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	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	Trna_tot	Trna_ref	Trna_var	Trna_alt1	Trna_alt2
LCE1E	353135	bcgsc.ca	37	1	152760096	152760096	+	Silent	SNP	A	A	T	rs115864544	bycluster;byfrequency;by1000genomes	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	LCE1E-90	NM_178353	exon2	c.A321T	p.G107G	CTGTGGAGGGGGC	.	80	49	170	29	A|0.901;T|0.099	0	0	0	0	0
LOR	4014	hgsc.bcm.edu	37	1	153233578	153233578	+	Silent	SNP	C	C	T	rs1143389	bycluster;byfrequency;by1000genomes	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	LOR-90	NM_000427	exon2	c.C153T	p.C51C	TGGCTGCGGCTAC	.	8	8	0	0	C|0.818;T|0.182	0	0	0	0	0
TOR3A	64222	hgsc.bcm.edu	37	1	179051300	179051300	+	Missense_Mutation	SNP	T	T	C	rs2296377	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	TOR3A-90	NM_022371	exon1	c.T37C	p.F13L	CTCTTTTTCCTGC	.	9	9	0	0	T|0.229;C|0.771	2	0	2	0	0
EIF2D	1939	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	206784680	206784680	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	EIF2D-92	NM_006893	exon2	c.C104G	p.T35S	TGATCAGTTCCAA	.	132	96	136	1	.	17	3	14	0	0
OR2T33	391195	broad.mit.edu	37	1	248436537	248436537	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	OR2T33-114	NM_001004695	exon1	c.G580C	p.E194Q	CGTTTTCGAAGAC	.	666	19	609	0	.	1	1	0	0	0
MUC2	4583	broad.mit.edu	37	11	1092953	1092953	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	MUC2-90	NM_002457	exon30	c.C4772T	p.T1591M	CCACTACGGTGAC	.	136	9	112	1	.	0	0	0	0	0
OR51F1	256892	bcgsc.ca	37	11	4790671	4790671	+	Silent	SNP	C	C	T	rs11033795	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	OR51F1-70	NM_001004752	exon1	c.G477A	p.L159L	TAGTGGCAATATT	.	144	6	155	1	C|0.706;T|0.294	0	0	0	0	0
ZDHHC13	54503	broad.mit.edu	37	11	19185906	19185906	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	ZDHHC13-90	NM_019028	exon12	c.G1292T	p.C431F	CATCATGTCTTGT	.	65	3	78	0	.	0	0	0	0	0
CCDC34	91057	bcgsc.ca	37	11	27362359	27362359	+	Missense_Mutation	SNP	T	T	G	rs17244028	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	CCDC34-90	NM_030771	exon5	c.A791C	p.E264A	TGTATTTCAGCTT	.	64	5	60	0	T|0.772;G|0.228	15	15	0	0	0
WT1	7490	hgsc.bcm.edu	37	11	32456694	32456694	+	Silent	SNP	C	C	A	rs2234582	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	WT1-6891	NM_024424	exon1	c.G198T	p.P66P	TTGCTGCGGCTCA	.	5	4	0	0	C|0.748;A|0.252	0	0	0	0	0
OR4A16	81327	ucsc.edu;bcgsc.ca	37	11	55111584	55111584	+	Missense_Mutation	SNP	A	A	T	rs10896659	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	OR4A16-69	NM_001005274	exon1	c.A908T	p.K303M	GTGAAAAGTTAAG	.	19	18	13	0	A|0.589;T|0.411	0	0	0	0	0
NUMA1	4926	bcgsc.ca	37	11	71717106	71717106	+	Silent	SNP	G	G	A	rs61745941	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	NUMA1-633	NM_006185	exon22	c.C5667T	p.A1889A	CACCCCGGCCTGG	.	94	6	82	1	G|0.969;A|0.031	80	80	0	0	0
PGM2L1	283209	bcgsc.ca	37	11	74109166	74109166	+	Missense_Mutation	SNP	A	A	G	rs12049823	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	PGM2L1-91	NM_173582	exon1	c.T41C	p.L14P	GCGTGGAGCAGGT	.	84	5	66	1	A|0.843;G|0.157	1	1	0	0	0
B3GNT6	192134	hgsc.bcm.edu	37	11	76751542	76751542	+	Splice_Site	DEL	T	T	-	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	.	NM_138706	exon2	c.946+1T>-	.	TGTGTCTTGGAGC	.	13	13	0	0	.	0	0	0	0	0
AKAP3	10566	bcgsc.ca	37	12	4737042	4737042	+	Silent	SNP	G	G	A	rs7972737	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	AKAP3-292	NM_006422	exon4	c.C1026T	p.H342H	GACGCTGTGGAGA	.	228	8	142	1	G|0.653;A|0.347	2	2	0	0	0
KANSL2	54934	broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	49075305	49075305	+	Silent	SNP	G	G	A	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	.	NM_017822	exon2	c.C111T	p.H37H	ACGAGGGTGAGAG	.	270	128	148	1	.	8	3	5	0	0
TUBA1C	84790	ucsc.edu	37	12	49666152	49666152	+	Silent	SNP	G	G	A	rs199599214	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	TUBA1C-90	NM_032704	exon4	c.G492A	p.K164K	CAAGAAGTCCAAG	.	379	21	221	15	G|0.998;A|0.002	1688	1138	550	0	0
KRT1	3848	broad.mit.edu	37	12	53069236	53069256	+	In_Frame_Del	DEL	TAGCTGCTACCTCCGGAGCCA	TAGCTGCTACCTCCGGAGCCA	-	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	KRT1-92	NM_006121	exon9	c.1656_1676del	p.552_559del	GAGCCGTAGCTGC	.	49	14	10	0	.	0	0	0	0	0
NAP1L1	4673	broad.mit.edu	37	12	76444319	76444319	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	NAP1L1-92	NM_004537	exon12	c.G1051A	p.D351N	CATCATCATCATC	.	144	4	120	0	.	0	0	0	0	0
TMEM119	338773	hgsc.bcm.edu	37	12	108986112	108986112	+	Silent	SNP	G	G	C	rs10861953	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	TMEM119-69	NM_181724	exon2	c.C48G	p.L16L	CCCCAGGAGCAGC	.	9	6	1	0	G|0.822;C|0.178	2	0	2	0	0
PARP4	143	ucsc.edu;bcgsc.ca	37	13	25016762	25016762	+	Missense_Mutation	SNP	G	G	A	rs113301501	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	PARP4-94	NM_006437	exon29	c.C3509T	p.T1170I	AATTGTGTTATGA	.	148	17	162	3	G|0.935;A|0.065	61	61	0	0	0
FAM194B	220081	hgsc.bcm.edu	37	13	46170735	46170735	+	Missense_Mutation	SNP	C	C	T	rs28460344		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	FAM194B-68	NM_182542	exon3	c.G406A	p.E136K	CTTCCTCCTCCAG	.	87	9	77	0	.	0	0	0	0	0
FAM179B	23116	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	45542716	45542716	+	Silent	SNP	A	A	G	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	FAM179B-93	NM_015091	exon19	c.A5115G	p.K1705K	TATCAAAAAGAGT	.	76	28	80	0	.	8	1	7	0	0
FERMT2	10979	bcgsc.ca	37	14	53341962	53341962	+	Silent	SNP	C	C	G	rs1130597	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	FERMT2-68	NM_001135000	exon8	c.G1077C	p.G359G	TTTACCCCCTTCC	.	64	4	109	0	G|0.274;C|0.726	11	11	0	0	0
L3HYPDH	112849	hgsc.bcm.edu	37	14	59950676	59950676	+	Missense_Mutation	SNP	A	A	C	rs34741399	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	.	NM_144581	exon1	c.T359G	p.L120R	GGCACAAGCCCGA	.	28	4	5	0	A|0.965;C|0.035	1	1	0	0	0
PCNXL4	64430	bcgsc.ca	37	14	60591887	60591887	+	Missense_Mutation	SNP	G	G	A	rs167437	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	.	NM_022495	exon8	c.G2296A	p.G766S	GTTTACGGTGGTG	.	168	6	204	0	G|0.537;T|0.066	19	19	0	0	0
FAM161B	145483	bcgsc.ca	37	14	74413129	74413129	+	Silent	SNP	C	C	G	rs7146634	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	FAM161B-91	NM_152445	exon2	c.G423C	p.G141G	CCATCTCCCTTTC	.	111	5	112	1	C|0.648;G|0.352	2	2	0	0	0
ISM2	145501	hgsc.bcm.edu	37	14	77965094	77965094	+	Silent	SNP	G	G	A	rs12431905	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	ISM2-91	NM_199296	exon1	c.C43T	p.L15L	GCAGCAGCACGCA	.	5	5	2	0	G|0.934;A|0.066	0	0	0	0	0
SERPINA1	5265	bcgsc.ca	37	14	94847415	94847415	+	Missense_Mutation	SNP	A	A	G	rs6647	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	SERPINA1-226	NM_001127701	exon5	c.T710C	p.V237A	GTGGTCACCTGGT	.	143	5	167	2	A|0.718;G|0.282	22	22	0	0	0
TDRD9	122402	broad.mit.edu;bcgsc.ca	37	14	104394850	104394850	+	Silent	SNP	C	C	T	rs9324066	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	TDRD9-70	NM_153046	exon1	c.C4T	p.L2L	AGGATGCTGCGGA	.	113	8	55	0	A|0.000;C|0.519;G|0.000;T|0.480	0	0	0	0	0
ZNF592	9640	bcgsc.ca	37	15	85333953	85333953	+	Silent	SNP	A	A	G	rs2241645	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	ZNF592-96	NM_014630	exon5	c.A2238G	p.Q746Q	ATGCCAAATGCTG	.	79	4	101	1	A|0.223;G|0.777	8	8	0	0	0
HDDC3	374659	hgsc.bcm.edu	37	15	91475756	91475756	+	Silent	SNP	C	C	G	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	HDDC3-91	NM_198527	exon1	c.G15C	p.A5A	CTGCGCCGCCTCA	.	8	7	0	0	.	16	0	16	0	0
RCCD1	91433	hgsc.bcm.edu	37	15	91499986	91499986	+	Missense_Mutation	SNP	G	G	T	rs4932380		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	RCCD1-90	NM_001017919	exon2	c.G22T	p.A8S	CCGGGGGCCTGGT	.	12	12	3	0	G|0.822;T|0.178	1	0	1	0	0
FAM173A	65990	hgsc.bcm.edu	37	16	771286	771286	+	Silent	SNP	C	C	T	rs11540049	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	FAM173A-91	NM_001271285	exon1	c.C12T	p.D4D	GCAGGACGACCCG	.	4	4	0	0	C|0.504;T|0.496	3	1	2	0	0
EME2	197342	hgsc.bcm.edu	37	16	1823444	1823444	+	Silent	SNP	C	C	G	rs761065		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	EME2-229	NM_001257370	exon1	c.C216G	p.V72V	GCAGGTCCTGAAG	.	9	9	1	0	C|0.615;G|0.385	1	0	1	0	0
ITGAM	3684	broad.mit.edu	37	16	31342579	31342579	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	ITGAM-226	NM_001145808	exon29	c.A3373C	p.T1125P	CTCATCACCGCCG	.	110	19	66	15	.	9	9	0	0	0
CBLN1	869	broad.mit.edu	37	16	49315298	49315298	+	Missense_Mutation	SNP	G	G	T	rs200550358		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	CBLN1-90	NM_004352	exon1	c.C79A	p.P27T	CGATGGGCTCCGT	.	86	8	27	2	.	6	6	0	0	0
RBL2	5934	hgsc.bcm.edu	37	16	53468699	53468699	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	RBL2-841	NM_005611	exon1	c.C231T	p.Y77Y	AAGCTACACGCTG	.	18	9	1	0	.	0	0	0	0	0
CCDC102A	92922	hgsc.bcm.edu	37	16	57562804	57562804	+	Missense_Mutation	SNP	G	G	A	rs12935069		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	CCDC102A-91	NM_033212	exon2	c.C286T	p.R96W	ACCACCGGCGCAT	.	7	7	0	0	G|0.001;A|0.999	0	0	0	0	0
ZFPM1	161882	hgsc.bcm.edu	37	16	88599697	88599705	+	In_Frame_Del	DEL	AGCCTCTGG	AGCCTCTGG	-	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	AGCCTCTGG	AGCCTCTGG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	ZFPM1-90	NM_153813	exon10	c.1331_1339del	p.444_447del	GAGCGGAGCCTCT	.	24	0	2	0	.	0	0	0	0	0
KRTAP4-5	85289	ucsc.edu	37	17	39305785	39305785	+	Missense_Mutation	SNP	A	A	T	rs411367		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	KRTAP4-5-90	NM_033188	exon1	c.T235A	p.C79S	AGCAGCAGGGGCG	.	59	11	35	1	A|0.354;T|0.646	0	0	0	0	0
CDK5RAP3	80279	bcgsc.ca	37	17	46053334	46053334	+	Silent	SNP	A	A	G	rs202125432	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	CDK5RAP3-226	NM_176096	exon8	c.A753G	p.E251E	GGTGGAACGACCC	.	87	7	90	0	A|0.949;G|0.051	52	52	0	0	0
STXBP4	252983	broad.mit.edu;bcgsc.ca	37	17	53063612	53063612	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	STXBP4-91	NM_178509	exon3	c.C32T	p.P11L	TATCACCCAGTCT	.	157	6	214	0	.	1	1	0	0	0
TCF3	6929	hgsc.bcm.edu	37	19	1619348	1619348	+	Silent	SNP	G	G	A	rs1052696	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	TCF3-721	NM_003200	exon15	c.C1293T	p.G431G	CATGGGGCCGGTG	.	8	7	1	0	G|0.903;A|0.097	0	0	0	0	0
TCF3	6929	hgsc.bcm.edu	37	19	1619350	1619350	+	Missense_Mutation	SNP	C	C	T	rs1052692	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	TCF3-721	NM_003200	exon15	c.G1291A	p.G431S	TGGGGCCGGTGAA	.	8	7	1	0	C|0.901;T|0.099	0	0	0	0	0
PRKCSH	5589	hgsc.bcm.edu	37	19	11558367	11558367	+	Silent	SNP	G	G	A	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	PRKCSH-90	NM_001001329	exon11	c.G963A	p.E321E	GGAGGAGGAGGAA	.	125	7	95	0	.	71	71	0	0	0
CILP2	148113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	19656298	19656298	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	CILP2-91	NM_153221	exon8	c.G2944A	p.E982K	GACCCCGAGCGTC	.	95	31	33	0	.	1	1	0	0	0
PLEKHF1	79156	hgsc.bcm.edu	37	19	30165225	30165225	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	PLEKHF1-226	NM_024310	exon2	c.G479A	p.R160H	GCATGCGCTGCAC	.	17	8	2	0	.	1	1	0	0	0
RGS9BP	388531	hgsc.bcm.edu	37	19	33167455	33167455	+	Missense_Mutation	SNP	G	G	T	rs259290	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	RGS9BP-90	NM_207391	exon1	c.G286T	p.A96S	CGACGCGCGCTGG	.	5	5	0	0	G|0.540;T|0.460	0	0	0	0	0
ERCC2	2068	hgsc.bcm.edu	37	19	45867259	45867259	+	Missense_Mutation	SNP	C	C	T	rs1799793	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	ERCC2-848	NM_000400	exon10	c.G934A	p.D312N	CTTCGTCGGGCAG	.	19	12	1	0	C|0.804;T|0.196	14	1	13	0	0
PTGIR	5739	hgsc.bcm.edu	37	19	47127324	47127324	+	Silent	SNP	C	C	G	rs2229128	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	PTGIR-522	NM_000960	exon2	c.G159C	p.V53V	TCCGGTCACCAGC	.	8	4	0	0	C|0.254;G|0.746	0	0	0	0	0
TPRX1	284355	ucsc.edu	37	19	48305650	48305650	+	Silent	SNP	C	C	T	rs112397458	bycluster;byfrequency;by1000genomes	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	TPRX1-90	NM_198479	exon2	c.G618A	p.P206P	TGGGATCGGGCCT	.	46	10	31	0	C|0.912;T|0.088	0	0	0	0	0
GYS1	2997	bcgsc.ca	37	19	49485548	49485548	+	Silent	SNP	G	G	A	rs5464	bycluster;byfrequency;by1000genomes	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	GYS1-524	NM_002103	exon7	c.C1026T	p.F342F	CTCCAGGAAGACG	.	253	10	151	1	G|0.713;A|0.287	94	94	0	0	0
ZNF814	730051	hgsc.bcm.edu	37	19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T	rs111727691		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	.	NM_001144989	exon3	c.C968A	p.P323H	TCATAAGGTCTTT	.	114	15	103	0	G|0.500;T|0.500	9	9	0	0	0
ZNF814	730051	hgsc.bcm.edu	37	19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T	rs113623532		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	.	NM_001144989	exon3	c.G965A	p.R322K	TAAGGTCTTTTCC	.	109	13	101	0	C|0.500;T|0.500	9	9	0	0	0
ZBTB45	84878	hgsc.bcm.edu	37	19	59028585	59028585	+	Silent	SNP	G	G	A	rs11545185	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	ZBTB45-90	NM_032792	exon2	c.C456T	p.R152R	GCGCAGGCGGTGA	.	9	4	0	0	G|0.844;A|0.156	7	3	4	0	0
CMPK2	129607	hgsc.bcm.edu	37	2	7005369	7005369	+	Silent	SNP	A	A	G	rs11678810		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	CMPK2-68	NM_001256478	exon1	c.T459C	p.C153C	CTCCTGACAGGCG	.	7	7	0	0	A|0.003;G|0.997	0	0	0	0	0
DYNC1I2	1781	bcgsc.ca	37	2	172585298	172585298	+	Silent	SNP	T	T	C	rs78255103	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	DYNC1I2-91	NM_001378	exon14	c.T1329C	p.D443D	TGGAGATGTCAAC	.	369	12	332	2	T|0.333;C|0.667	164	164	0	0	0
TTN	7273	bcgsc.ca	37	2	179421694	179421694	+	Missense_Mutation	SNP	A	A	G	rs9808377	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	TTN-636	NM_001267550	exon330	c.T88187C	p.I29396T	GAGATGATGAATT	.	119	5	108	1	A|0.549;G|0.451	0	0	0	0	0
PRR21	643905	bcgsc.ca	37	2	240982243	240982243	+	Missense_Mutation	SNP	G	G	A	rs80033040	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	PRR21-70	NM_001080835	exon1	c.C157T	p.R53W	AGAGCCGTGGATG	.	115	9	182	3	G|0.966;A|0.034	0	0	0	0	0
TCF15	6939	hgsc.bcm.edu	37	20	590456	590456	+	Silent	SNP	A	A	G	rs282164	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	TCF15-90	NM_004609	exon1	c.T426C	p.R142R	CGCGGCACGGAAG	.	11	11	0	0	A|0.165;G|0.835	0	0	0	0	0
CST1	1469	broad.mit.edu	37	20	23728528	23728528	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	CST1-91	NM_001898	exon3	c.G351A	p.L117L	AGAGCACAACTGT	.	176	11	118	0	.	0	0	0	0	0
SCARF2	91179	hgsc.bcm.edu	37	22	20780097	20780097	+	Silent	SNP	G	G	C	rs759609	bycluster;byfrequency;by1000genomes	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	SCARF2-341	NM_153334	exon11	c.C2181G	p.R727R	CGGGGGGCGCGGC	.	4	4	0	0	G|0.826;C|0.174	0	0	0	0	0
PI4KAP2	375133	bcgsc.ca	37	22	21832428	21832428	+	RNA	SNP	A	A	G	rs128478		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	PI4KAP2-68	.	.	.	.	GTTGGCATCCTTG	.	63	29	165	27	G|1.000;|0.000	0	0	0	0	0
SEMA5B	54437	hgsc.bcm.edu	37	3	122631896	122631896	+	Missense_Mutation	SNP	A	A	T	rs2276782	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	SEMA5B-157	NM_001256347	exon18	c.T2681A	p.V894D	AGGAGGACCTCCA	.	9	5	0	0	T|0.412;A|0.588	0	0	0	0	0
ADCY5	111	hgsc.bcm.edu	37	3	123167249	123167249	+	Silent	SNP	G	G	A	rs4678027		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	ADCY5-94	NM_183357	exon1	c.C144T	p.G48G	GGCAGAGCCCCCG	.	4	4	0	0	G|0.028;A|0.972	0	0	0	0	0
MUC4	4585	hgsc.bcm.edu	37	3	195508147	195508194	+	In_Frame_Del	DEL	GTGGATGCTGAGGAAGTGCTGGTGACAGGAAGAGGGGTGGCGTGACCT	GTGGATGCTGAGGAAGTGCTGGTGACAGGAAGAGGGGTGGCGTGACCT	-	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	GTGGATGCTGAGGAAGTGCTGGTGACAGGAAGAGGGGTGGCGTGACCT	GTGGATGCTGAGGAAGTGCTGGTGACAGGAAGAGGGGTGGCGTGACCT	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	MUC4-90	NM_018406	exon2	c.10257_10304del	p.3419_3435del	TGACCGGTGGATG	.	725	0	459	0	.	0	0	0	0	0
TACC3	10460	ucsc.edu	37	4	1729795	1729795	+	Silent	SNP	A	A	G	rs200539908	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	TACC3-91	NM_006342	exon4	c.A666G	p.E222E	CGAGGAAGAATGC	.	90	25	44	0	A|0.992;G|0.008	4	4	0	0	0
CCDC96	257236	hgsc.bcm.edu	37	4	7044357	7044357	+	Silent	SNP	A	A	G	rs871133		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	CCDC96-90	NM_153376	exon1	c.T309C	p.V103V	AGCCCCAACCTCG	.	14	14	0	0	A|0.036;G|0.964	4	0	4	0	0
CCDC96	257236	hgsc.bcm.edu	37	4	7044380	7044380	+	Missense_Mutation	SNP	C	C	T	rs871134		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	CCDC96-90	NM_153376	exon1	c.G286A	p.E96K	CGGGCTCGGGCTG	.	7	7	0	0	C|0.472;T|0.528	2	0	2	0	0
PDCD6	10016	hgsc.bcm.edu	37	5	271858	271869	+	In_Frame_Del	DEL	CCGGCCCTGGGG	CCGGCCCTGGGG	-	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	CCGGCCCTGGGG	CCGGCCCTGGGG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	PDCD6-290	NM_013232	exon1	c.23_34del	p.8_12del	ACCGCCCCGGCCC	.	25	10	3	0	.	0	0	0	0	0
NSUN2	54888	hgsc.bcm.edu	37	5	6633042	6633042	+	Silent	SNP	C	C	T	rs10062086	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	NSUN2-91	NM_017755	exon1	c.G51A	p.E17E	CGCGTCCTCCGGC	.	4	4	1	0	C|0.687;T|0.313	9	4	5	0	0
C9	735	broad.mit.edu;bcgsc.ca	37	5	39341264	39341264	+	Nonsense_Mutation	SNP	G	G	A	rs144138616		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	C9-90	NM_001737	exon4	c.C460T	p.R154X	CTGTTCGTGCCAG	.	218	7	143	0	G|1.000;A|0.000	0	0	0	0	0
SOWAHA	134548	hgsc.bcm.edu	37	5	132149684	132149684	+	Missense_Mutation	SNP	G	G	C	rs40274	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	.	NM_175873	exon1	c.G371C	p.R124P	TGGTCCGGGTGCC	.	5	5	0	0	G|0.980;C|0.020	0	0	0	0	0
PROB1	389333	hgsc.bcm.edu	37	5	138730037	138730037	+	Missense_Mutation	SNP	T	T	C	rs11748963		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	.	NM_001161546	exon1	c.A734G	p.Q245R	GCGGCCTGCAGGG	.	17	7	2	0	T|0.632;C|0.368	1	1	0	0	0
RUNX2	860	hgsc.bcm.edu	37	6	45390514	45390514	+	Silent	SNP	G	G	A	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	RUNX2-417	NM_001024630	exon3	c.G243A	p.A81A	GGCGGCGGCGGCT	.	6	4	2	0	.	0	0	0	0	0
POU3F2	5454	hgsc.bcm.edu	37	6	99283376	99283376	+	Silent	SNP	T	T	G	rs195860		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	POU3F2-90	NM_005604	exon1	c.T627G	p.G209G	GGCCGGTCTGCAC	.	12	12	0	0	T|0.089;G|0.911	0	0	0	0	0
TTLL2	83887	bcgsc.ca	37	6	167753691	167753691	+	Silent	SNP	C	C	T	rs877653	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	TTLL2-92	NM_031949	exon3	c.C303T	p.S101S	GCAAAGCGTCCTC	.	125	6	162	1	C|0.724;T|0.276	0	0	0	0	0
SMOC2	64094	hgsc.bcm.edu	37	6	168842113	168842113	+	Silent	SNP	T	T	G	rs73270928	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	SMOC2-91	NM_022138	exon1	c.T63G	p.A21A	GCCCGCTCAGAAG	.	31	25	9	0	T|0.654;G|0.346	0	0	0	0	0
TNRC18	84629	hgsc.bcm.edu	37	7	5352635	5352635	+	Silent	SNP	T	T	G	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	TNRC18-46	NM_001080495	exon27	c.A7887C	p.S2629S	GGAGGATGAGGAG	.	24	9	5	0	.	2	1	1	0	0
USP42	84132	hgsc.bcm.edu	37	7	6193521	6193521	+	Missense_Mutation	SNP	G	G	C	rs61729726	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	USP42-659	NM_032172	exon15	c.G2336C	p.R779P	CGCCCCGCGATCC	.	11	5	1	0	G|0.456;C|0.544	4	4	0	0	0
PODXL	5420	hgsc.bcm.edu;broad.mit.edu	37	7	131241030	131241035	+	In_Frame_Del	DEL	GGCGAC	GGCGAC	-	rs11277659	alternate_allele	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	GGCGAC	GGCGAC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	PODXL-136	NM_001018111	exon1	c.84_89del	p.28_30del	TGGGAGGGCGACG	.	54	14	9	0	.	0	0	0	0	0
EPPK1	83481	bcgsc.ca	37	8	144940267	144940267	+	Silent	SNP	G	G	A	rs28441354		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	EPPK1-25	NM_031308	exon1	c.C7155T	p.G2385G	GAAGAAGCCCTTG	.	322	14	123	1	G|0.995;A|0.005	1	1	0	0	0
PLEC	5339	hgsc.bcm.edu	37	8	144990528	144990528	+	Silent	SNP	A	A	G	rs7014582	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	PLEC-141	NM_201380	exon32	c.T13872C	p.A4624A	GGAGCCAGCGGTA	.	22	10	5	0	A|0.536;G|0.464	65	34	31	0	0
C9orf66	157983	hgsc.bcm.edu	37	9	214706	214706	+	Missense_Mutation	SNP	G	G	C	rs540473	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	C9orf66-514	NM_152569	exon1	c.C691G	p.R231G	AGTATCGGGAGGC	.	5	5	1	0	G|0.516;C|0.484	0	0	0	0	0
ZNF618	114991	bcgsc.ca	37	9	116810204	116810204	+	Silent	SNP	G	G	A	rs12378906	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	ZNF618-22	NM_133374	exon13	c.G999A	p.Q333Q	CAACCAGTCCCGA	.	314	9	305	2	G|0.927;A|0.073	8	8	0	0	0
FPGS	2356	hgsc.bcm.edu	37	9	130565267	130565267	+	Missense_Mutation	SNP	A	A	G	rs10760502	byfrequency	TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	FPGS-90	NM_004957	exon1	c.A64G	p.I22V	CGCGGCATAACGA	.	6	6	0	0	A|0.235;G|0.765	1	0	1	0	0
SALL3	27164	hgsc.bcm.edu	37	18	76752544	76752545	+	Missense_Mutation	DNP	GC	GC	TT	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	GC	GC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	SALL3-155	NM_171999	exon2	c.C554T	p.A185L	AGGGCGCGCGCGC	.	9	4	0	0	C|0.967;T|0.033	0	0	0	0	0
ZNF814	730051	hgsc.bcm.edu	37	19	58385798	58385799	+	Missense_Mutation	DNP	CC	CC	TT	novel		TCGA-OR-A5JR-01A-11D-A29I-10	TCGA-OR-A5JR-10A-01D-A29L-10	CC	CC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	6625a9c0-ac73-4f14-a02d-7a8e64f7b2bb	8ea6498c-da66-42fc-bb2a-b4f5e02c0438	.	.	NM_001144989	exon3	c.G959A	p.G320E	CTTTTCCCAGTGT	.	97	6	91	0	.	0	0	0	0	0