#INFO: 1000G => 1000 Genomes Project call set
#INFO: DGV => Database of Genomic Variants
#INFO: COSMIC => COSMIC v86
#INFO: Cancer_census => Cancer Census COSMIC v86
#chr	start	end	type	log2	tool	tumor--normal	info	focal	cytoband
chrX	10446	44887174	DEL	-1.73242079264775	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=P2RY8|Tier1,CRLF2|Tier1,ZRSR2|Tier1,EIF1AX|Tier2,FAM47C|Tier2,BCOR|Tier1,DDX3X|Tier1,KDM6A|Tier1;DisruptL=;DisruptR=KDM6A	no	chrXp22.33-p11.3
chrX	44887175	47658808	DEL	-0.696755842654952	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ARAF|Tier2,KDM6A|Tier1,RBM10|Tier1;DisruptL=KDM6A;DisruptR=UXT	yes	chrXp11.3-p11.23
chrX	47658809	56991083	DEL	-1.73940073132426	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SSX1|Tier1,WAS|Tier1,SSX4|Tier1,GATA1|Tier1,TFE3|Tier1,SSX2|Tier1,SMC1A|Tier2,KDM5C|Tier1;DisruptL=UXT;DisruptR=SPIN3	yes	chrXp11.23-p11.21
chrX	56991084	57170167	DEL	-0.750684302895406	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=SPIN3;DisruptR=	yes	chrXp11.21
chrX	57170168	57361936	DEL	-1.71021027601264	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=FAAH2	yes	chrXp11.21
chrX	57361937	62463002	DEL	-0.289746558931545	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=FAAH2;DisruptR=	yes	chrXp11.21-q11.1
chrX	62463003	65752559	DUP	0.203314318585815	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=AMER1|Tier1,MSN|Tier1;DisruptL=;DisruptR=	yes	chrXq11.1-q12
chrX	65752560	73870954	NEU	-0.177938101574837	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=FOXO4|Tier1,ZMYM3|Tier2,NONO|Tier1,MED12|Tier1,AR|Tier1;DisruptL=;DisruptR=	yes	chrXq12-q13.2
chrX	73870955	76245723	DUP	0.288497591429533	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chrXq13.2-q13.3
chrX	76245724	84380545	DUP	0.601432296210426	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ATRX|Tier1;DisruptL=;DisruptR=HDX	yes	chrXq13.3-q21.1
chrX	84380546	87101846	DUP	0.279959825656591	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=HDX;DisruptR=	yes	chrXq21.1-q21.31
chrX	87101847	88321165	DUP	0.585090605188128	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chrXq21.31
chrX	88321166	100877555	DUP	0.276987735260403	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chrXq21.31-q22.1
chrX	100877556	106655099	DEL	-0.663705369652851	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=BTK|Tier1;DisruptL=;DisruptR=CXorf57	yes	chrXq22.1-q22.3
chrX	106655100	106901143	NEU	-0.0718017061137764	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=CXorf57;DisruptR=RIPPLY1,CLDN2,MORC4	yes	chrXq22.3
chrX	106901144	115886049	DEL	-0.634815098290312	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=IRS4|Tier1;DisruptL=RIPPLY1,CLDN2,MORC4;DisruptR=	yes	chrXq22.3-q23
chrX	115886050	116456070	NEU	-0.0600180788237999	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=SLC6A14	yes	chrXq23
chrX	116456071	117971510	DUP	0.293568535186115	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=SLC6A14;DisruptR=KLHL13	yes	chrXq23-q24
chrX	117971511	118882103	DUP	1.07249014872496	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=KLHL13;DisruptR=LINC01285	yes	chrXq24
chrX	118882104	139747068	DUP	0.243444349007488	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=DCAF12L2|Tier2,STAG2|Tier1,ELF4|Tier1,PHF6|Tier1,SEPT6|Tier2,GPC3|Tier1,BCORL1|Tier1;DisruptL=LINC01285;DisruptR=ATP11C	no	chrXq24-q27.1
chrX	139747069	140075558	DEL	-1.8526819127166	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ATP11C;DisruptR=	yes	chrXq27.1
chrX	140075559	153146260	DEL	-0.799218372135039	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chrXq27.1-q28
chrX	153149106	153586440	DUP	0.442704693043589	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=ATP2B3|Tier1;DisruptL=;DisruptR=	yes	chrXq28
chrX	153586441	156030795	NEU	-0.180578270726493	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=RPL10|Tier1,MTCP1|Tier1,FLNA|Tier2;DisruptL=;DisruptR=	yes	chrXq28
chr1	10028	6465256	NEU	0.162390511861026	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=TNFRSF14|Tier1,SKI|Tier2,RPL22|Tier1,PRDM16|Tier1;DisruptL=;DisruptR=TNFRSF25	yes	chr1p36.33-p36.31
chr1	6465257	8673995	NEU	-0.117163436561528	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CAMTA1|Tier1;DisruptL=TNFRSF25;DisruptR=RERE	yes	chr1p36.31-p36.23
chr1	8673996	8950766	DUP	0.661911350386526	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=RERE;DisruptR=CA6	yes	chr1p36.23
chr1	8950767	19769880	NEU	-0.180573434675417	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CASP9|Tier2,PAX7|Tier1,MTOR|Tier1,PRDM2|Tier2,SPEN|Tier1,SDHB|Tier1,ARHGEF10L|Tier2;DisruptL=CA6;DisruptR=TMCO4	yes	chr1p36.23-p36.13
chr1	19769881	23063290	DUP	0.250953126006712	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=TMCO4;DisruptR=KDM1A,AL031428.1	yes	chr1p36.13-p36.12
chr1	23063291	47818851	NEU	-0.154573885656901	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ID3|Tier2,MDS2|Tier2,MYCL|Tier1,TAL1|Tier1,LCK|Tier1,SFPQ|Tier1,THRAP3|Tier2,CSF3R|Tier1,MPL|Tier1,MUTYH|Tier1,STIL|Tier1,ARID1A|Tier1;DisruptL=KDM1A,AL031428.1;DisruptR=AC096541.1,TRABD2B	no	chr1p36.12-p33
chr1	47818852	51383048	DUP	0.235024817318037	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CDKN2C|Tier1,EPS15|Tier1;DisruptL=AC096541.1,TRABD2B;DisruptR=EPS15	yes	chr1p33-p32.3
chr1	51383049	83866422	NEU	-0.15650505531394	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=JUN|Tier1,FUBP1|Tier1,JAK1|Tier1,EPS15|Tier1;DisruptL=EPS15;DisruptR=TTLL7	no	chr1p32.3-p31.1
chr1	83866423	84289901	DUP	0.64677724864349	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=TTLL7;DisruptR=	yes	chr1p31.1
chr1	84289902	94125587	NEU	-0.135197755692923	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=BCL10|Tier1,RPL5|Tier1;DisruptL=;DisruptR=	yes	chr1p31.1-p22.1
chr1	94125588	94476855	DUP	0.683729270615448	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=ABCD3	yes	chr1p22.1-p21.3
chr1	94476856	103478104	NEU	-0.142781697872618	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ABCD3;DisruptR=AC095032.1	yes	chr1p21.3-p21.1
chr1	103478105	107356412	DEL	-0.749820055126303	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AC095032.1;DisruptR=NTNG1	yes	chr1p21.1-p13.3
chr1	107356413	150474851	NEU	-0.145803965096703	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=RBM15|Tier1,NRAS|Tier1,FAM46C|Tier1,BCL9|Tier1,TRIM33|Tier1,NOTCH2|Tier1,ATP1A1|Tier1,PDE4DIP|Tier1;DisruptL=NTNG1;DisruptR=RPRD2	no	chr1p13.3-q21.2
chr1	150474852	150749711	DUP	0.68835491610426	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV;COSMIC;DisruptL=RPRD2;DisruptR=CTSS	yes	chr1q21.2-q21.3
chr1	150749712	186672516	NEU	-0.110057115428863	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MLLT11|Tier1,S100A7|Tier2,TPM3|Tier1,LMNA|Tier1,PRCC|Tier1,NTRK1|Tier1,FCRL4|Tier1,FCGR2B|Tier1,DDR2|Tier1,PRRX1|Tier1,ABL2|Tier1,TPR|Tier1,ARNT|Tier1,SDHC|Tier1,MUC1|Tier1,PBX1|Tier1;DisruptL=CTSS;DisruptR=PTGS2	no	chr1q21.3-q31.1
chr1	186672517	203360618	DUP	0.281758663053538	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ELF3|Tier2,CDC73|Tier1,PTPRC|Tier1;DisruptL=PTGS2;DisruptR=	yes	chr1q31.1-q32.1
chr1	203360619	205097486	DUP	0.740004450492394	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MDM4|Tier1;DisruptL=;DisruptR=RBBP5	yes	chr1q32.1
chr1	205097487	212301736	DUP	0.463711894032751	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SLC45A3|Tier1,ELK4|Tier1;DisruptL=RBBP5;DisruptR=AL360091.3,PPP2R5A	yes	chr1q32.1-q32.3
chr1	212301737	213004741	DUP	0.959125216614562	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AL360091.3,PPP2R5A;DisruptR=ANGEL2	yes	chr1q32.3
chr1	213004742	217112255	DUP	0.614522887815487	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ANGEL2;DisruptR=ESRRG	yes	chr1q32.3-q41
chr1	217112256	217777417	DUP	0.329845488730082	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ESRRG;DisruptR=SPATA17	yes	chr1q41
chr1	217777418	220805315	DUP	0.893068802143558	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=SPATA17;DisruptR=MARC1	yes	chr1q41
chr1	220805316	223431462	DUP	1.13394128811201	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=MARC1;DisruptR=	yes	chr1q41
chr1	223431463	234776417	NEU	-0.120705410332972	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=H3F3A|Tier1;DisruptL=;DisruptR=	yes	chr1q41-q42.3
chr1	234776418	242120686	DUP	0.288529442923014	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=FH|Tier1,RGS7|Tier2;DisruptL=;DisruptR=PLD5	yes	chr1q42.3-q43
chr1	242120687	248946322	DUP	0.566757791098143	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=AKT3|Tier2;DisruptL=PLD5;DisruptR=	yes	chr1q43-q44
chr2	10005	37825578	DEL	-0.663197842496562	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MYCN|Tier1,C2orf44|Tier1,NCOA1|Tier1,ASXL2|Tier2,DNMT3A|Tier1,STRN|Tier1,ALK|Tier1,BIRC6|Tier2;DisruptL=;DisruptR=	no	chr2p25.3-p22.2
chr2	37825579	62620851	DEL	-0.246495471549651	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SIX2|Tier2,EPAS1|Tier1,MSH6|Tier1,FBXO11|Tier1,BCL11A|Tier1,REL|Tier1,XPO1|Tier1,EML4|Tier1,MSH2|Tier1;DisruptL=;DisruptR=AC092155.1	no	chr2p22.2-p15
chr2	63608437	94141931	DEL	-0.636708509714021	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=PCBP1|Tier2,DCTN1|Tier1;DisruptL=WDPCP;DisruptR=	no	chr2p15-q11.1
chr2	95642457	105664599	DEL	-0.330285579997176	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=TMEM127|Tier1,AFF3|Tier1;DisruptL=;DisruptR=	yes	chr2q11.1-q12.2
chr2	105664600	109199259	DEL	-0.696541986428974	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=RANBP2|Tier1,RGPD3|Tier2;DisruptL=;DisruptR=SH3RF3	yes	chr2q12.2-q13
chr2	109199785	114973555	DEL	-0.403025290239464	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=PAX8|Tier1;DisruptL=SH3RF3;DisruptR=DPP10	yes	chr2q13-q14.1
chr2	114973556	242183395	DEL	-0.70866876899258	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CXCR4|Tier1,HOXD13|Tier1,HOXD11|Tier1,FEV|Tier1,ACKR3|Tier1,ACVR1|Tier1,NFE2L2|Tier1,CASP8|Tier1,CD28|Tier2,CREB1|Tier1,IDH1|Tier1,BARD1|Tier1,ATIC|Tier1,ACSL3|Tier1,ERCC3|Tier1,COL3A1|Tier2,SF3B1|Tier1,CUL3|Tier2,LRP1B|Tier1,ACVR2A|Tier1,ITGAV|Tier2,PMS1|Tier2,ERBB4|Tier1,PAX3|Tier1;DisruptL=DPP10;DisruptR=	no	chr2q14.1-q37.3
chr3	10005	9676603	NEU	-0.166548377635806	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SRGAP3|Tier2;DisruptL=;DisruptR=MTMR14	yes	chr3p26.3-p25.3
chr3	9676604	10083193	DUP	0.82348177264628	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=FANCD2|Tier1;DisruptL=MTMR14;DisruptR=FANCD2,FANCD2OS	yes	chr3p25.3
chr3	10083194	37547020	NEU	-0.151830410735615	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=VHL|Tier1,CCR4|Tier2,PPARG|Tier1,RAF1|Tier1,MLH1|Tier1,FANCD2|Tier1,XPC|Tier1,TGFBR2|Tier1,FBLN2|Tier2;DisruptL=FANCD2,FANCD2OS;DisruptR=ITGA9	no	chr3p25.3-p22.2
chr3	37547021	37719800	DUP	0.513966954630611	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ITGA9;DisruptR=ITGA9	yes	chr3p22.2
chr3	37719801	39770242	NEU	-0.174375217096961	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MYD88|Tier1;DisruptL=ITGA9;DisruptR=	yes	chr3p22.2-p22.1
chr3	39770243	41312675	DUP	0.786376381302738	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CTNNB1|Tier1;DisruptL=;DisruptR=ULK4	yes	chr3p22.1
chr3	41312676	52565237	DEL	-0.742170315829046	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=BAP1|Tier1,NCKIPSD|Tier2,RHOA|Tier1,SETD2|Tier1,PBRM1|Tier1;DisruptL=ULK4;DisruptR=SMIM4,PBRM1	yes	chr3p22.1-p21.1
chr3	52565238	52629453	DEL	-7.16395331147551	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=PBRM1|Tier1;DisruptL=SMIM4,PBRM1;DisruptR=PBRM1	yes	chr3p21.1
chr3	52629454	85183422	DEL	-0.759244990775244	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MITF|Tier1,PBRM1|Tier1,CACNA1D|Tier1,FOXP1|Tier1,FHIT|Tier1,ROBO2|Tier2;DisruptL=PBRM1;DisruptR=CADM2	no	chr3p21.1-p12.1
chr3	85183423	93455911	DUP	0.297309760423666	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=EPHA3|Tier2;DisruptL=CADM2;DisruptR=	yes	chr3p12.1-q11.1
chr3	93481450	95005470	DUP	0.694630929566397	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=LINC00879	yes	chr3q11.1-q11.2
chr3	95005471	170316551	DUP	0.283378708027476	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=FOXL2|Tier1,TFG|Tier1,GATA2|Tier1,RPN1|Tier1,CNBP|Tier1,GMPS|Tier2,MECOM|Tier1,CBLB|Tier1,POLQ|Tier1,STAG1|Tier2,PIK3CB|Tier1,ATR|Tier1,WWTR1|Tier1,MLF1|Tier1;DisruptL=LINC00879;DisruptR=	no	chr3q11.2-q26.2
chr3	170316552	173659062	DUP	0.683114596646562	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=NLGN1	yes	chr3q26.2-q26.31
chr3	173659063	194248003	DUP	0.341742387842264	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SOX2|Tier1,EIF4A2|Tier1,TBL1XR1|Tier1,PIK3CA|Tier1,ETV5|Tier1,BCL6|Tier1,MAP3K13|Tier1,IGF2BP2|Tier2,MB21D2|Tier2,LPP|Tier1,TP63|Tier1;DisruptL=NLGN1;DisruptR=LINC02036,LINC02037	no	chr3q26.31-q29
chr3	194248004	198139690	DUP	0.652228407725765	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MUC4|Tier2,TFRC|Tier2;DisruptL=LINC02036,LINC02037;DisruptR=	yes	chr3q29
chr4	10011	14827697	DEL	-0.319790434370846	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=FGFR3|Tier1,WHSC1|Tier1;DisruptL=;DisruptR=LINC00504	yes	chr4p16.3-p15.33
chr4	14827698	15664843	DUP	0.477993617701079	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=LINC00504;DisruptR=FBXL5	yes	chr4p15.33-p15.32
chr4	15664844	52771714	DEL	-0.252542523042101	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=RHOH|Tier1,SLC34A2|Tier1,PHOX2B|Tier1,TEC|Tier2,N4BP2|Tier2;DisruptL=FBXL5;DisruptR=	no	chr4p15.32-q12
chr4	52771742	57339073	DUP	0.650796883948463	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=FIP1L1|Tier1,CHIC2|Tier2,KIT|Tier1,KDR|Tier1,PDGFRA|Tier1;DisruptL=;DisruptR=	yes	chr4q12
chr4	57339074	59832563	DUP	0.877386110088138	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr4q12-q13.1
chr4	59832564	62845465	DEL	-0.750075398710684	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr4q13.1
chr4	62845466	65266704	DUP	1.03203174036118	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV;COSMIC;DisruptL=;DisruptR=	yes	chr4q13.1
chr4	65266705	89026738	DEL	-0.726555881013597	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=PTPN13|Tier1,AFF1|Tier1;DisruptL=;DisruptR=FAM13A	no	chr4q13.1-q22.1
chr4	89026739	91384037	DEL	-0.556686246034916	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=FAM13A;DisruptR=CCSER1	yes	chr4q22.1
chr4	91384038	91964419	DEL	-8.15824192085114	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV;COSMIC;DisruptL=CCSER1;DisruptR=	yes	chr4q22.1
chr4	91964420	190066290	DEL	-0.718108215665854	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=IL2|Tier1,FBXW7|Tier1,CASP3|Tier2,RAP1GDS1|Tier1,TET2|Tier1,LEF1|Tier1,FAT4|Tier1,FAT1|Tier1;DisruptL=;DisruptR=DBET	no	chr4q22.1-q35.2
chr5	11484	12810903	DUP	0.781324648487251	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SDHA|Tier1,TERT|Tier1,CTNND2|Tier2;DisruptL=;DisruptR=	yes	chr5p15.33-p15.2
chr5	12810904	12820362	DEL	-8.38699408066103	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=LINC01194	yes	chr5p15.2
chr5	12820363	32366972	DUP	0.654740812323852	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CDH10|Tier2,DROSHA|Tier1;DisruptL=;DisruptR=ZFR	yes	chr5p15.2-p13.3
chr5	32366973	164930824	DUP	0.26250323298084	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=RAD17|Tier2,IL7R|Tier1,LIFR|Tier1,MAP3K1|Tier1,APC|Tier1,PDGFRB|Tier1,CD74|Tier1,ITK|Tier1,PWWP2A|Tier2,IL6ST|Tier1,PIK3R1|Tier1,ACSL6|Tier2,AFF4|Tier1,ARHGAP26|Tier1,CSF1R|Tier2,EBF1|Tier1;DisruptL=ZFR;DisruptR=AC109466.1	no	chr5p13.3-q34
chr5	164930825	180949083	DUP	0.658955275445574	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=NPM1|Tier1,FGFR4|Tier1,TLX3|Tier1,FLT4|Tier1,NSD1|Tier1;DisruptL=AC109466.1;DisruptR=BTNL8	yes	chr5q34-q35.3
chr5	180949084	181003477	DEL	-8.72433167888861	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV,1000G;COSMIC;DisruptL=BTNL8;DisruptR=BTNL3	yes	chr5q35.3
chr5	181003478	181449255	DUP	0.606264899033637	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=BTNL3;DisruptR=	yes	chr5q35.3
chr6	89830	607294	NEU	-0.126255603099321	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV;COSMIC;Cancer_census=IRF4|Tier1;DisruptL=;DisruptR=EXOC2	yes	chr6p25.3
chr6	607295	882087	DEL	-1.65842400187709	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV;DisruptL=EXOC2;DisruptR=	yes	chr6p25.3
chr6	882088	24909815	NEU	-0.0462161100798397	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=DEK|Tier1;DisruptL=;DisruptR=RIPOR2	no	chr6p25.3-p22.3
chr6	24909816	32487100	DEL	-0.660618797459426	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=HIST1H3B|Tier1,HIST1H4I|Tier1,HLA-A|Tier1,POU5F1|Tier1,TRIM27|Tier1;DisruptL=RIPOR2;DisruptR=	yes	chr6p22.3-p21.32
chr6	32487101	36092605	DUP	0.31015246384497	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=DAXX|Tier1,HMGA1|Tier1,FANCE|Tier1;DisruptL=;DisruptR=Z95152.1,MAPK14	yes	chr6p21.32-p21.31
chr6	36092606	37947068	NEU	-0.0837963965211756	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CDKN1A|Tier2,PIM1|Tier1,SRSF3|Tier1;DisruptL=Z95152.1,MAPK14;DisruptR=ZFAND3	yes	chr6p21.31-p21.2
chr6	37947069	38141254	DUP	1.19057334090609	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ZFAND3;DisruptR=ZFAND3	yes	chr6p21.2
chr6	38141255	41251784	DUP	0.54995620507025	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ZFAND3;DisruptR=	yes	chr6p21.2-p21.1
chr6	41251785	52221178	DUP	0.29558522200017	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=TFEB|Tier1,CCND3|Tier1,NFKBIE|Tier1,HSP90AB1|Tier1;DisruptL=;DisruptR=	yes	chr6p21.1-p12.2
chr6	52221179	52679253	DUP	0.677289093257231	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=TMEM14A	yes	chr6p12.2
chr6	52679254	54303155	NEU	-0.112251705623557	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=TMEM14A;DisruptR=	yes	chr6p12.2-p12.1
chr6	54303156	54849666	DEL	-0.665915173870901	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=FAM83B	yes	chr6p12.1
chr6	54849667	59823890	DEL	-1.61037835868916	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=BMP5|Tier2;DisruptL=FAM83B;DisruptR=	yes	chr6p12.1-q11.1
chr6	60241646	78257462	NEU	0.159092581382362	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr6q11.1-q14.1
chr6	78257463	78326601	DEL	-7.48800619648698	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=	yes	chr6q14.1
chr6	78326602	129707604	NEU	0.151064692194691	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=PRDM1|Tier1,CCNC|Tier2,FOXO3|Tier1,ROS1|Tier1,GOPC|Tier1,RSPO3|Tier1,PTPRK|Tier1,EPHA7|Tier2;DisruptL=;DisruptR=ARHGAP18	no	chr6q14.1-q22.33
chr6	129707605	130003966	DUP	1.13296528338616	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ARHGAP18;DisruptR=	yes	chr6q22.33-q23.1
chr6	130003967	166891771	NEU	0.135632037522742	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SGK1|Tier2,MYB|Tier1,BCLAF1|Tier2,TNFAIP3|Tier1,ECT2L|Tier2,EZR|Tier1,ARID1B|Tier1,QKI|Tier1,ESR1|Tier1;DisruptL=;DisruptR=AL159163.1,RPS6KA2	no	chr6q23.1-q27
chr6	166891772	170740360	DUP	0.382788546651371	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=FGFR1OP|Tier1,MLLT4|Tier1;DisruptL=AL159163.1,RPS6KA2;DisruptR=	yes	chr6q27
chr7	16339	43477638	DEL	-0.559868993594197	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=HOXA11|Tier1,HOXA13|Tier1,CARD11|Tier1,PMS2|Tier1,RAC1|Tier1,ETV1|Tier1,HNRNPA2B1|Tier1,HOXA9|Tier1,FKBP9|Tier2,SFRP4|Tier1,JAZF1|Tier2;DisruptL=AC215522.3;DisruptR=HECW1	no	chr7p22.3-p13
chr7	43477639	57487363	DUP	0.631794926043397	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ZNF479|Tier2,EGFR|Tier1,IKZF1|Tier1;DisruptL=HECW1;DisruptR=	yes	chr7p13-p11.2
chr7	57497083	62116180	DUP	0.961130451799653	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=	yes	chr7p11.2-q11.21
chr7	62454737	62742771	DEL	-0.243055087830579	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;Intergenic;Closest=	yes	chr7q11.21
chr7	62742772	69920123	DEL	-0.796801292023739	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SBDS|Tier1;DisruptL=;DisruptR=AUTS2	yes	chr7q11.21-q11.22
chr7	69920124	70236679	DEL	-1.79342739594644	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AUTS2;DisruptR=AUTS2	yes	chr7q11.22
chr7	70236680	84167674	DEL	-0.737274333744057	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ELN|Tier2,HIP1|Tier1;DisruptL=AUTS2;DisruptR=SEMA3A	yes	chr7q11.22-q21.11
chr7	84167675	84789192	NEU	-0.0586450663332738	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=SEMA3A;DisruptR=	yes	chr7q21.11
chr7	84789193	92202778	DEL	-0.724469136983929	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=GRM3|Tier2,AKAP9|Tier2;DisruptL=;DisruptR=AC000120.1,KRIT1	yes	chr7q21.11-q21.2
chr7	92202779	92380732	DEL	-1.6513711166938	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC000120.1,KRIT1;DisruptR=ANKIB1	yes	chr7q21.2
chr7	92380733	116918672	DEL	-0.728544404532958	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CDK6|Tier1,TRRAP|Tier1,CUX1|Tier1,MET|Tier1;DisruptL=ANKIB1;DisruptR=CAPZA2	no	chr7q21.2-q31.2
chr7	116918673	125559131	NEU	-0.157804170815812	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=POT1|Tier1;DisruptL=CAPZA2;DisruptR=	yes	chr7q31.2-q31.33
chr7	125559132	137445253	DEL	-0.746315133262323	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SMO|Tier1,SND1|Tier1;DisruptL=;DisruptR=DGKI	yes	chr7q31.33-q33
chr7	137445254	144556595	NEU	-0.156857151984194	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=KIAA1549|Tier2,FAM131B|Tier2,CREB3L2|Tier1,TRIM24|Tier1,BRAF|Tier1;DisruptL=DGKI;DisruptR=TPK1	yes	chr7q33-q35
chr7	144556596	159335873	DEL	-0.778653215165846	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=EZH2|Tier1,MNX1|Tier2,KMT2C|Tier1,CNTNAP2|Tier2;DisruptL=TPK1;DisruptR=	yes	chr7q35-q36.3
chr8	71162	36461420	DEL	-0.745374476213353	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ARHGEF10|Tier2,LEPROTL1|Tier2,PCM1|Tier1,WRN|Tier1,NRG1|Tier1;DisruptL=;DisruptR=	no	chr8p23.3-p12
chr8	36461421	43475932	NEU	-0.151534973869614	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=WHSC1L1|Tier1,FGFR1|Tier1,IKBKB|Tier1,ANK1|Tier2,HOOK3|Tier1;DisruptL=;DisruptR=	yes	chr8p12-p11.1
chr8	43475933	43646293	DUP	1.94328399797958	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=	yes	chr8p11.1
chr8	43646294	45740170	NEU	-0.115317609705028	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=	yes	chr8p11.1-q11.1
chr8	45740171	60480053	DUP	0.721292223155639	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=TCEA1|Tier1,PLAG1|Tier1,CHCHD7|Tier1;DisruptL=;DisruptR=LINC01301	yes	chr8q11.1-q12.1
chr8	60480054	69392451	DUP	0.940865575164908	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=PREX2|Tier1;DisruptL=LINC01301;DisruptR=	yes	chr8q12.1-q13.2
chr8	69392452	96324265	DUP	0.699652934786086	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=HEY1|Tier1,NBN|Tier1,CDH17|Tier2,NCOA2|Tier1,RUNX1T1|Tier1,CNBD1|Tier2;DisruptL=;DisruptR=PTDSS1	no	chr8q13.2-q22.1
chr8	96324266	97238581	DUP	1.07543825263349	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=PTDSS1;DisruptR=	yes	chr8q22.1
chr8	97238582	101450436	DUP	0.719284292488478	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=COX6C|Tier2,PABPC1|Tier2;DisruptL=;DisruptR=AP001208.2	yes	chr8q22.1-q22.3
chr8	101450437	113847102	DUP	1.46815101967385	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=EIF3E|Tier1,UBR5|Tier1,RSPO2|Tier1,CSMD3|Tier2;DisruptL=AP001208.2;DisruptR=	yes	chr8q22.3-q23.3
chr8	113847103	114412877	DUP	0.696888029167748	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=	yes	chr8q23.3
chr8	114412878	121696690	DUP	1.13340725046321	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=RAD21|Tier1,EXT1|Tier1;DisruptL=;DisruptR=AC104233.1	yes	chr8q23.3-q24.13
chr8	121696691	145078494	DUP	1.23244885529427	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MYC|Tier1,RECQL4|Tier1,NDRG1|Tier1,FAM135B|Tier2;DisruptL=AC104233.1;DisruptR=	no	chr8q24.13-q24.3
chr9	10000	28551864	DEL	-1.48778184627176	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CD274|Tier1,PDCD1LG2|Tier1,PSIP1|Tier1,CDKN2A|Tier1,JAK2|Tier1,NFIB|Tier1,MLLT3|Tier1,PTPRD|Tier2;DisruptL=;DisruptR=LINGO2	no	chr9p24.3-p21.1
chr9	28551865	30540068	DUP	0.706356221243526	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=LINGO2;DisruptR=LINC01242	yes	chr9p21.1
chr9	30540069	45516998	NEU	-0.0509402502425434	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=FANCG|Tier1,PAX5|Tier1;DisruptL=LINC01242;DisruptR=	yes	chr9p21.1-q12
chr9	45516999	66040021	DEL	-0.768293742939348	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=	no	chr9q12-q21.11
chr9	66040022	138313848	NEU	-0.151835590607385	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=OMD|Tier2,KLF4|Tier1,TAL2|Tier1,SET|Tier1,SYK|Tier1,PTCH1|Tier1,XPA|Tier1,NR4A3|Tier1,ABL1|Tier1,RALGDS|Tier2,BRD3|Tier1,NOTCH1|Tier1,GNAQ|Tier1,WNK2|Tier2,FANCC|Tier1,TNC|Tier2,CNTRL|Tier1,PPP6C|Tier1,NUP214|Tier1,TSC1|Tier1,FNBP1|Tier2;DisruptL=;DisruptR=	no	chr9q21.11-q34.3
chr10	10287	3411101	DUP	0.372914558664325	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=LARP4B|Tier2;DisruptL=;DisruptR=	yes	chr10p15.3-p15.2
chr10	3411102	23965103	DUP	0.668025430977722	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=KLF6|Tier1,GATA3|Tier1,MLLT10|Tier1;DisruptL=;DisruptR=KIAA1217	no	chr10p15.2-p12.2
chr10	23965104	27758013	DUP	0.964964713510024	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ABI1|Tier1;DisruptL=KIAA1217;DisruptR=MKX-AS1	yes	chr10p12.2-p12.1
chr10	27758014	29240715	DUP	0.691953333573787	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=MKX-AS1;DisruptR=	yes	chr10p12.1
chr10	29240716	37167257	DUP	0.247554717868894	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=KIF5B|Tier1,ZEB1|Tier2;DisruptL=;DisruptR=ANKRD30A	yes	chr10p12.1-p11.21
chr10	37167258	39580116	DUP	0.537738457637327	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=ANKRD30A;DisruptR=	yes	chr10p11.21-p11.1
chr10	39580117	63904755	DUP	0.356248173010653	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=NCOA4|Tier1,RET|Tier1,A1CF|Tier2,CCDC6|Tier1;DisruptL=;DisruptR=AC022387.1	no	chr10p11.1-q21.3
chr10	63904756	133787316	NEU	-0.175834121436996	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=TLX1|Tier1,PRF1|Tier1,NUTM2B|Tier1,NUTM2A|Tier1,CYP2C8|Tier2,NFKB2|Tier1,TET1|Tier1,KAT6B|Tier1,BMPR1A|Tier1,PTEN|Tier1,FAS|Tier1,CPEB3|Tier2,SUFU|Tier1,NT5C2|Tier1,VTI1A|Tier2,TCF7L2|Tier1,KIAA1598|Tier2,FGFR2|Tier1,MGMT|Tier2;DisruptL=AC022387.1;DisruptR=	no	chr10q21.3-q26.3
chr11	128355	4827727	NEU	-0.23114432262076	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=HRAS|Tier1,NUP98|Tier1,CARS|Tier1;DisruptL=LINC01001;DisruptR=MMP26	yes	chr11p15.5-p15.4
chr11	4827728	7289777	DUP	0.600191704082175	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=MMP26;DisruptR=SYT9	yes	chr11p15.4
chr11	7289778	7844446	DUP	0.997162755384013	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=SYT9;DisruptR=AC044810.3,AC044810.2	yes	chr11p15.4
chr11	7844447	10522050	DUP	0.578796052809746	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=LMO1|Tier1;DisruptL=AC044810.3,AC044810.2;DisruptR=RNF141	yes	chr11p15.4
chr11	10522051	11283093	NEU	-0.155665995552056	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=RNF141;DisruptR=GALNT18	yes	chr11p15.4
chr11	11283094	12343415	DUP	0.56328740080531	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=GALNT18;DisruptR=MICAL2	yes	chr11p15.4-p15.3
chr11	12343416	27802256	NEU	-0.183836187170885	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MYOD1|Tier1,FANCF|Tier1;DisruptL=MICAL2;DisruptR=AC103796.1	yes	chr11p15.3-p14.1
chr11	27802257	29804998	DUP	0.594987152460831	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AC103796.1;DisruptR=AC107973.1	yes	chr11p14.1
chr11	29804999	36593149	NEU	-0.157060769223881	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=WT1|Tier1,LMO2|Tier1;DisruptL=AC107973.1;DisruptR=RAG2,RAG1	yes	chr11p14.1-p12
chr11	36593150	39290297	DUP	0.594476981314884	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=RAG2,RAG1;DisruptR=	yes	chr11p12
chr11	39290298	45539524	NEU	-0.202294922788272	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=EXT2|Tier1;DisruptL=;DisruptR=AC103855.2	yes	chr11p12-p11.2
chr11	45539525	48860163	DUP	0.540739315568864	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CREB3L1|Tier1,DDB2|Tier1;DisruptL=AC103855.2;DisruptR=	yes	chr11p11.2-p11.12
chr11	48860164	49740712	DUP	1.03363939529582	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV;COSMIC;DisruptL=;DisruptR=AC136759.1	yes	chr11p11.12
chr11	49740713	54537482	DUP	0.510963985334505	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AC136759.1;DisruptR=	yes	chr11p11.12-q11
chr11	54537483	58828468	NEU	0.147425268931269	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CLP1|Tier2,CTNND1|Tier2;DisruptL=;DisruptR=	yes	chr11q11-q12.1
chr11	58828469	59869482	DUP	0.43280486108643	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr11q12.1
chr11	59869483	60292995	DUP	0.834441916581633	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=MS4A4A	yes	chr11q12.1-q12.2
chr11	60292996	65505149	NEU	-0.155015460110588	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=FEN1|Tier2,MEN1|Tier1,MALAT1|Tier2,SDHAF2|Tier1;DisruptL=MS4A4A;DisruptR=MALAT1	yes	chr11q12.2-q13.1
chr11	65505150	67782749	DUP	0.244752046837208	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=MALAT1;DisruptR=	yes	chr11q13.1-q13.2
chr11	67782750	69098161	NEU	-0.18207347773054	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=TPCN2	yes	chr11q13.2-q13.3
chr11	69098162	69779346	DUP	2.90792924743999	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=CCND1|Tier1;DisruptL=TPCN2;DisruptR=	yes	chr11q13.3
chr11	69779347	70550613	DUP	1.95533526678893	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=SHANK2	yes	chr11q13.3-q13.4
chr11	70550614	72659617	NEU	-0.217123025297269	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=NUMA1|Tier1;DisruptL=SHANK2;DisruptR=PDE2A	yes	chr11q13.4
chr11	72659618	73059914	DUP	0.283715092417924	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=PDE2A;DisruptR=FCHSD2	yes	chr11q13.4
chr11	73059915	74628478	NEU	-0.0887120035190214	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=FCHSD2;DisruptR=POLD3	yes	chr11q13.4
chr11	74628479	78640369	DUP	0.630473391841354	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=POLD3;DisruptR=	yes	chr11q13.4-q14.1
chr11	78640370	80765305	NEU	-0.196419138454143	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr11q14.1
chr11	80765306	121197406	DEL	-0.742141382743052	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SDHD|Tier1,FAT3|Tier2,BIRC3|Tier1,POU2AF1|Tier1,PAFAH1B2|Tier1,DDX6|Tier1,BCL9L|Tier1,FOXR1|Tier2,EED|Tier2,MAML2|Tier1,ATM|Tier1,DDX10|Tier1,ZBTB16|Tier1,CBL|Tier1,ARHGEF12|Tier1,PICALM|Tier1,KMT2A|Tier1;DisruptL=;DisruptR=	no	chr11q14.1-q23.3
chr11	121197407	121473002	NEU	-0.206909827013359	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=SORL1	yes	chr11q23.3-q24.1
chr11	121473003	133551052	DEL	-0.793700907758826	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=KCNJ5|Tier1,FLI1|Tier1;DisruptL=SORL1;DisruptR=	yes	chr11q24.1-q25
chr11	133551053	135076522	DEL	-1.86436361266953	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr11q25
chr12	41087	56255606	NEU	-0.155461676799245	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=PTPN6|Tier2,CDKN1B|Tier1,HOXC13|Tier1,HOXC11|Tier1,KDM5A|Tier1,CCND2|Tier1,CHD4|Tier1,ZNF384|Tier1,KRAS|Tier1,COL2A1|Tier1,KMT2D|Tier1,PRPF40B|Tier2,SMARCD1|Tier1,ATF1|Tier1,ETV6|Tier1,ETNK1|Tier1,PPFIBP1|Tier1,ARID2|Tier1,ERBB3|Tier1,ERC1|Tier1;DisruptL=;DisruptR=ANKRD52	no	chr12p13.33-q13.3
chr12	56255607	61144793	DUP	0.853465094126381	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=NAB2|Tier1,GLI1|Tier2,DDIT3|Tier1,CDK4|Tier1,NACA|Tier2,STAT6|Tier1,LRIG3|Tier1;DisruptL=ANKRD52;DisruptR=	yes	chr12q13.3-q14.1
chr12	61144794	65713849	NEU	-0.137220411871809	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=WIF1|Tier1;DisruptL=;DisruptR=	yes	chr12q14.1-q14.3
chr12	65713850	67923115	DUP	2.43751576610213	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=HMGA2|Tier1;DisruptL=;DisruptR=	yes	chr12q14.3-q15
chr12	67923116	69782592	DUP	1.6226997176003	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MDM2|Tier1;DisruptL=;DisruptR=RAB3IP	yes	chr12q15
chr12	69782593	69869146	NEU	-0.174585169321525	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=RAB3IP;DisruptR=MYRFL	yes	chr12q15
chr12	69869147	71964313	DUP	1.48386284317098	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=PTPRB|Tier1;DisruptL=MYRFL;DisruptR=TPH2	yes	chr12q15-q21.1
chr12	71964314	72511936	DUP	2.09700184520745	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=TPH2;DisruptR=TRHDE	yes	chr12q21.1
chr12	72511937	112325530	NEU	-0.156861592009548	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=BTG1|Tier1,USP44|Tier2,SH2B3|Tier1,CHST11|Tier2,ALDH2|Tier2;DisruptL=TRHDE;DisruptR=HECTD4	no	chr12q21.1-q24.13
chr12	112325531	112386380	DUP	2.47611958649697	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=HECTD4;DisruptR=	yes	chr12q24.13
chr12	112386381	125881976	NEU	-0.209108062887736	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=TBX3|Tier1,SETD1B|Tier2,ZCCHC8|Tier2,PTPN11|Tier1,HNF1A|Tier1,BCL7A|Tier1,CLIP1|Tier1,NCOR2|Tier1;DisruptL=;DisruptR=	yes	chr12q24.13-q24.32
chr12	125881977	133264924	NEU	0.136312987620628	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=POLE|Tier1;DisruptL=;DisruptR=	yes	chr12q24.32-q24.33
chr13	16000006	17402857	DUP	0.431878889535423	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=;Intergenic;Closest=	yes	chr13p11.2-p11.1
chr13	17417970	23788056	DEL	-0.389176610654975	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ZNF198|Tier1;DisruptL=;DisruptR=MIPEP	yes	chr13p11.1-q12.12
chr13	23788057	24952905	NEU	0.0312524409016876	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=MIPEP;DisruptR=TPTE2P1	yes	chr13q12.12-q12.13
chr13	24952906	28880401	DUP	0.303598897637474	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CDX2|Tier1,FLT3|Tier1;DisruptL=TPTE2P1;DisruptR=MTUS2	yes	chr13q12.13-q12.3
chr13	28880402	68670604	DEL	-0.741613977662178	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CYSLTR2|Tier2,BRCA2|Tier1,LHFP|Tier2,FOXO1|Tier1,RB1|Tier1,NBEA|Tier2,LCP1|Tier2;DisruptL=MTUS2;DisruptR=	no	chr13q12.3-q21.33
chr13	68670605	68694604	DEL	-6.84782495275923	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV,1000G;DisruptL=;DisruptR=	yes	chr13q21.33
chr13	68694605	97331911	DEL	-0.719298628256566	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SOX21|Tier2,GPC5|Tier2;DisruptL=;DisruptR=MBNL2	no	chr13q21.33-q32.1
chr13	97331912	97689209	DEL	-1.6597916683381	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=MBNL2;DisruptR=	yes	chr13q32.1-q32.2
chr13	97689210	98509394	DEL	-0.751674524876152	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=STK24	yes	chr13q32.2
chr13	98509395	107326494	DUP	0.35597786078123	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ERCC5|Tier1;DisruptL=STK24;DisruptR=FAM155A	yes	chr13q32.2-q33.3
chr13	107326495	110418575	DUP	0.550509830072072	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=FAM155A;DisruptR=COL4A2	yes	chr13q33.3-q34
chr13	110418576	114354111	NEU	-0.215336102363864	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=COL4A2;DisruptR=	yes	chr13q34
chr14	16140244	20575058	NEU	0.119248644953633	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=CCNB1IP1|Tier1;DisruptL=;DisruptR=	yes	chr14p11.1-q11.2
chr14	20575059	21264197	DUP	0.694241481429683	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=HNRNPC	yes	chr14q11.2
chr14	21264198	41140316	NEU	0.0985569567852812	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=NKX2-1|Tier1,FOXA1|Tier1,ARHGAP5|Tier2,BAZ1A|Tier2;DisruptL=HNRNPC;DisruptR=	yes	chr14q11.2-q21.1
chr14	41140317	41200380	DEL	-7.53636462911679	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=	yes	chr14q21.1
chr14	41200381	91109906	NEU	0.0862846211220301	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SIX1|Tier1,NIN|Tier1,KTN1|Tier1,MAX|Tier1,HIF1A|Tier1,TSHR|Tier1,RAD51B|Tier1,GPHN|Tier1;DisruptL=;DisruptR=DGLUCY	no	chr14q21.1-q32.11
chr14	91109907	91493434	DUP	0.59603042629931	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=DGLUCY;DisruptR=PPP4R3A	yes	chr14q32.11-q32.12
chr14	91493435	104243063	NEU	0.0108682635432299	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=TCL1A|Tier1,DICER1|Tier1,TRIP11|Tier1,GOLGA5|Tier1,BCL11B|Tier1,HSP90AA1|Tier1;DisruptL=PPP4R3A;DisruptR=AL590079.1	yes	chr14q32.12-q32.33
chr14	104243064	105433357	DUP	1.8105651479203	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=AKT1|Tier1;DisruptL=AL590079.1;DisruptR=TEX22,MTA1	yes	chr14q32.33
chr14	105433358	106883618	DUP	1.20339538796228	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV;COSMIC;DisruptL=TEX22,MTA1;DisruptR=	yes	chr14q32.33
chr15	17083473	56746778	NEU	-0.126844022364764	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=NUTM1|Tier1,BUB1B|Tier1,KNSTRN|Tier2,B2M|Tier1,CASC5|Tier1,USP8|Tier1,MYO5A|Tier1;DisruptL=;DisruptR=AC090517.4	no	chr15p11.2-q21.3
chr15	56746779	65078751	DUP	0.604054448257953	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=TCF12|Tier1;DisruptL=AC090517.4;DisruptR=	yes	chr15q21.3-q22.31
chr15	65078752	72000143	NEU	0.191022094077794	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MAP2K1|Tier1,SMAD3|Tier1;DisruptL=;DisruptR=AC022872.1,MYO9A	yes	chr15q22.31-q23
chr15	72000144	72362589	DUP	0.831832080412268	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AC022872.1,MYO9A;DisruptR=AC009690.1,HEXA	yes	chr15q23
chr15	72362590	101981087	NEU	0.142385533804755	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=FES|Tier1,PML|Tier1,POLG|Tier2,IDH2|Tier1,BLM|Tier1,CRTC3|Tier1,CHD2|Tier2,NTRK3|Tier1;DisruptL=AC009690.1,HEXA;DisruptR=	no	chr15q23-q26.3
chr16	10005	13284477	NEU	-0.0951851568826254	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=TRAF7|Tier1,SOCS1|Tier1,RMI2|Tier1,TNFRSF17|Tier1,AXIN1|Tier1,TSC2|Tier1,RUNDC2A|Tier2,CREBBP|Tier1,GRIN2A|Tier1,CIITA|Tier1,NTHL1|Tier2;DisruptL=;DisruptR=U91319.1	yes	chr16p13.3-p13.12
chr16	13284478	34502581	DUP	0.311866348272102	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=FUS|Tier1,ERCC4|Tier1,PALB2|Tier1,IL21R|Tier1,MYH11|Tier1,PRKCB|Tier2;DisruptL=U91319.1;DisruptR=	no	chr16p13.12-p11.2
chr16	34596149	90226217	NEU	-0.180190016081108	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=MAF|Tier1,CYLD|Tier1,HERPUD1|Tier1,CDH11|Tier1,CBFB|Tier1,RFWD3|Tier2,CBFA2T3|Tier1,CTCF|Tier1,CDH1|Tier1,ZFHX3|Tier1,FANCA|Tier1;DisruptL=;DisruptR=	no	chr16p11.2-q24.3
chr17	168977	21658447	DUP	0.216865584970261	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=TP53|Tier1,YWHAE|Tier1,USP6|Tier1,PER1|Tier1,FLCN|Tier1,RABEP1|Tier1,GAS7|Tier1,MAP2K4|Tier1,NCOR1|Tier1,SPECC1|Tier2;DisruptL=DOC2B;DisruptR=	no	chr17p13.3-p11.2
chr17	22044138	34345057	DEL	-0.254870558958534	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=NF1|Tier1,SUZ12|Tier1;DisruptL=;DisruptR=	yes	chr17p11.2-q12
chr17	34345058	36041470	DUP	0.250240109740102	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=TAF15|Tier1;DisruptL=;DisruptR=	yes	chr17q12
chr17	36041471	39577425	DEL	-0.71112305889253	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MLLT6|Tier1,LASP1|Tier1,CDK12|Tier1;DisruptL=;DisruptR=	yes	chr17q12
chr17	39577426	39805109	DUP	0.245068065687465	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ERBB2|Tier1;DisruptL=;DisruptR=IKZF3	yes	chr17q12-q21.1
chr17	39805110	43301596	DEL	-0.715254382152286	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CCR7|Tier2,RARA|Tier1,SMARCE1|Tier1,STAT5B|Tier1,STAT3|Tier1,BRCA1|Tier1;DisruptL=IKZF3;DisruptR=LINC00854	yes	chr17q21.1-q21.31
chr17	43301597	47874812	NEU	0.168991168623362	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ETV4|Tier1;DisruptL=LINC00854;DisruptR=	yes	chr17q21.31-q21.32
chr17	47874813	48072289	DUP	1.19561329742961	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=CBX1	yes	chr17q21.32
chr17	48072290	55607901	DUP	0.204924913602767	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SPOP|Tier1,KAT7|Tier2,COL1A1|Tier1,HLF|Tier1;DisruptL=CBX1;DisruptR=	yes	chr17q21.32-q22
chr17	55607902	59518846	DUP	0.821210651759635	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=RNF43|Tier1,MSI2|Tier1;DisruptL=;DisruptR=LINC01476	yes	chr17q22-q23.1
chr17	59518847	67102559	NEU	-0.139306271039043	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=PPM1D|Tier1,CD79B|Tier1,DDX5|Tier1,CLTC|Tier1,BRIP1|Tier1,AXIN2|Tier1;DisruptL=LINC01476;DisruptR=HELZ	yes	chr17q23.1-q24.2
chr17	67102560	83247341	DUP	0.793435794136766	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=H3F3B|Tier1,SRSF2|Tier1,CANT1|Tier1,PRKAR1A|Tier1,ASPSCR1|Tier1,SEPT9|Tier2,RNF213|Tier1;DisruptL=HELZ;DisruptR=	yes	chr17q24.2-q25.3
chr18	10010	276979	DUP	0.227807883519478	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV;COSMIC;DisruptL=;DisruptR=	yes	chr18p11.32
chr18	276980	1091192	DUP	1.05014221509118	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=AP005328.1	yes	chr18p11.32
chr18	1091193	1158563	DEL	-0.319419104917766	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=AP005328.1;DisruptR=AP005328.1	yes	chr18p11.32
chr18	1158564	3047603	DUP	0.933668194321343	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AP005328.1;DisruptR=	yes	chr18p11.32-p11.31
chr18	3047604	7909753	DUP	1.15443728077165	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=PTPRM	yes	chr18p11.31-p11.23
chr18	7909754	11293417	DUP	1.47179035783631	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=PTPRM;DisruptR=	yes	chr18p11.23-p11.21
chr18	11293418	11707457	DUP	1.09199855300875	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=GNAL	yes	chr18p11.21
chr18	11707458	20553041	NEU	0.148737120057397	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=GNAL;DisruptR=	yes	chr18p11.21-q11.1
chr18	20553042	23307595	DEL	-0.262164570806976	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=TMEM241	yes	chr18q11.1-q11.2
chr18	23307596	23971374	DUP	1.23020312157277	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=TMEM241;DisruptR=AC010754.1	yes	chr18q11.2
chr18	23971375	24279287	DUP	0.548273629483977	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AC010754.1;DisruptR=OSBPL1A	yes	chr18q11.2
chr18	24279288	24683977	DEL	-0.262132614460008	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=OSBPL1A;DisruptR=	yes	chr18q11.2
chr18	24683978	30129850	DEL	-0.702852943671167	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SS18|Tier1,ZNF521|Tier1;DisruptL=;DisruptR=	yes	chr18q11.2-q12.1
chr18	30129851	40264437	DEL	-0.897504714118573	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr18q12.1-q12.3
chr18	40264438	49181719	DEL	-0.287875273536123	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SMAD2|Tier1,SETBP1|Tier1;DisruptL=;DisruptR=DYM	yes	chr18q12.3-q21.1
chr18	49181720	57411729	DEL	-0.931762360233605	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SMAD4|Tier1,DCC|Tier2;DisruptL=DYM;DisruptR=	yes	chr18q21.1-q21.31
chr18	57411730	59280927	DEL	-0.483922733549493	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MALT1|Tier1;DisruptL=;DisruptR=CPLX4	yes	chr18q21.31-q21.32
chr18	59280928	61626459	DEL	-0.888204956782555	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=CPLX4;DisruptR=AC105094.2	yes	chr18q21.32-q21.33
chr18	61626460	67194496	DUP	0.409500602625316	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=KDSR|Tier1,BCL2|Tier1;DisruptL=AC105094.2;DisruptR=	yes	chr18q21.33-q22.1
chr18	67194497	73989168	NEU	0.178011488420988	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=AC090125.1	yes	chr18q22.1-q22.3
chr18	73989169	80263172	DUP	0.425844300142982	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=AC090125.1;DisruptR=	yes	chr18q22.3-q23
chr19	90733	12858860	NEU	-0.182514722240739	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=FSTL3|Tier1,CD209|Tier2,KEAP1|Tier1,STK11|Tier1,TCF3|Tier1,GNA11|Tier1,MAP2K2|Tier1,SH3GL1|Tier1,MLLT1|Tier1,MUC16|Tier2,VAV1|Tier2,DNM2|Tier1,SMARCA4|Tier1;DisruptL=;DisruptR=HOOK2,MAST1	yes	chr19p13.3-p13.13
chr19	12858861	12880012	DEL	-7.26348333346458	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=HOOK2,MAST1;DisruptR=DNASE2	yes	chr19p13.13
chr19	12880013	14687523	NEU	-0.157406837413209	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=LYL1|Tier1,CALR|Tier1,PRKACA|Tier1,DNAJB1|Tier1;DisruptL=DNASE2;DisruptR=ADGRE3	yes	chr19p13.13-p13.12
chr19	14687524	15684658	DUP	1.94036745539687	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=BRD4|Tier1;DisruptL=ADGRE3;DisruptR=CYP4F12	yes	chr19p13.12
chr19	15684659	20137237	NEU	-0.024606598432035	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=TPM4|Tier1,JAK3|Tier1,ELL|Tier1,CRTC1|Tier1;DisruptL=CYP4F12;DisruptR=AC011447.2,AC011447.3	yes	chr19p13.12-p12
chr19	20137238	20490394	DUP	0.903033474177566	bicseq2	HCC-1143_80--HCC-1143BL_40	known=DGV;DisruptL=AC011447.2,AC011447.3;DisruptR=AC008554.1	yes	chr19p12
chr19	20490395	23544109	NEU	-0.181291745187585	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ZNF429|Tier2;DisruptL=AC008554.1;DisruptR=ZNF675	yes	chr19p12
chr19	23544110	24018595	DUP	0.362688176435516	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ZNF675;DisruptR=	yes	chr19p12
chr19	24018596	58607515	NEU	-0.105824759419373	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CEBPA|Tier1,BCL3|Tier1,BCL2L12|Tier2,KLK2|Tier1,TFPT|Tier2,CCNE1|Tier1,CD79A|Tier1,CIC|Tier1,CBLC|Tier1,ERCC2|Tier1,BAX|Tier1,POLD1|Tier1,PPP2R1A|Tier1,ZNF331|Tier1,CNOT3|Tier1,CEP89|Tier2,LSM14A|Tier2,AKT2|Tier1;DisruptL=;DisruptR=	no	chr19p12-q13.43
chr20	67260	8764419	DUP	0.529458486195768	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SIRPA|Tier2;DisruptL=;DisruptR=PLCB1	yes	chr20p13-p12.3
chr20	8764420	21885644	DUP	0.78857797027008	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=CRNKL1|Tier2;DisruptL=PLCB1;DisruptR=	yes	chr20p12.3-p11.22
chr20	21885645	28506070	DUP	0.940102227272049	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=	yes	chr20p11.22-q11.1
chr20	29339193	30761316	NEU	0.151132990081343	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;DisruptL=;DisruptR=	yes	chr20q11.1-q11.21
chr20	31245066	31539738	DUP	1.2197270737823	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=HM13	yes	chr20q11.21
chr20	31539739	34230620	DUP	1.85344535344003	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ASXL1|Tier1;DisruptL=HM13;DisruptR=ASIP	yes	chr20q11.21-q11.22
chr20	34230621	36912830	DUP	1.25642697561249	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=ASIP;DisruptR=SAMHD1	yes	chr20q11.22-q11.23
chr20	36912831	39349550	DUP	1.01666822746823	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=SRC|Tier1;DisruptL=SAMHD1;DisruptR=	yes	chr20q11.23-q12
chr20	39349551	64334067	NEU	0.185485241728428	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=MAFB|Tier1,TOP1|Tier1,SDC4|Tier1,SALL4|Tier1,GNAS|Tier1,SS18L1|Tier1,PTK6|Tier1,PLCG1|Tier1,NFATC2|Tier1,PTPRT|Tier1;DisruptL=;DisruptR=	no	chr20q12-q13.33
chr21	13282812	13507200	DUP	0.395199651585114	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr21q11.2
chr21	13507201	15873584	DUP	1.46846267608385	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=USP25	yes	chr21q11.2-q21.1
chr21	15873585	17474345	DUP	0.286094859614575	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=USP25;DisruptR=	yes	chr21q21.1
chr21	17474346	17986205	DUP	1.59820845031939	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=CHODL	yes	chr21q21.1
chr21	17986206	18484759	DUP	0.47974744225096	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=CHODL;DisruptR=TMPRSS15,AL109763.1	yes	chr21q21.1
chr21	18484760	20111383	NEU	0.0993833820272748	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=TMPRSS15,AL109763.1;DisruptR=	yes	chr21q21.1
chr21	20111384	26635290	NEU	-0.153572710586549	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=	yes	chr21q21.1-q21.3
chr21	26635291	31947284	DEL	-0.634536049376747	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=;DisruptR=HUNK	yes	chr21q21.3-q22.11
chr21	31947285	32739659	DUP	0.734474303515442	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=HUNK;DisruptR=PAXBP1-AS1,PAXBP1	yes	chr21q22.11
chr21	32739660	34714666	DUP	0.27526929392765	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=OLIG2|Tier1;DisruptL=PAXBP1-AS1,PAXBP1;DisruptR=CLIC6	yes	chr21q22.11-q22.12
chr21	34714667	34819639	DEL	-1.22527495119003	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=RUNX1|Tier1;DisruptL=CLIC6;DisruptR=RUNX1	yes	chr21q22.12
chr21	34819640	34847754	DEL	-7.87445248300763	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=RUNX1|Tier1;DisruptL=RUNX1;DisruptR=RUNX1	yes	chr21q22.12
chr21	34847755	40764259	DEL	-0.477961653702394	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=RUNX1|Tier1,ERG|Tier1;DisruptL=RUNX1;DisruptR=DSCAM	yes	chr21q22.12-q22.2
chr21	40764260	41078298	DUP	1.15163195966485	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=DSCAM;DisruptR=	yes	chr21q22.2
chr21	41078299	41825925	DEL	-0.331231030637504	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=TMPRSS2|Tier1;DisruptL=;DisruptR=PRDM15	yes	chr21q22.2-q22.3
chr21	41825926	42103908	DUP	1.13229425470384	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=PRDM15;DisruptR=UMODL1-AS1,UMODL1	yes	chr21q22.3
chr21	42103909	44064549	NEU	-0.0758811106959548	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=U2AF1|Tier1;DisruptL=UMODL1-AS1,UMODL1;DisruptR=TRAPPC10	yes	chr21q22.3
chr21	44064550	46107841	DUP	1.22087947073456	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=TRAPPC10;DisruptR=COL6A2	yes	chr21q22.3
chr21	46107842	46699872	NEU	-0.0621603203556886	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=COL6A2;DisruptR=	yes	chr21q22.3
chr22	10514978	24015968	DUP	0.871841346848739	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;Cancer_census=SEPT5|Tier2,DGCR8|Tier2,LZTR1|Tier1,MAPK1|Tier1,SMARCB1|Tier1,CLTCL1|Tier1,BCR|Tier1;DisruptL=;DisruptR=CABIN1	yes	chr22p11.2-q11.23
chr22	24015969	29344638	DUP	1.12803596999529	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=ZNRF3|Tier2,EWSR1|Tier1,MN1|Tier1,CHEK2|Tier1;DisruptL=CABIN1;DisruptR=AP1B1	yes	chr22q11.23-q12.2
chr22	29344639	46073918	DUP	0.708398116705091	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;Cancer_census=APOBEC3B|Tier1,ZNF278|Tier1,ISX|Tier2,PDGFB|Tier1,MKL1|Tier1,NF2|Tier1,MYH9|Tier1,EP300|Tier1;DisruptL=AP1B1;DisruptR=MIRLET7BHG	yes	chr22q12.2-q13.31
chr22	46073919	46234133	DUP	1.28055277284805	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=MIRLET7BHG;DisruptR=PPARA	yes	chr22q13.31
chr22	46234134	50808368	DUP	0.635891209611808	bicseq2	HCC-1143_80--HCC-1143BL_40	known=;COSMIC;DisruptL=PPARA;DisruptR=	yes	chr22q13.31-q13.33