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	chromosome_name_WU	start_WU	stop_WU	reference_WU	variant_WU	type_WU	gene_name_WU	transcript_name_WU	transcript_species_WU	transcript_source_WU	transcript_version_WU	strand_WU	transcript_status_WU	trv_type_WU	c_position_WU	amino_acid_change_WU	ucsc_cons_WU	domain_WU	all_domains_WU	deletion_substructures_WU	transcript_error_WU
TMEM37	140738	genome.wustl.edu	36	2	119911121	119911122	+	In_Frame_Ins	INS	-	-	GTGTGC			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	119911121	119911122	-	GTGTGC	INS	TMEM37	NM_183240	human	genbank	54_36p	+1	validated	in_frame_ins	c.208_209	p.T70in_frame_insSVP	0.975:0.000	NULL	NULL	-	no_errors
MAP3K4	4216	genome.wustl.edu	36	6	161439341	161439343	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	CTG	CTG			CTG	CTG	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	6	161439341	161439343	CTG	-	DEL	MAP3K4	NM_005922	human	genbank	54_36p	+1	reviewed	in_frame_del	c.3566_3568	p.A1193in_frame_del	0.981:0.960:0.963	NULL	HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase	-	no_errors
ZAN	7455	genome.wustl.edu	36	7	100223498	100223532	+	Frame_Shift_Del	DEL	GCTTCAGCTACCGCTTGCAAGGCCGCATGACCTAT	GCTTCAGCTACCGCTTGCAAGGCCGCATGACCTAT	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	GCTTCAGCTACCGCTTGCAAGGCCGCATGACCTAT	GCTTCAGCTACCGCTTGCAAGGCCGCATGACCTAT			GCTTCAGCTACCGCTTGCAAGGCCGCATGACCTAT	GCTTCAGCTACCGCTTGCAAGGCCGCATGACCTAT	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	7	100223498	100223532	GCTTCAGCTACCGCTTGCAAGGCCGCATGACCTAT	-	DEL	ZAN	ENST00000349350	human	ensembl	54_36p	+1	known	frame_shift_del	c.7028_7062	p.F2344fs	0.088:0.076:0.047:0.031:0.008:0.004:0.007:0.317:0.790:0.908:0.967:0.964:0.963:0.997:1.000:0.999:0.997:0.968:0.891:0.954:1.000:1.000:1.000:0.999:0.998:0.998:1.000:0.999:1.000:1.000:1.000:1.000:1.000:0.990:0.736	HMMPfam_VWD,HMMSmart_SM00216	HMMPfam_MAM,HMMSmart_SM00137,PatternScan_MAM_1,HMMSmart_SM00214,HMMPfam_VWD,HMMSmart_SM00216,superfamily_Serine proterase inhibitors,HMMPfam_TIL_assoc,HMMPfam_EGF,HMMSmart_SM00181,HMMSmart_SM00215,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_C8,HMMPfam_TIL,superfamily_EGF/Laminin	-	no_errors
LOC647211	647211	genome.wustl.edu	36	16	33312183	33312184	+	RNA	INS	-	-	TAG			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	16	33312183	33312184	-	TAG	INS	LOC647211	XR_017499	human	genbank	54_36p	+1	model	rna	NULL	NULL	1.000:1.000	-	-	-	pseudogene
PRUNE2	158471	genome.wustl.edu	36	9	78513955	78513956	+	In_Frame_Ins	INS	-	-	TGACTGTTGCAG			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	9	78513955	78513956	-	TGACTGTTGCAG	INS	PRUNE2	ENST00000376718	human	ensembl	54_36p	-1	known	in_frame_ins	c.1978_1977	p.659in_frame_insLQQS	0.000:0.000	NULL	HMMSmart_SM00516,superfamily_CRAL/TRIO domain,superfamily_Ferritin-like	-	no_errors
ZNF275	10838	genome.wustl.edu	36	X	152263419	152263427	+	In_Frame_Del	DEL	GTGACCTCT	GTGACCTCT	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	GTGACCTCT	GTGACCTCT			GTGACCTCT	GTGACCTCT	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	X	152263419	152263427	GTGACCTCT	-	DEL	ZNF275	ENST00000370251	human	ensembl	54_36p	+1	known	splice_site_del	c.1+4_12	e1-1	0.009:0.010:0.009:0.004:0.003:0.006:0.011:0.009:0.004	-	-	-	no_errors
MYH7	4625	genome.wustl.edu	36	14	22959285	22959286	+	Splice_Site	INS	-	-	G			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	14	22959285	22959286	-	G	INS	MYH7	NM_000257	human	genbank	54_36p	-1	reviewed	splice_site_ins	c.3337-3_3337-2	e25-2	1.000:0.822	-	-	-	no_errors
LOC441736	441736	genome.wustl.edu	36	15	100133921	100133928	+	RNA	DEL	CTCTGCTG	CTCTGCTG	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	CTCTGCTG	CTCTGCTG			CTCTGCTG	CTCTGCTG	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	15	100133921	100133928	CTCTGCTG	-	DEL	LOC441736	XR_042320	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.666:0.741:0.817:0.895:0.974:0.993:0.997:0.999	-	-	-	pseudogene
LOC389662	389662	genome.wustl.edu	36	8	57551882	57551885	+	RNA	DEL	TTTG	TTTG	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	TTTG	TTTG			TTTG	TTTG	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	8	57551882	57551885	TTTG	-	DEL	LOC389662	XR_016813	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.140:0.140:0.141:0.141	-	-	-	pseudogene
C2orf42	54980	genome.wustl.edu	36	2	70262095	70262095	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	70262095	70262095	G	A	SNP	C2orf42	NM_017880	human	genbank	54_36p	-1	predicted	missense	c.527	p.P176L	1.000	NULL	PatternScan_THIOL_PROTEASE_CYS	-	no_errors
ENSG00000217945	0	genome.wustl.edu	36	NT_113961	149191	149195	+	Frame_Shift_Del	DEL	AAGAT	AAGAT	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	AAGAT	AAGAT			AAGAT	AAGAT	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	NT_113961	149191	149195	AAGAT	-	DEL	ENSG00000217945	ENST00000402318	human	ensembl	54_36p	+1	novel	frame_shift_del	c.1946_1950	p.D650fs	NULL	NULL	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat	-	no_start_codon
AP1S3	130340	genome.wustl.edu	36	2	224348892	224348892	+	Silent	SNP	G	G	A			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	224348892	224348892	G	A	SNP	AP1S3	NM_001039569	human	genbank	54_36p	-1	validated	silent	c.261	p.Y87	1.000	HMMPfam_Clat_adaptor_s,superfamily_SNARE-like	HMMPfam_Clat_adaptor_s,superfamily_SNARE-like,PatternScan_CLAT_ADAPTOR_S	-	no_errors
SRSF2	6427	genome.wustl.edu	36	17	72244554	72244554	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	17	72244554	72244554	G	C	SNP	SFRS2	NM_003016	human	genbank	54_36p	-1	provisional	missense	c.284	p.P95R	0.970	superfamily_RNA-binding domain RBD	HMMPfam_RRM_1,HMMSmart_SM00360,HMMSmart_SM00361,superfamily_RNA-binding domain RBD	-	no_errors
MUC4	4585	genome.wustl.edu	36	3	197002507	197002508	+	In_Frame_Ins	INS	-	-	GTCTCCTGCGTAACA			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	197002507	197002508	-	GTCTCCTGCGTAACA	INS	MUC4	NM_018406	human	genbank	54_36p	-1	reviewed	in_frame_ins	c.339_338	p.114in_frame_insVTQET	0.000:0.000	NULL	HMMPfam_VWD,HMMSmart_SM00216,HMMPfam_NIDO,HMMSmart_SM00539,HMMPfam_AMOP,HMMSmart_SM00723,PatternScan_SUGAR_TRANSPORT_2,HMMSmart_SM00181,PatternScan_EGF_1,superfamily_EGF/Laminin	-	no_errors
ASMTL	8623	genome.wustl.edu	36	X	1506792	1506792	+	Silent	SNP	G	G	A			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	X	1506792	1506792	G	A	SNP	ASMTL	NM_004192	human	genbank	54_36p	-1	validated	silent	c.732	p.G244	0.004	NULL	"HMMPfam_Methyltransf_2,HMMPfam_Maf,superfamily_""Winged helix"" DNA-binding domain,superfamily_Maf/Ham1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases"	-	no_errors
LOC388996	388996	genome.wustl.edu	36	2	91141572	91141580	+	RNA	DEL	GATGCTGTG	GATGCTGTG	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	GATGCTGTG	GATGCTGTG			GATGCTGTG	GATGCTGTG	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	91141572	91141580	GATGCTGTG	-	DEL	LOC388996	XR_017571	human	genbank	54_36p	+1	model	rna	NULL	NULL	0.999:0.996:0.997:0.997:0.997:1.000:0.999:1.000:1.000	-	-	-	pseudogene
KRTAP10-7	386675	genome.wustl.edu	36	21	44845084	44845098	+	In_Frame_Del	DEL	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG			CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	21	44845084	44845098	CTGCTGCGCCCCCAG	-	DEL	KRTAP10-7	NM_198689	human	genbank	54_36p	+1	validated	in_frame_del	c.135_149	p.PSCCA49in_frame_del	0.999:0.999:1.000:0.999:0.995:0.979:0.353:0.334:0.435:0.672:0.824:0.909:0.920:0.914:0.918	NULL	HMMPfam_Keratin_B2	-	no_errors
CEACAMP2	1091	genome.wustl.edu	36	19	47751918	47751918	+	Splice_Site	SNP	G	G	C			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	19	47751918	47751918	G	C	SNP	CEACAMP2	ENST00000402513	human	ensembl	54_36p	-1	known	splice_site	c.NULL	NULL	0.002	-	-	-	no_coding_region:pseudogene
ZNF283	284349	genome.wustl.edu	36	19	49043007	49043012	+	In_Frame_Del	DEL	GGAGAT	GGAGAT	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	GGAGAT	GGAGAT			GGAGAT	GGAGAT	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	19	49043007	49043012	GGAGAT	-	DEL	ZNF283	NM_181845	human	genbank	54_36p	+1	validated	in_frame_del	c.414_419	p.EM139in_frame_del	0.046:0.037:0.003:0.003:0.004:0.006	NULL	superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_KRAB,HMMSmart_SM00349,superfamily_C2H2 and C2HC zinc fingers,HMMPfam_zf-C2H2,HMMSmart_SM00355,PatternScan_ZINC_FINGER_C2H2_1	-	no_errors
SCRN3	79634	genome.wustl.edu	36	2	175000827	175000839	+	Frame_Shift_Del	DEL	TCAAATTTATCAG	TCAAATTTATCAG	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	TCAAATTTATCAG	TCAAATTTATCAG			TCAAATTTATCAG	TCAAATTTATCAG	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	175000827	175000839	TCAAATTTATCAG	-	DEL	SCRN3	NM_024583	human	genbank	54_36p	+1	validated	frame_shift_del	c.1233_1245	p.Y414fs	0.987:0.985:0.984:0.995:1.000:1.000:0.998:1.000:0.998:0.987:0.030:0.000:0.004	NULL	NULL	-	no_errors
LOC391771	391771	genome.wustl.edu	36	5	23339715	23339715	+	RNA	SNP	C	C	T			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	5	23339715	23339715	C	T	SNP	LOC391771	XR_038806	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.996	-	-	-	pseudogene
OR5H6	79295	genome.wustl.edu	36	3	99466178	99466186	+	In_Frame_Del	DEL	TGTAACCAC	TGTAACCAC	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	TGTAACCAC	TGTAACCAC			TGTAACCAC	TGTAACCAC	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	99466178	99466186	TGTAACCAC	-	DEL	OR5H6	NM_001005479	human	genbank	54_36p	+1	provisional	in_frame_del	c.360_368	p.VTT124in_frame_del	0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000	HMMPfam_7tm_1,superfamily_SSF81321	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	-	no_errors
LOC728748	728748	genome.wustl.edu	36	X	73535890	73535891	+	RNA	INS	-	-	CTTGAAGAACTGTC			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	X	73535890	73535891	-	CTTGAAGAACTGTC	INS	LOC728748	XR_037583	human	genbank	54_36p	-1	model	rna	NULL	NULL	1.000:0.993	-	-	-	pseudogene
ENSG00000215398	0	genome.wustl.edu	36	14	18187129	18187129	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	14	18187129	18187129	A	-	DEL	ENSG00000215398	ENST00000400208	human	ensembl	54_36p	+1	known	frame_shift_del	c.435	p.S146fs	0.001	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat	PatternScan_ASP_PROTEASE,HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat	-	no_start_codon
CCDC144B	284047	genome.wustl.edu	36	17	18438784	18438785	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	17	18438784	18438785	-	A	INS	CCDC144B	ENST00000285176	human	ensembl	54_36p	-1	known	frame_shift_ins	c.1864_1865	p.E622fs	0.998:0.993	NULL	NULL	-	no_errors
NFKBIZ	64332	genome.wustl.edu	36	3	103058719	103058720	+	Splice_Site	INS	-	-	ACTTTTAGAAAGCTTTAATAACC			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	103058719	103058720	-	ACTTTTAGAAAGCTTTAATAACC	INS	NFKBIZ	NM_031419	human	genbank	54_36p	+1	reviewed	splice_site_ins	c.1935+2_1935+1	e10+2	0.997:0.000	-	-	-	no_errors
EPDR1	54749	genome.wustl.edu	36	7	37926788	37926800	+	Frame_Shift_Del	DEL	AGGCAGTGGCAGC	AGGCAGTGGCAGC	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	AGGCAGTGGCAGC	AGGCAGTGGCAGC			AGGCAGTGGCAGC	AGGCAGTGGCAGC	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	7	37926788	37926800	AGGCAGTGGCAGC	-	DEL	EPDR1	NM_017549	human	genbank	54_36p	+1	reviewed	frame_shift_del	c.82_94	p.Q31fs	0.083:0.084:0.084:0.084:0.084:0.084:0.083:0.082:0.080:0.077:0.074:0.070:0.065	NULL	HMMPfam_Ependymin,PatternScan_EPENDYMIN_1,PatternScan_EPENDYMIN_2	-	no_errors
LOC100132306	100132306	genome.wustl.edu	36	1	147914910	147914920	+	RNA	DEL	AGTTCTAAACA	AGTTCTAAACA	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	AGTTCTAAACA	AGTTCTAAACA			AGTTCTAAACA	AGTTCTAAACA	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	147914910	147914920	AGTTCTAAACA	-	DEL	LOC100132306	XR_037921	human	genbank	54_36p	+1	model	rna	NULL	NULL	1.000:1.000:1.000:1.000:1.000:1.000:0.999:1.000:1.000:1.000:1.000	-	-	-	pseudogene
CARD10	29775	genome.wustl.edu	36	22	36236255	36236260	+	In_Frame_Del	DEL	CTCCTT	CTCCTT	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	CTCCTT	CTCCTT			CTCCTT	CTCCTT	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	22	36236255	36236260	CTCCTT	-	DEL	CARD10	NM_014550	human	genbank	54_36p	-1	reviewed	in_frame_del	c.819_814	p.KE272in_frame_del	0.883:0.892:0.901:0.911:0.921:0.932	NULL	superfamily_DEATH_like,HMMPfam_CARD,superfamily_SSF52540	-	no_errors
TTLL3	26140	genome.wustl.edu	36	3	9832765	9832766	+	Frame_Shift_Ins	INS	-	-	AGTA			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	9832765	9832766	-	AGTA	INS	TTLL3	ENST00000310252	human	ensembl	54_36p	+1	known	frame_shift_ins	c.320_321	p.M107fs	0.998:1.000	NULL	HMMPfam_TTL,superfamily_Glutathione synthetase ATP-binding domain-like	-	no_errors
LOC642943	642943	genome.wustl.edu	36	9	94689865	94689870	+	RNA	DEL	GGGGCA	GGGGCA	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	GGGGCA	GGGGCA			GGGGCA	GGGGCA	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	9	94689865	94689870	GGGGCA	-	DEL	LOC642943	XR_039168	human	genbank	54_36p	+1	model	rna	NULL	NULL	0.058:0.057:0.056:0.055:0.053:0.051	-	-	-	pseudogene
LOC727860	727860	genome.wustl.edu	36	10	39005121	39005122	+	RNA	INS	-	-	A			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	10	39005121	39005122	-	A	INS	LOC727860	XR_037651	human	genbank	54_36p	-1	model	rna	NULL	NULL	1.000:1.000	-	-	-	pseudogene
KRTAP10-2	386679	genome.wustl.edu	36	21	44795188	44795202	+	In_Frame_Del	DEL	CTTGCAGCAGACAGG	CTTGCAGCAGACAGG	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	CTTGCAGCAGACAGG	CTTGCAGCAGACAGG			CTTGCAGCAGACAGG	CTTGCAGCAGACAGG	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	21	44795188	44795202	CTTGCAGCAGACAGG	-	DEL	KRTAP10-2	NM_198693	human	genbank	54_36p	-1	reviewed	in_frame_del	c.582_568	p.PVCCK190in_frame_del	0.001:0.000:0.038:0.263:0.912:0.967:0.990:0.984:0.905:0.270:0.059:0.015:0.006:0.075:0.088	NULL	HMMPfam_Keratin_B2	-	no_errors
ZNF408	79797	genome.wustl.edu	36	11	46681293	46681304	+	In_Frame_Del	DEL	AGTGGTGACAGA	AGTGGTGACAGA	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	AGTGGTGACAGA	AGTGGTGACAGA			AGTGGTGACAGA	AGTGGTGACAGA	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	11	46681293	46681304	AGTGGTGACAGA	-	DEL	ZNF408	NM_024741	human	genbank	54_36p	+1	provisional	in_frame_del	c.576_587	p.VTEV194in_frame_del	0.000:0.000:0.000:0.012:0.059:0.062:0.227:0.271:0.845:0.898:0.983:0.982	NULL	superfamily_SSF57667,HMMPfam_zf-C2H2,HMMSmart_ZnF_C2H2,PatternScan_ZINC_FINGER_C2H2_1	-	no_errors
LAMA1	284217	genome.wustl.edu	36	18	6946505	6946516	+	In_Frame_Del	DEL	CAGCTCCAGCTC	CAGCTCCAGCTC	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	CAGCTCCAGCTC	CAGCTCCAGCTC			CAGCTCCAGCTC	CAGCTCCAGCTC	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	18	6946505	6946516	CAGCTCCAGCTC	-	DEL	LAMA1	ENST00000344342	human	ensembl	54_36p	-1	known	in_frame_del	c.577_566	p.GAGA189in_frame_del	0.008:0.000:0.000:0.000:0.000:0.000:0.000:0.001:0.004:0.008:0.008:0.007	NULL	HMMSmart_SM00282,HMMPfam_Laminin_G_1,superfamily_Concanavalin A-like lectins/glucanases	-	no_errors
MIR516B2	574485	genome.wustl.edu	36	19	58920554	58920555	+	RNA	INS	-	-	AAAGA			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	19	58920554	58920555	-	AAAGA	INS	MIRN516B2	ENST00000385190	human	ensembl	54_36p	+1	known	rna	NULL	NULL	0.000:0.000	-	-	-	no_errors
HSP90AB3P	3327	genome.wustl.edu	36	4	89032295	89032296	+	In_Frame_Ins	INS	-	-	ATT			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	89032295	89032296	-	ATT	INS	HSP90AB3P	ENST00000327934	human	ensembl	54_36p	+1	known	in_frame_ins	c.277_278	p.M93in_frame_insNL	0.997:1.000	HMMPfam_HATPase_c,HMMSmart_HATPase_c,superfamily_ATP_bd_ATPase	HMMPfam_HATPase_c,HMMSmart_HATPase_c,superfamily_ATP_bd_ATPase,superfamily_Ribosomal_S5_D2-typ_fold,HMMPfam_HSP90,superfamily_SSF110942	-	no_errors
LOC388996	388996	genome.wustl.edu	36	2	91159321	91159325	+	RNA	DEL	CAACT	CAACT	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	CAACT	CAACT			CAACT	CAACT	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	91159321	91159325	CAACT	-	DEL	LOC388996	XR_017571	human	genbank	54_36p	+1	model	rna	NULL	NULL	0.999:0.998:0.992:0.997:0.996	-	-	-	pseudogene
DENND4B	9909	genome.wustl.edu	36	1	152173903	152173911	+	In_Frame_Del	DEL	CTGCTGCTG	CTGCTGCTG	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	CTGCTGCTG	CTGCTGCTG			CTGCTGCTG	CTGCTGCTG	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	152173903	152173911	CTGCTGCTG	-	DEL	DENND4B	NM_014856	human	genbank	54_36p	-1	validated	in_frame_del	c.2730_2722	p.QQQ908in_frame_del	0.852:0.853:0.853:0.867:0.882:0.897:0.913:0.962:0.976	NULL	HMMSmart_uDENN,HMMPfam_uDENN,HMMPfam_DENN,HMMSmart_DENN,HMMPfam_dDENN,HMMSmart_dDENN,HMMPfam_PPR	-	no_errors
PKD1L2	114780	genome.wustl.edu	36	16	79718974	79718975	+	Frame_Shift_Ins	INS	-	-	TACTGCCAAGCCTGGGGAAAGC			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	16	79718974	79718975	-	TACTGCCAAGCCTGGGGAAAGC	INS	PKD1L2	ENST00000299598	human	ensembl	54_36p	-1	known	frame_shift_ins	c.6251_6250	p.T2084fs	1.000:1.000	HMMPfam_PKD_channel	HMMPfam_GPS,HMMSmart_SM00303,PatternScan_CHANNEL_COLICIN,HMMPfam_PLAT,HMMSmart_SM00308,HMMPfam_Lectin_C,HMMSmart_SM00034,superfamily_Lipase/lipooxygenase domain (PLAT/LH2 domain),HMMPfam_PKD_channel,superfamily_C-type lectin-like	-	no_errors
MST1P9	11223	genome.wustl.edu	36	1	16960129	16960133	+	Frame_Shift_Del	DEL	GTGCT	GTGCT	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	GTGCT	GTGCT			GTGCT	GTGCT	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	16960129	16960133	GTGCT	-	DEL	MSTP9	ENST00000334998	human	ensembl	54_36p	-1	known	frame_shift_del	c.123_119	p.Q40fs	0.887:0.863:0.855:0.990:0.991	HMMPfam_PAN_1,HMMSmart_SM00473,superfamily_Hairpin loop containing domain-like	HMMPfam_Kringle,HMMSmart_SM00130,HMMPfam_Trypsin,HMMSmart_SM00020,HMMPfam_PAN_1,HMMSmart_SM00473,superfamily_Trypsin-like serine proteases,superfamily_Kringle-like,PatternScan_KRINGLE_1,superfamily_Hairpin loop containing domain-like	-	no_errors
MT-CO2	0	genome.wustl.edu	36	MT	7782	7782	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	MT	7782	7782	A	G	SNP	MT-CO2	ENST00000361739	human	ensembl	54_36p	+1	known	missense	c.196	p.T66A	NULL	HMMPfam_COX2_TM,superfamily_Cytochrome c oxidase subunit II-like transmembrane region	PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins,HMMPfam_COX2_TM,superfamily_Cytochrome c oxidase subunit II-like transmembrane region	-	no_errors
OTOP1	133060	genome.wustl.edu	36	4	4249850	4249855	+	In_Frame_Del	DEL	CGTTGC	CGTTGC	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	CGTTGC	CGTTGC			CGTTGC	CGTTGC	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	4249850	4249855	CGTTGC	-	DEL	OTOP1	NM_177998	human	genbank	54_36p	-1	provisional	in_frame_del	c.1612_1607	p.GN536in_frame_del	0.000:0.000:0.000:0.000:0.000:0.002	NULL	HMMPfam_DUF270	-	no_errors
NPM1	4869	genome.wustl.edu	36	5	170770152	170770153	+	Frame_Shift_Ins	INS	-	-	TCTG			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Verified	Valid	Somatic		Capture				Illumina GAIIx	5	170770152	170770153	0	TCTG	INS	NPM1	NM_002520	human	genbank	54_36p	1	validated	frame_shift_ins	c.863_864	p.W288fs	1.000:1.000	NULL	Nucleoplasmin;HMMPfam_Nucleoplasmin;Nucleoplasmin-like	-	NA
PRSS16	10279	genome.wustl.edu	36	6	27331044	27331058	+	In_Frame_Del	DEL	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT			AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	6	27331044	27331058	AAGGAGAGCCAGATT	-	DEL	PRSS16	NM_005865	human	genbank	54_36p	+1	reviewed	in_frame_del	c.1516_1530	p.ESQIK507in_frame_del	0.008:0.021:0.022:0.020:0.048:0.068:0.213:0.244:0.303:0.312:0.297:0.218:0.073:0.000:0.000	NULL	HMMPfam_Peptidase_S28,superfamily_SSF53474	-	no_errors
EPSTI1	94240	genome.wustl.edu	36	13	42360434	42360435	+	Frame_Shift_Ins	INS	-	-	TCAGG			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	13	42360434	42360435	-	TCAGG	INS	EPSTI1	NM_001002264	human	genbank	54_36p	-1	validated	frame_shift_ins	c.1185_1184	p.E395fs	0.071:0.095	NULL	NULL	-	no_errors
HIF3A	64344	genome.wustl.edu	36	19	51507544	51507547	+	Frame_Shift_Del	DEL	TATT	TATT	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	TATT	TATT			TATT	TATT	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	19	51507544	51507547	TATT	-	DEL	HIF3A	ENST00000244303	human	ensembl	54_36p	+1	known	frame_shift_del	c.679_682	p.Y227fs	0.000:0.001:0.001:0.001	NULL	NULL	-	no_errors
HSP90AB3P	3327	genome.wustl.edu	36	4	89032293	89032294	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	89032293	89032294	-	C	INS	HSP90AB3P	ENST00000327934	human	ensembl	54_36p	+1	known	frame_shift_ins	c.275_276	p.M93fs	1.000:1.000	HMMPfam_HATPase_c,HMMSmart_HATPase_c,superfamily_ATP_bd_ATPase	HMMPfam_HATPase_c,HMMSmart_HATPase_c,superfamily_ATP_bd_ATPase,superfamily_Ribosomal_S5_D2-typ_fold,HMMPfam_HSP90,superfamily_SSF110942	-	no_errors
PRUNE2	158471	genome.wustl.edu	36	9	78508196	78508210	+	In_Frame_Del	DEL	GTGACAGCCTGCAAC	GTGACAGCCTGCAAC	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	GTGACAGCCTGCAAC	GTGACAGCCTGCAAC			GTGACAGCCTGCAAC	GTGACAGCCTGCAAC	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	9	78508196	78508210	GTGACAGCCTGCAAC	-	DEL	PRUNE2	ENST00000376718	human	ensembl	54_36p	-1	known	in_frame_del	c.7076_7062	p.LQAVT2355in_frame_del	0.994:0.955:0.952:0.911:0.888:0.272:0.194:0.036:0.048:0.066:0.066:0.023:0.016:0.001:0.000	NULL	HMMSmart_SM00516,superfamily_CRAL/TRIO domain,superfamily_Ferritin-like	-	no_errors
MIR509-2	100126301	genome.wustl.edu	36	X	146148031	146148031	+	RNA	DEL	T	T	-			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	X	146148031	146148031	T	-	DEL	MIRN509-2	ENST00000390724	human	ensembl	54_36p	-1	known	rna	NULL	NULL	0.026	-	-	-	no_errors
UNC5A	90249	genome.wustl.edu	36	5	176239049	176239049	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2903-03A-01W-0761-09	TCGA-AB-2903-11A-01W-0732-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	5	176239049	176239049	C	T	SNP	UNC5A	NM_133369	human	genbank	54_36p	+1	validated	missense	c.2317	p.R773W	1.000	superfamily_DEATH_like,HMMSmart_DEATH,HMMPfam_Death	superfamily_SSF48726,HMMPfam_I-set,HMMSmart_IG,superfamily_TSP1,HMMSmart_TSP1,HMMPfam_TSP_1,HMMPfam_ZU5,HMMSmart_ZU5,superfamily_DEATH_like,HMMSmart_DEATH,HMMPfam_Death	-	no_errors
