227944	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTCCAAAATAGAT		325	13	0.04	369	0	0				0	0				
LOC646762	0	bcgsc.ca	37	7	29700039	29700039	+	RNA	SNP	C	C	T	rs1728603	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTAAAACGCTTCC		156	20	0.13	174	0	0				0	0				
.	0	broad.mit.edu	37	7	38284884	38284885	+	RNA	INS	-	-	GG	rs200076851	by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTGTCAAGGTGTG		7	5	0.71	4	0	0				0	0				
.	0	bcgsc.ca	37	7	39874281	39874281	+	RNA	SNP	T	T	C	rs113205984	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCAGAATGACAAT		163	14	0.09	204	0	0				35	35	1.00			
.	0	bcgsc.ca	37	7	48886607	48886607	+	RNA	SNP	A	A	G	rs28657654	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AAGATCATGGTGA		194	17	0.09	230	1	0.0043478261				2	0	0.00			
.	2667	bcgsc.ca	37	7	48943352	48943352	+	RNA	SNP	T	T	C	rs887451	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTGTTATAGAGGC		23	5	0.22	25	0	0				0	0				
.	0	bcgsc.ca	37	7	51668140	51668140	+	RNA	SNP	G	G	A	rs4538818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAATTCGAACTTT		132	7	0.05	158	0	0				0	0				
.	0	bcgsc.ca	37	7	51668190	51668190	+	RNA	SNP	G	G	A	rs4541850	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGGGGAGGCTGGC		159	7	0.04	185	0	0				0	0				
.	653175	bcgsc.ca	37	7	53256324	53256324	+	RNA	SNP	T	T	C	rs35856447	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAAAGATGGGAAC		215	22	0.10	238	2	0.0084033613				11	0	0.00			
.	222005	bcgsc.ca	37	7	54487594	54487594	+	RNA	SNP	C	C	T	rs35588876	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAATTCCGAGGCC		35	4	0.11	48	0	0				2	0	0.00			
.	0	bcgsc.ca	37	7	55706496	55706496	+	RNA	SNP	T	T	C	rs7791528	bycluster;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TACCAATAGCACC		39	8	0.21	42	0	0				0	0				
.	360132	bcgsc.ca	37	7	55774888	55774888	+	RNA	SNP	C	C	T	rs12666519	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGAAGCGTGCCA		328	25	0.08	335	0	0				13	0	0.00			
.	0	bcgsc.ca	37	7	56356744	56356744	+	RNA	SNP	G	G	T	rs3813510	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGTCTGCTGGGT		56	5	0.09	81	1	0.012345679				0	0				
.	0	bcgsc.ca	37	7	63602199	63602199	+	RNA	SNP	A	A	G	rs191758847	by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTGGCAATGACAA		31	4	0.13	31	0	0				2	0	0.00			
CCT6P3	0	broad.mit.edu	37	7	64528813	64528814	+	RNA	INS	-	-	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTGTAACTTTTTT		9	2	0.22	7	0	0				0	0				
.	0	bcgsc.ca	37	7	65266945	65266945	+	RNA	SNP	G	G	A	rs73701013	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTTCCTGTATGTA		45	5	0.11	39	0	0				0	0				
AUTS2	26053	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	70255922	70255922	+	Silent	SNP	G	G	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_015570	exon19	c.G3720T	p.L1240L	TCCTCTGTCCGCA		69	11	0.16	83	0	0				121	30	0.25			
LOC100133091	22932	bcgsc.ca	37	7	76247668	76247668	+	Silent	SNP	G	G	A	rs1636619	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGCACCGTGGCTC		489	43	0.09	529	4	0.0075614367				1	0	0.00			
.	0	bcgsc.ca	37	7	79726151	79726151	+	RNA	SNP	G	G	T	rs10239304	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AAACATGATGACT		33	10	0.30	28	0	0				0	0				
ZNF804B	219578	bcgsc.ca	37	7	88964226	88964227	+	Missense_Mutation	DNP	CC	CC	AG	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	ZNF804B,NS,carcinoma,0,1	ZNF804B	NM_181646	exon4	c.C1931G	p.P644S	TGCAGTCCTCATT		162	7	0.04	194	0	0		322	1	0	0				
KEL	3792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	142651427	142651427	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_000420	exon8	c.G768C	p.Q256H	TCCCAGCTGATTC		73	22	0.30	103	0	0				91	24	0.26			
.	0	bcgsc.ca;mdanderson.org	37	7	154989982	154989982	+	Missense_Mutation	SNP	G	G	A	rs28664023	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CACCCCGAATCAC		180	26	0.14	204	0	0				0	0				
.	0	bcgsc.ca	37	7	155174898	155174898	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GGGGAGCCTGGCT		66	6	0.09	39	0	0				0	0				
FAM86B2	653333	bcgsc.ca	37	8	12287957	12287957	+	Missense_Mutation	SNP	C	C	T	rs2898329		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	FAM86B2	NM_001137610	exon4	c.G244A	p.E82K	CAGCCTCGTGCTG		272	20	0.07	296	3	0.0101351351		19		0	0				
.	0	bcgsc.ca	37	8	13880224	13880224	+	RNA	SNP	G	G	A	rs4831261	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCGGCCGTATAAT		119	9	0.08	140	0	0				0	0				
.	0	bcgsc.ca	37	8	13880562	13880562	+	RNA	SNP	G	G	T	rs7003822	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACGTAAGACAATC		151	19	0.13	230	0	0				0	0				
.	137012	bcgsc.ca	37	8	15663805	15663805	+	RNA	SNP	C	C	A	rs73199378	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGTACACCACATG		56	6	0.11	70	0	0				0	0				
.	724059	bcgsc.ca	37	8	20792070	20792070	+	RNA	SNP	G	G	C	rs11776249	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AATCCAGTTGCAG		55	11	0.20	45	0	0				0	0				
C8orf58	541565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	22459522	22459522	+	Missense_Mutation	SNP	C	C	T	rs147143680		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_001013842	exon4	c.C695T	p.P232L	CTTTACCGTCCCC		108	28	0.26	111	0	0	0			57	18	0.32			
.	29778	bcgsc.ca	37	8	29885662	29885662	+	RNA	SNP	G	G	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTGCAGGTAGCAC		70	9	0.13	85	0	0				2	0	0.00			
.	29778	bcgsc.ca	37	8	29886264	29886264	+	RNA	DEL	A	A	-	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTAATAAAAACC		79	16	0.20	77	0	0				3	0	0.00			
.	0	bcgsc.ca	37	8	30841331	30841331	+	RNA	SNP	C	C	T	rs2080720	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTATTACCCACTG		35	9	0.26	40	0	0				0	0				
.	0	bcgsc.ca	37	8	30841522	30841522	+	RNA	SNP	A	A	G	rs2344121	bycluster;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGAGGAAGCCCCT		55	5	0.09	63	0	0				0	0				
.	0	broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	57294571	57294571	+	RNA	SNP	C	C	G	rs10216409	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ATGGTGCTTTTAA		120	21	0.18	166	1	0.0060240964				0	0				
.	0	bcgsc.ca	37	8	61851466	61851466	+	RNA	SNP	T	T	C	rs3748648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTGATCTCCTACA		168	9	0.05	189	0	0				1	0	0.00			
.	0	bcgsc.ca	37	8	70042263	70042263	+	RNA	SNP	A	A	G	rs67905920	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCGTGCAGAGATG		50	9	0.18	57	0	0				2	0	0.00			
.	6661	bcgsc.ca	37	8	88801868	88801868	+	RNA	SNP	T	T	G	rs16873107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGAGGTCTTGGG		84	5	0.06	93	1	0.0107526882				0	0				
FAM83A	84985	bcgsc.ca	37	8	124221677	124221681	+	Frame_Shift_Del	DEL	AAACA	AAACA	-	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AAACA	AAACA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	FAM83A	NM_207006	exon5	c.1045_1049del	p.349_350del	GAAAGTAAACAAA		97	3	0.03	92	0	0		64		0	0				
.	0	bcgsc.ca	37	8	125933052	125933052	+	RNA	SNP	T	T	C	rs17395997	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTTAAATTTAGAG		66	7	0.11	108	1	0.0092592593				0	0				
.	0	bcgsc.ca	37	8	143719983	143719983	+	RNA	SNP	G	G	C	rs2280881	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CATGACGCCAGTG		180	18	0.10	179	0	0				0	0				
.	100132467	bcgsc.ca	37	9	6669375	6669375	+	RNA	SNP	C	C	G	rs2297556	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TTGCTGCATTGTT		65	7	0.11	74	0	0				0	0				
.	0	bcgsc.ca	37	9	29826486	29826486	+	RNA	SNP	G	G	A	rs79694178	byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AACTACGCTTAAC		30	5	0.17	34	0	0				0	0				
.	441391	bcgsc.ca	37	9	30689445	30689445	+	RNA	SNP	G	G	A	rs200326968	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGAGGAGGAAGTG		443	18	0.04	492	0	0				37	0	0.00			
.	441391	bcgsc.ca	37	9	30689459	30689459	+	RNA	SNP	A	A	C	rs201295283	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGGAACAAGGGGA		430	20	0.05	483	0	0				4	2	0.50			
.	441391	bcgsc.ca	37	9	30690005	30690005	+	RNA	SNP	A	A	C	rs78196531		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GCCCCCACCATCT		233	15	0.06	276	1	0.0036231884				1	0	0.00			
.	0	bcgsc.ca	37	9	40610136	40610136	+	RNA	SNP	G	G	A	rs76194885	bycluster;byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CAGTGGGGCATCA		405	22	0.05	577	1	0.0017331023				2	0	0.00			
CNTNAP3B	728577	bcgsc.ca	37	9	43822686	43822686	+	Missense_Mutation	SNP	C	C	A	rs62555055		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	CNTNAP3B	NM_001201380	exon8	c.C1240A	p.R414S	CTTCAACGTGGTT		235	25	0.11	298	2	0.0067114094		37		0	0				
CNTNAP3B	728577	bcgsc.ca	37	9	43822704	43822704	+	Missense_Mutation	SNP	G	G	A	rs62555056		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	CNTNAP3B	NM_001201380	exon8	c.G1258A	p.V420I	AGTTTCGTCCTCT		236	22	0.09	301	0	0		37		0	0				
.	0	bcgsc.ca	37	9	76089841	76089841	+	RNA	SNP	C	C	A	rs278746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGCGAGCAGCCCA		31	4	0.13	36	0	0				0	0				
.	0	bcgsc.ca	37	9	80834173	80834173	+	RNA	SNP	A	A	G	rs878922	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGACTTATGTCCA		101	17	0.17	110	1	0.0090909091				0	0				
.	0	bcgsc.ca	37	9	88401021	88401021	+	RNA	SNP	A	A	G	rs11141102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GATCATAAGGCTG		208	15	0.07	253	1	0.0039525692				0	0				
LOC286238	0	bcgsc.ca	37	9	91262493	91262494	+	RNA	DNP	AG	AG	CT	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_001100111	exon2	c.C149A	.	ATTTCCAGGTCTC		138	8	0.06	144	1	0.0069444444				0	0				
LOC286238	0	bcgsc.ca	37	9	91262522	91262522	+	RNA	SNP	T	T	A	rs28429833	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_001100111	exon2	c.A121T	p.N41Y	TTGGATTAAGCAC		131	7	0.05	149	0	0				0	0				
.	100287922	bcgsc.ca	37	9	99983312	99983312	+	RNA	SNP	C	C	T	rs12235734	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CGCTACCTGTCCT		42	6	0.14	45	0	0				0	0				
LAMC3	10319	bcgsc.ca	37	9	133901819	133901820	+	Missense_Mutation	DNP	CC	CC	AG	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	LAMC3	NM_006059	exon2	c.C522G	p.P174Q	GCCGGCCCGAGGG		170	6	0.04	188	0	0		167		72	0	0.00			
.	0	bcgsc.ca	37	9	138340462	138340462	+	RNA	SNP	A	A	G	rs10732637	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAAGGGATAGATC		32	10	0.31	41	0	0				0	0				
.	0	bcgsc.ca	37	9	141035935	141035935	+	RNA	SNP	T	T	C	rs115489568	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCTCTCTAGCAGT		80	9	0.11	51	0	0				0	0				
.	0	bcgsc.ca	37	9	141038257	141038257	+	RNA	SNP	T	T	G	rs2507153	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGGACTTGGCCCC		36	5	0.14	29	0	0				0	0				
.	0	bcgsc.ca	37	9	141038277	141038277	+	RNA	SNP	A	A	G	rs28521831	bycluster	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCCACCAGGGCAT		30	6	0.20	23	0	0				0	0				
LOC100873065	729650	bcgsc.ca	37	X	22454639	22454639	+	RNA	SNP	C	C	T	rs7391306	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AAGTTTCTGAGAC		98	5	0.05	100	0	0				0	0				
ARX	170302	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	X	25031217	25031217	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	NM_139058	exon2	c.C895T	p.P299S	CTTCCGGGTGCAG		90	42	0.47	67	0	0				2	1	0.50			
MAGEB16	139604	ucsc.edu	37	X	35821055	35821056	+	Missense_Mutation	DNP	AT	AT	GA	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AT	AT					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	MAGEB16	NM_001099921	exon2	c.T743A	p.M280E	CCCAGAATGCTCA		171	20	0.12	163	3	0.018404908		64		0	0				
KDM6A	7403	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	X	44918601	44918602	+	Frame_Shift_Del	DEL	TA	TA	-	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	TA	TA					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	KDM6A	NM_021140	exon12	c.1083_1084del	p.361_362del	ACTCTCTATGAAT		216	0	0.00	228	0	0		274		19	0	0.00			
.	0	bcgsc.ca	37	X	55683421	55683421	+	RNA	SNP	A	A	G	rs187148944	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AGGCCTATATGTT		141	6	0.04	105	0	0				0	0				
.	0	bcgsc.ca	37	X	65176531	65176531	+	RNA	SNP	T	T	C	rs199968155		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AACTGGTCCTGAA		309	17	0.06	217	0	0				81	0	0.00			
.	0	bcgsc.ca	37	X	65176539	65176539	+	RNA	SNP	G	G	C	rs112831485	byfrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTGAAGGTGCAGA		317	18	0.06	233	0	0				55	0	0.00			
FAM155B	27112	ucsc.edu	37	X	68749750	68749750	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	FAM155B	NM_015686	exon3	c.G1370T	p.G457V	GATTGGGGCTGGA		54	5	0.09	56	0	0		44		50	0	0.00			
.	254700	bcgsc.ca	37	X	89367831	89367831	+	RNA	SNP	C	C	T	rs111832781	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GTCGTCCGTTTCG		36	6	0.17	32	0	0				1	0	0.00			
.	254700	bcgsc.ca	37	X	89368160	89368160	+	RNA	SNP	G	G	A	rs112135433	bycluster;byfrequency;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	ACGTGGGTTCATG		84	6	0.07	78	0	0				0	0				
.	0	bcgsc.ca	37	X	99405357	99405357	+	RNA	SNP	T	T	C	rs5967081	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AACAGATTTCCTA		86	11	0.13	62	0	0				0	0				
.	84443	bcgsc.ca	37	X	106846552	106846552	+	Silent	SNP	G	G	A	rs141655380	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	AACTTCGGCGACT		244	8	0.03	266	0	0				2	0	0.00			
.	286423	bcgsc.ca	37	X	122250996	122250996	+	Missense_Mutation	SNP	G	G	T	rs6648942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	GAGTATGTGGCCT		230	16	0.07	243	1	0.0041152263				1	0	0.00			
.	0	bcgsc.ca	37	X	134807372	134807372	+	RNA	SNP	A	A	G	rs7890081	bycluster;by2hit2allele;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CTTCTCAAGTTGC		172	26	0.15	134	0	0				0	0				
.	0	bcgsc.ca	37	X	134814932	134814932	+	RNA	SNP	G	G	T	rs111943338	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGGAACGTTTCTG		218	27	0.12	194	1	0.0051546392				0	0				
.	0	bcgsc.ca	37	X	141260813	141260813	+	RNA	SNP	G	G	T	rs1883360	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TGTATAGCTTGGC		39	7	0.18	45	0	0				0	0				
.	0	bcgsc.ca	37	X	147279972	147279972	+	RNA	SNP	T	T	C	rs142596624	bycluster;by1000genomes	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	TCTGGATACTTAA		41	4	0.10	53	0	0				0	0				
.	286544	bcgsc.ca	37	Y	14107272	14107272	+	RNA	SNP	C	C	T	novel		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	.	.	.	.	.	.	CCATGGCGGGCCA		67	16	0.24	108	0	0				5	0	0.00			
