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	chromosome_name	start	stop	reference	variant	type	gene_name	transcript_name	transcript_species	transcript_source	transcript_version	strand	transcript_status	trv_type	c_position	amino_acid_change	ucsc_cons	domain	all_domains	deletion_substructures	transcript_error
ABCB8	11194	broad.mit.edu	36	7	150372194	150372194	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	7	150372194	150372194	C	A	SNP	ABCB8	NM_007188	human	genbank	54_36p	1	reviewed	missense	c.1969	p.R657S	0.01	HMMPfam_ABC_tran,HMMSmart_AAA,superfamily_SSF52540	HMMPfam_ABC_membrane,HMMPfam_ABC_tran,HMMSmart_AAA,superfamily_ABC_TM_1,PatternScan_ABC_TRANSPORTER_1,superfamily_SSF52540	-	no_errors
ADAMTSL3	57188	broad.mit.edu	36	15	82485191	82485191	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	15	82485191	82485191	G	A	SNP	ADAMTSL3	NM_207517	human	genbank	54_36p	1	validated	missense	c.4655	p.R1552Q	0.98	NULL	HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_PLAC,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin	-	no_errors
ADCY2	108	broad.mit.edu	36	5	7467689	7467689	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	5	7467689	7467689	G	T	SNP	ADCY2	NM_020546	human	genbank	54_36p	1	reviewed	missense	c.214	p.V72F	0.81	NULL	HMMSmart_CYCc,superfamily_A/G_cyclase,HMMPfam_Guanylate_cyc,PatternScan_GUANYLATE_CYCLASE_1,HMMPfam_DUF1053	-	no_errors
ALMS1	7840	broad.mit.edu	36	2	73466540	73466545	+	In_Frame_Del	DEL	GGAGGA	-	GGAGGA	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	GGAGGA	GGAGGA					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	2	73466540	73466545	GGAGGA	-	DEL	ALMS1	NM_015120	human	genbank	54_36p	1	reviewed	in_frame_del	c.36_41	p.EE16in_frame_del	0.986:0.995:0.998:1.000:1.000:1.000	NULL	NULL	(deletion:cds_exon[73466505,73466828])	no_errors
B3GALT2	8707	broad.mit.edu	36	1	191416457	191416457	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	1	191416457	191416457	C	T	SNP	B3GALT2	NM_003783	human	genbank	54_36p	-1	reviewed	missense	c.859	p.A287T	1	HMMPfam_Galactosyl_T	HMMPfam_Galactosyl_T	-	no_errors
C3orf59	151963	broad.mit.edu	36	3	193999851	193999851	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	3	193999851	193999851	C	G	SNP	C3orf59	NM_178496	human	genbank	54_36p	-1	validated	missense	c.488	p.C163S	1	NULL	NULL	-	no_errors
CDK12	51755	broad.mit.edu	36	17	34902577	34902577	+	Nonsense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Sanger_PCR_WGA			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	17	34902577	34902577	G	A	SNP	CRKRS	NM_016507	human	genbank	54_36p	1	validated	nonsense	c.2156	p.W719*	1	superfamily_Protein kinase-like (PK-like)	HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase	-	no_errors
COL6A6	131873	broad.mit.edu	36	3	131764946	131764946	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	3	131764946	131764946	G	C	SNP	COL6A6	NM_001102608	human	genbank	54_36p	1	provisional	missense	c.409	p.V137L	1	HMMPfam_VWA,HMMSmart_SM00327,superfamily_vWA-like	HMMPfam_VWA,HMMSmart_SM00327,HMMPfam_Collagen,superfamily_vWA-like	-	no_errors
CRLS1	54675	broad.mit.edu	36	20	5960658	5960658	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	20	5960658	5960658	C	G	SNP	CRLS1	NM_019095	human	genbank	54_36p	1	validated	missense	c.661	p.R221G	1	HMMPfam_CDP-OH_P_transf	PatternScan_CDP_ALCOHOL_P_TRANSF,HMMPfam_CDP-OH_P_transf	-	no_errors
CYP2E1	1571	broad.mit.edu	36	10	135192003	135192003	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	10	135192003	135192003	C	G	SNP	CYP2E1	NM_000773	human	genbank	54_36p	1	reviewed	missense	c.206	p.T69R	0.97	HMMPfam_p450,superfamily_Cytochrome_P450	HMMPfam_p450,superfamily_Cytochrome_P450,PatternScan_CYTOCHROME_P450	-	no_errors
DGKH	160851	broad.mit.edu	36	13	41681575	41681575	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	13	41681575	41681575	A	G	SNP	DGKH	NM_178009	human	genbank	54_36p	1	reviewed	missense	c.2824	p.R942G	1	NULL	HMMPfam_DAGK_acc,HMMSmart_SM00045,HMMPfam_DAGK_cat,HMMSmart_SM00046,HMMSmart_SM00454,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_C1_1,HMMSmart_SM00109,PatternScan_ZF_DAG_PE_1,superfamily_SAM/Pointed domain,HMMPfam_SAM_2,superfamily_PH domain-like,superfamily_Cysteine-rich domain	-	no_errors
E2F7	144455	broad.mit.edu	36	12	75947794	75947794	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	12	75947794	75947794	T	A	SNP	E2F7	NM_203394	human	genbank	54_36p	-1	validated	missense	c.1832	p.K611I	0.77	NULL	superfamily_Winged helix DNA-binding domain,HMMPfam_E2F_TDP	-	no_errors
GIF	2694	broad.mit.edu	36	11	59369478	59369478	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	11	59369478	59369478	G	A	SNP	GIF	NM_005142	human	genbank	54_36p	-1	reviewed	silent	c.25	p.L9	0	HMMPfam_Cobalamin_bind	HMMPfam_Cobalamin_bind,PatternScan_COBALAMIN_BINDING	-	no_errors
IL11RA	3590	broad.mit.edu	36	9	34647128	34647128	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	9	34647128	34647128	G	A	SNP	IL11RA	NM_004512	human	genbank	54_36p	1	reviewed	missense	c.428	p.R143H	1	superfamily_Fibronectin type III,HMMSmart_SM00060	superfamily_Immunoglobulin,HMMSmart_SM00409,HMMPfam_ig,superfamily_Fibronectin type III,HMMSmart_SM00060,PatternScan_HEMATOPO_REC_L_F3,HMMPfam_fn3	-	no_errors
LPA	4018	broad.mit.edu	36	6	160935006	160935006	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	6	160935006	160935006	C	T	SNP	LPA	NM_005577	human	genbank	54_36p	-1	validated	silent	c.3603	p.Q1201	0.02	HMMPfam_Kringle,HMMSmart_SM00130,superfamily_Kringle-like	HMMPfam_Kringle,HMMSmart_SM00130,HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases,superfamily_Kringle-like,PatternScan_KRINGLE_1,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER	-	no_errors
LRRIQ3	127255	broad.mit.edu	36	1	74279941	74279941	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	1	74279941	74279941	C	G	SNP	LRRIQ3	NM_001105659	human	genbank	54_36p	-1	inferred	missense	c.1262	p.S421T	0	NULL	superfamily_Outer arm dynein light chain 1,HMMPfam_LRR_1	-	no_errors
MLL3	58508	broad.mit.edu	36	7	151510449	151510449	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	7	151510449	151510449	A	C	SNP	MLL3	NM_170606	human	genbank	54_36p	-1	reviewed	missense	c.5429	p.L1810W	0.99	NULL	PatternScan_HMGI_Y,HMMPfam_HMG_box,HMMSmart_SM00398,HMMPfam_SET,HMMSmart_SM00317,HMMSmart_SM00184,HMMSmart_SM00249,HMMSmart_SM00508,HMMPfam_FYRN,HMMPfam_FYRC,superfamily_FYVE/PHD zinc finger,HMMPfam_AT_hook,HMMSmart_SM00542,HMMSmart_SM00541,PatternScan_ZF_PHD_1,HMMPfam_PHD,PatternScan_ATPASE_ALPHA_BETA,superfamily_SET domain	-	no_errors
MME	4311	broad.mit.edu	36	3	156347676	156347676	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	3	156347676	156347676	A	G	SNP	MME	NM_000902	human	genbank	54_36p	1	reviewed	missense	c.1466	p.N489S	0.05	superfamily_Metalloproteases (zincins) catalytic domain	HMMPfam_Peptidase_M13_N,HMMPfam_Peptidase_M13,superfamily_Metalloproteases (zincins) catalytic domain	-	no_errors
MTMR1	8776	broad.mit.edu	36	X	149656477	149656477	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	X	149656477	149656477	T	A	SNP	MTMR1	NM_003828	human	genbank	54_36p	1	reviewed	missense	c.1348	p.S450T	0.9	superfamily_(Phosphotyrosine protein) phosphatases II,HMMSmart_SM00404	HMMSmart_SM00568,superfamily_PH domain-like,HMMPfam_GRAM,superfamily_(Phosphotyrosine protein) phosphatases II,HMMPfam_Myotub-related,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1	-	no_errors
MYL2	4633	broad.mit.edu	36	12	109837929	109837929	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	12	109837929	109837929	C	A	SNP	MYL2	NM_000432	human	genbank	54_36p	-1	reviewed	missense	c.142	p.D48Y	1	superfamily_EF-hand,HMMSmart_SM00054,HMMPfam_efhand,PatternScan_EF_HAND_1	superfamily_EF-hand,HMMSmart_SM00054,HMMPfam_efhand,PatternScan_EF_HAND_1	-	no_errors
NUP160	23279	broad.mit.edu	36	11	47770961	47770961	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	11	47770961	47770961	T	C	SNP	NUP160	NM_015231	human	genbank	54_36p	-1	validated	missense	c.3403	p.I1135V	1	NULL	PatternScan_HIS_ACID_PHOSPHAT_1	-	no_errors
OR4C13	283092	broad.mit.edu	36	11	49930659	49930659	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	11	49930659	49930659	A	G	SNP	OR4C13	NM_001001955	human	genbank	54_36p	1	provisional	missense	c.109	p.M37V	0	superfamily_SSF81321	PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321,HMMPfam_7tm_1	-	no_errors
PCDHB16	57717	broad.mit.edu	36	5	140544180	140544180	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	5	140544180	140544180	A	G	SNP	PCDHB16	NM_020957	human	genbank	54_36p	1	reviewed	missense	c.1862	p.N621S	0.67	HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin	HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin	-	no_errors
PDE4DIP	9659	broad.mit.edu	36	1	143663557	143663557	+	Splice_Site	SNP	C	C	T	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	1	143663557	143663557	C	T	SNP	PDE4DIP	NM_014644	human	genbank	54_36p	-1	validated	splice_site	c.518+1	e4+1	1	-	-	-	no_errors
PDIK1L	149420	broad.mit.edu	36	1	26321116	26321116	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	1	26321116	26321116	C	G	SNP	PDIK1L	NM_152835	human	genbank	54_36p	1	validated	missense	c.487	p.R163G	1	superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase,HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST	superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase,HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ATP,PatternScan_PROTEIN_KINASE_ST	-	no_errors
PNLIP	5406	broad.mit.edu	36	10	118305559	118305559	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	10	118305559	118305559	G	C	SNP	PNLIP	NM_000936	human	genbank	54_36p	1	reviewed	missense	c.869	p.S290T	1	HMMPfam_Lipase,superfamily_alpha/beta-Hydrolases	HMMPfam_Lipase,superfamily_alpha/beta-Hydrolases,PatternScan_LIPASE_SER,superfamily_Lipase/lipooxygenase domain (PLAT/LH2 domain),HMMPfam_PLAT,HMMSmart_SM00308	-	no_errors
PPA2	27068	broad.mit.edu	36	4	106594233	106594233	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	4	106594233	106594233	T	C	SNP	PPA2	NM_176869	human	genbank	54_36p	-1	reviewed	missense	c.238	p.M80V	0.95	superfamily_Inorganic pyrophosphatase	superfamily_Inorganic pyrophosphatase,HMMPfam_Pyrophosphatase,PatternScan_PPASE	-	no_errors
PPAPDC1A	196051	broad.mit.edu	36	10	122324720	122324720	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	10	122324720	122324720	G	A	SNP	PPAPDC1A	NM_001030059	human	genbank	54_36p	1	validated	missense	c.533	p.R178Q	1	superfamily_Acid phosphatase/Vanadium-dependent haloperoxidase,HMMSmart_SM00014,HMMPfam_PAP2	PatternScan_TUBULIN_B_AUTOREG,superfamily_Acid phosphatase/Vanadium-dependent haloperoxidase,HMMSmart_SM00014,HMMPfam_PAP2	-	no_errors
PRELP	5549	broad.mit.edu	36	1	201719889	201719889	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	1	201719889	201719889	C	T	SNP	PRELP	NM_002725	human	genbank	54_36p	1	reviewed	silent	c.954	p.L318	1	HMMPfam_LRR_1,superfamily_L domain-like	HMMPfam_LRRNT,HMMSmart_SM00013,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00364,superfamily_L domain-like	-	no_errors
RAD23A	5886	broad.mit.edu	36	19	12924845	12924845	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	19	12924845	12924845	G	C	SNP	RAD23A	NM_005053	human	genbank	54_36p	1	reviewed	missense	c.1074	p.Q358H	1	superfamily_UBA_like	PatternScan_UBIQUITIN_1,superfamily_SSF54236,HMMSmart_UBQ,HMMPfam_ubiquitin,superfamily_UBA_like,HMMPfam_UBA,HMMSmart_UBA,superfamily_XPC-bd,HMMSmart_STI1,HMMPfam_XPC-binding	-	no_errors
SPTA1	6708	broad.mit.edu	36	1	156879836	156879836	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	1	156879836	156879836	C	A	SNP	SPTA1	NM_003126	human	genbank	54_36p	-1	reviewed	missense	c.4342	p.G1448W	1	superfamily_Spectrin repeat,HMMPfam_Spectrin,HMMSmart_SM00150	superfamily_Spectrin repeat,HMMPfam_Spectrin,HMMSmart_SM00150,superfamily_SH3-domain,HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_EF-hand,HMMPfam_efhand_Ca_insen	-	no_errors
TP53	7157	broad.mit.edu	36	17	7520087	7520121	+	Frame_Shift_Del	DEL	AACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGG	AACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGG	-	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	AACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGG	AACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGG	AACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGG	-	AACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGG	AACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGG	Unknown	Valid	Somatic	Phase_I	Capture	Sanger_PCR_WGA			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	17	7520087	7520121	AACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGG	-	DEL	TP53	NM_000546	human	genbank	54_36p	-1	reviewed	frame_shift_del	c.325_291	p.Q100fs	0.330:0.183:0.165:0.162:0.166:0.178:0.151:0.019:0.003:0.025:0.345:0.734:0.731:0.078:0.860:0.941:0.999:0.999:0.993:0.668:0.645:0.642:0.600:0.610:0.602:0.560:0.575:0.595:0.590:0.909:0.938:0.944:1.000:1.000:1.000	superfamily_p53-like transcription factors,HMMPfam_P53	PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD	(deletion:cds_exon[7520037,7520315])	no_errors
TRIB3	57761	broad.mit.edu	36	20	319976	319976	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	20	319976	319976	C	G	SNP	TRIB3	NM_021158	human	genbank	54_36p	1	reviewed	missense	c.337	p.R113G	0	superfamily_Kinase_like	superfamily_Kinase_like,HMMPfam_Pkinase	-	no_errors
VGLL1	51442	broad.mit.edu	36	X	135458788	135458788	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	X	135458788	135458788	G	A	SNP	VGLL1	NM_016267	human	genbank	54_36p	1	provisional	missense	c.589	p.G197R	0.25	NULL	HMMPfam_Vg_Tdu,HMMSmart_SM00711	-	no_errors
WIPI2	26100	broad.mit.edu	36	7	5224105	5224105	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	7	5224105	5224105	C	T	SNP	WIPI2	NM_015610	human	genbank	54_36p	1	validated	silent	c.603	p.H201	1	HMMSmart_SM00320,superfamily_WD40 repeat-like	HMMSmart_SM00320,superfamily_WD40 repeat-like	-	no_errors
ZFP57	346171	broad.mit.edu	36	6	29749153	29749153	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	6	29749153	29749153	C	G	SNP	ZFP57	NM_001109809	human	genbank	54_36p	-1	inferred	missense	c.654	p.K218N	0.75	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667	HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667	-	no_errors
ZNF445	353274	broad.mit.edu	36	3	44471659	44471659	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	3	44471659	44471659	C	G	SNP	ZNF445	NM_181489	human	genbank	54_36p	-1	validated	missense	c.387	p.L129F	1	HMMPfam_SCAN,HMMSmart_SCAN	HMMPfam_SCAN,HMMSmart_SCAN,superfamily_Krueppel-associated_box,HMMPfam_KRAB,HMMSmart_KRAB,superfamily_SSF57667,HMMPfam_zf-C2H2,HMMSmart_ZnF_C2H2,PatternScan_ZINC_FINGER_C2H2_1	-	no_errors
ZNF583	147949	broad.mit.edu	36	19	61626618	61626618	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-31-1953-01A-01W-0699-08	TCGA-31-1953-10A-01W-0699-08	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	---			Illumina GAIIx	a8a53d5f-6fdd-41fa-9b3b-baf270a2b997	712bf481-0073-4fdd-a1a5-323ea080bfdd	19	61626618	61626618	G	A	SNP	ZNF583	NM_152478	human	genbank	54_36p	1	provisional	missense	c.779	p.R260K	0.01	superfamily_SSF57667,HMMPfam_zf-C2H2,HMMSmart_ZnF_C2H2,PatternScan_ZINC_FINGER_C2H2_1	superfamily_Krueppel-associated_box,HMMPfam_KRAB,HMMSmart_KRAB,superfamily_SSF57667,HMMPfam_zf-C2H2,HMMSmart_ZnF_C2H2,PatternScan_ZINC_FINGER_C2H2_1	-	no_errors
