#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 -1.73187277448838 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=P2RY8,CRLF2,ZRSR2,EIF1AX,FAM47C,BCOR,DDX3X,KDM6A;DisruptL=;DisruptR=KDM6A no chrXp22.33-p11.3 chrX 44887175 47658808 DEL -0.694867507995076 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ARAF,KDM6A,RBM10;DisruptL=KDM6A;DisruptR=UXT yes chrXp11.3-p11.23 chrX 47658809 56991083 DEL -1.73652933711447 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SSX1,WAS,SSX4,GATA1,TFE3,SSX2,SMC1A,KDM5C;DisruptL=UXT;DisruptR=SPIN3 yes chrXp11.23-p11.21 chrX 56991084 57170267 DEL -0.768377479334792 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SPIN3;DisruptR= yes chrXp11.21 chrX 57170268 57361936 DEL -1.71664650842954 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=FAAH2 yes chrXp11.21 chrX 57361937 57506640 NEU -0.205890342252425 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAAH2;DisruptR= yes chrXp11.21 chrX 57506641 57682097 DEL -0.760353602437335 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chrXp11.21 chrX 57682198 58538907 NEU -0.232103321407404 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chrXp11.21-p11.1 chrX 58538908 65752159 NEU 0.196062154500607 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=AMER1,MSN;DisruptL=;DisruptR= yes chrXp11.1-q12 chrX 65752160 73870954 NEU -0.180376697151362 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=FOXO4,ZMYM3,NONO,MED12,AR;DisruptL=;DisruptR= yes chrXq12-q13.2 chrX 73870955 76244723 DUP 0.283831213478883 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chrXq13.2-q13.3 chrX 76244724 84380645 DUP 0.595268597866807 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ATRX;DisruptL=;DisruptR=HDX yes chrXq13.3-q21.1 chrX 84380646 87103946 DUP 0.278331545319598 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=HDX;DisruptR= yes chrXq21.1-q21.31 chrX 87103947 88322772 DUP 0.582154496499178 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chrXq21.31 chrX 88322773 100877555 DUP 0.272134228467576 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chrXq21.31-q22.1 chrX 100877556 106655099 DEL -0.659875112629486 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=BTK;DisruptL=;DisruptR=CXorf57 yes chrXq22.1-q22.3 chrX 106655100 106901143 NEU -0.079824052907948 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=CXorf57;DisruptR=RIPPLY1,CLDN2,MORC4 yes chrXq22.3 chrX 106901144 115725483 DEL -0.634369406631009 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=IRS4;DisruptL=RIPPLY1,CLDN2,MORC4;DisruptR= yes chrXq22.3-q23 chrX 115725484 116456786 NEU -0.0645045764432444 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=SLC6A14 yes chrXq23 chrX 116456787 117971410 DUP 0.294032716859252 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=SLC6A14;DisruptR=KLHL13 yes chrXq23-q24 chrX 117971411 118882103 DUP 1.06657213466317 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=KLHL13;DisruptR=LINC01285 yes chrXq24 chrX 118882104 139747068 DUP 0.24062609719122 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=DCAF12L2,STAG2,ELF4,PHF6,SEPT6,GPC3,BCORL1;DisruptL=LINC01285;DisruptR=ATP11C no chrXq24-q27.1 chrX 139747069 140075558 DEL -1.84723426438723 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ATP11C;DisruptR= yes chrXq27.1 chrX 140075559 153146260 DEL -0.80169115056085 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chrXq27.1-q28 chrX 153149106 153586440 DUP 0.440573891990643 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=ATP2B3;DisruptL=;DisruptR= yes chrXq28 chrX 153586441 156030795 NEU -0.186278266703881 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=RPL10,MTCP1,FLNA;DisruptL=;DisruptR= yes chrXq28 chr1 10028 6465256 NEU 0.164113166863963 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=TNFRSF14,SKI,RPL22,PRDM16;DisruptL=;DisruptR=TNFRSF25 yes chr1p36.33-p36.31 chr1 6465257 8115684 NEU -0.186499423395274 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CAMTA1;DisruptL=TNFRSF25;DisruptR=AL034417.2 yes chr1p36.31-p36.23 chr1 8115685 8673895 NEU 0.0804631774677909 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL034417.2;DisruptR=RERE yes chr1p36.23 chr1 8673896 8950366 DUP 0.658080960488197 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=RERE;DisruptR=CA6 yes chr1p36.23 chr1 8950367 19771880 NEU -0.181383910577795 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CASP9,PAX7,MTOR,PRDM2,SPEN,SDHB,ARHGEF10L;DisruptL=CA6;DisruptR=TMCO4 yes chr1p36.23-p36.13 chr1 19771881 23063090 DUP 0.242953722972102 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=TMCO4;DisruptR=KDM1A,AL031428.1 yes chr1p36.13-p36.12 chr1 23063091 47818851 NEU -0.155759513664001 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ID3,MDS2,MYCL,TAL1,LCK,SFPQ,THRAP3,CSF3R,MPL,MUTYH,STIL,ARID1A;DisruptL=KDM1A,AL031428.1;DisruptR=AC096541.1,TRABD2B no chr1p36.12-p33 chr1 47818852 51383048 DUP 0.227736387398213 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CDKN2C,EPS15;DisruptL=AC096541.1,TRABD2B;DisruptR=EPS15 yes chr1p33-p32.3 chr1 51383049 52861923 NEU -0.087798446820374 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=EPS15;DisruptL=EPS15;DisruptR=ZYG11A yes chr1p32.3 chr1 52861924 53005829 DEL -0.698176342288448 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ZYG11A;DisruptR=SCP2 yes chr1p32.3 chr1 53005833 83866322 NEU -0.159944116619155 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=JUN,FUBP1,JAK1;DisruptL=SCP2;DisruptR=TTLL7 no chr1p32.3-p31.1 chr1 83866323 84289901 DUP 0.641485837454027 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=TTLL7;DisruptR= yes chr1p31.1 chr1 84289902 94125487 NEU -0.138874759593928 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=BCL10,RPL5;DisruptL=;DisruptR= yes chr1p31.1-p22.1 chr1 94125488 94476955 DUP 0.66668179211075 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=ABCD3 yes chr1p22.1-p21.3 chr1 94476956 103478704 NEU -0.14745457475771 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ABCD3;DisruptR=AC095032.1 yes chr1p21.3-p21.1 chr1 103478705 107356812 DEL -0.748476435564636 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AC095032.1;DisruptR=NTNG1 yes chr1p21.1-p13.3 chr1 107356813 121384880 NEU -0.165746426883596 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=RBM15,NRAS,FAM46C,TRIM33,NOTCH2,ATP1A1;DisruptL=NTNG1;DisruptR=SRGAP2C,SRGAP2-AS1 yes chr1p13.3-p11.2 chr1 121384881 124734467 DUP 0.302092236562876 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SRGAP2C,SRGAP2-AS1;DisruptR= yes chr1p11.2-q11 chr1 124752057 150474751 NEU -0.138075747802932 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=BCL9,PDE4DIP;DisruptL=;DisruptR=RPRD2 no chr1q11-q21.2 chr1 150474752 150749711 DUP 0.685951336633822 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;COSMIC;DisruptL=RPRD2;DisruptR=CTSS yes chr1q21.2-q21.3 chr1 150749712 169257068 NEU -0.121150726994736 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MLLT11,S100A7,TPM3,LMNA,PRCC,NTRK1,FCRL4,FCGR2B,DDR2,ARNT,SDHC,MUC1,PBX1;DisruptL=CTSS;DisruptR=NME7 yes chr1q21.3-q24.2 chr1 169257069 169275461 DEL -8.5403882287172 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;COSMIC;DisruptL=NME7;DisruptR=NME7 yes chr1q24.2 chr1 169275462 186672816 NEU -0.103918222224636 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=PRRX1,ABL2,TPR;DisruptL=NME7;DisruptR=PTGS2 yes chr1q24.2-q31.1 chr1 186672817 200934768 DUP 0.29200006140006 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CDC73,PTPRC;DisruptL=PTGS2;DisruptR=MROH3P yes chr1q31.1-q32.1 chr1 200934769 202013977 NEU 0.107824703234401 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ELF3;DisruptL=MROH3P;DisruptR=ELF3,AL691482.3 yes chr1q32.1 chr1 202013978 202476271 DUP 0.615245787583378 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ELF3;DisruptL=ELF3,AL691482.3;DisruptR=PPP1R12B yes chr1q32.1 chr1 202476272 203360618 NEU 0.124610772931901 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=PPP1R12B;DisruptR= yes chr1q32.1 chr1 203360619 205097986 DUP 0.740125842001456 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MDM4;DisruptL=;DisruptR=RBBP5 yes chr1q32.1 chr1 205097987 211808611 DUP 0.475070783221211 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SLC45A3,ELK4;DisruptL=RBBP5;DisruptR=LPGAT1 yes chr1q32.1-q32.3 chr1 211808612 212301636 DUP 0.277874371703419 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LPGAT1;DisruptR=AL360091.3,PPP2R5A yes chr1q32.3 chr1 212301637 212996331 DUP 0.957667759731855 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AL360091.3,PPP2R5A;DisruptR=ANGEL2 yes chr1q32.3 chr1 212996332 217111255 DUP 0.613053975481472 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ANGEL2;DisruptR=ESRRG yes chr1q32.3-q41 chr1 217111256 217777417 DUP 0.323710633548837 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ESRRG;DisruptR=SPATA17 yes chr1q41 chr1 217777418 220805315 DUP 0.887247923308628 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=SPATA17;DisruptR=MARC1 yes chr1q41 chr1 220805316 221668389 DUP 1.03835666058052 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=MARC1;DisruptR= yes chr1q41 chr1 221668390 222786580 DUP 1.26055391712443 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chr1q41 chr1 222786581 223431562 DUP 1.01862802271431 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chr1q41 chr1 223431563 234957836 NEU -0.121103889250402 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=H3F3A;DisruptL=;DisruptR=AL391832.1,AL391832.2 yes chr1q41-q42.3 chr1 234957837 242121907 DUP 0.291926261115833 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=FH,RGS7;DisruptL=AL391832.1,AL391832.2;DisruptR=PLD5 yes chr1q42.3-q43 chr1 242121908 248946322 DUP 0.568413522956941 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=AKT3;DisruptL=PLD5;DisruptR= yes chr1q43-q44 chr2 10005 24576134 DEL -0.684700482636262 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MYCN,C2orf44;DisruptL=;DisruptR=NCOA1 no chr2p25.3-p23.3 chr2 24576135 24695332 NEU -0.190079479051605 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=NCOA1;DisruptL=NCOA1;DisruptR=NCOA1 yes chr2p23.3 chr2 24695333 37783334 DEL -0.635550391829276 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=NCOA1,ASXL2,DNMT3A,STRN,ALK,BIRC6;DisruptL=NCOA1;DisruptR= yes chr2p23.3-p22.2 chr2 37783435 62620851 DEL -0.247524616392694 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SIX2,EPAS1,MSH6,FBXO11,BCL11A,REL,XPO1,EML4,MSH2;DisruptL=;DisruptR=AC092155.1 no chr2p22.2-p15 chr2 63608437 88772978 DEL -0.644253081102805 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=PCBP1,DCTN1;DisruptL=WDPCP;DisruptR=ANKRD36BP2 no chr2p15-p11.2 chr2 88778964 99488531 NEU -0.209633401186215 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=TMEM127;DisruptL=ANKRD36BP2;DisruptR=REV1 yes chr2p11.2-q11.2 chr2 103111952 105668984 DEL -0.399547917285717 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AC073987.1;DisruptR= yes chr2q12.1-q12.2 chr2 105668985 109199259 DEL -0.697123127844434 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=RANBP2,RGPD3;DisruptL=;DisruptR=SH3RF3 yes chr2q12.2-q13 chr2 109199785 114973555 DEL -0.399931155263099 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=PAX8;DisruptL=SH3RF3;DisruptR=DPP10 yes chr2q13-q14.1 chr2 114973556 152347874 DEL -0.730063302716474 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CXCR4,ERCC3,LRP1B,ACVR2A;DisruptL=DPP10;DisruptR=FMNL2 no chr2q14.1-q23.3 chr2 152347875 152457123 DEL -1.24386008632178 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FMNL2;DisruptR=FMNL2 yes chr2q23.3 chr2 152457124 242183395 DEL -0.701583605174824 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=HOXD13,HOXD11,FEV,ACKR3,ACVR1,NFE2L2,CASP8,CD28,CREB1,IDH1,BARD1,ATIC,ACSL3,COL3A1,SF3B1,CUL3,ITGAV,PMS1,ERBB4,PAX3;DisruptL=FMNL2;DisruptR= no chr2q23.3-q37.3 chr3 10005 9307881 NEU -0.181911601259986 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SRGAP3;DisruptL=;DisruptR=SRGAP3,AC026191.1 yes chr3p26.3-p25.3 chr3 9307882 9404941 DUP 0.651241805698061 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=SRGAP3,AC026191.1;DisruptR=SETD5 yes chr3p25.3 chr3 9404942 9676503 NEU -0.132223382226586 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=SETD5;DisruptR=MTMR14 yes chr3p25.3 chr3 9676504 10083193 DUP 0.817708052055956 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=FANCD2;DisruptL=MTMR14;DisruptR=FANCD2,FANCD2OS yes chr3p25.3 chr3 10083194 37547020 NEU -0.154127827519746 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=VHL,CCR4,PPARG,RAF1,MLH1,FANCD2,XPC,TGFBR2,FBLN2;DisruptL=FANCD2,FANCD2OS;DisruptR=ITGA9 no chr3p25.3-p22.2 chr3 37547021 37719800 DUP 0.519265202921599 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ITGA9;DisruptR=ITGA9 yes chr3p22.2 chr3 37719801 39770242 NEU -0.179146770752829 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MYD88;DisruptL=ITGA9;DisruptR= yes chr3p22.2-p22.1 chr3 39770243 41312675 DUP 0.781304571092826 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CTNNB1;DisruptL=;DisruptR=ULK4 yes chr3p22.1 chr3 41312676 52565237 DEL -0.740206626107188 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=BAP1,NCKIPSD,RHOA,SETD2,PBRM1;DisruptL=ULK4;DisruptR=SMIM4,PBRM1 yes chr3p22.1-p21.1 chr3 52565238 52629453 DEL -6.69317231079691 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=PBRM1;DisruptL=SMIM4,PBRM1;DisruptR=PBRM1 yes chr3p21.1 chr3 52629454 85183522 DEL -0.75972192833664 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MITF,PBRM1,CACNA1D,FOXP1,FHIT,ROBO2;DisruptL=PBRM1;DisruptR=CADM2 no chr3p21.1-p12.1 chr3 85183523 93455911 DUP 0.29574511855103 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=EPHA3;DisruptL=CADM2;DisruptR= yes chr3p12.1-q11.1 chr3 93481450 95006170 DUP 0.696386915427004 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=LINC00879 yes chr3q11.1-q11.2 chr3 95006171 170316051 DUP 0.280130683238444 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=FOXL2,TFG,GATA2,RPN1,CNBP,GMPS,MECOM,CBLB,POLQ,STAG1,PIK3CB,ATR,WWTR1,MLF1;DisruptL=LINC00879;DisruptR= no chr3q11.2-q26.2 chr3 170316052 173658862 DUP 0.677153416788488 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=NLGN1 yes chr3q26.2-q26.31 chr3 173658863 194247703 DUP 0.340666392459149 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SOX2,EIF4A2,TBL1XR1,PIK3CA,ETV5,BCL6,MAP3K13,IGF2BP2,MB21D2,LPP,TP63;DisruptL=NLGN1;DisruptR=LINC02036,LINC02037 no chr3q26.31-q29 chr3 194247704 198139690 DUP 0.648167756767031 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MUC4,TFRC;DisruptL=LINC02036,LINC02037;DisruptR= yes chr3q29 chr4 10011 7325437 DEL -0.329234163992031 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=FGFR3,WHSC1;DisruptL=;DisruptR=SORCS2 yes chr4p16.3-p16.1 chr4 7325438 7334737 DEL -8.6013902007306 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SORCS2;DisruptR=SORCS2 yes chr4p16.1 chr4 7334738 9455743 DEL -0.330168501623589 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=SORCS2;DisruptR= yes chr4p16.1 chr4 9455744 9479035 DEL -6.89734650544388 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;DisruptL=;DisruptR= yes chr4p16.1 chr4 9479036 14827697 DEL -0.297404389678022 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=LINC00504 yes chr4p16.1-p15.33 chr4 14827698 15665043 DUP 0.482208952574665 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=LINC00504;DisruptR=FBXL5 yes chr4p15.33-p15.32 chr4 15665044 22959993 DEL -0.263617125352956 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=FBXL5;DisruptR= yes chr4p15.32-p15.2 chr4 22959994 22967180 DEL -7.25057965729075 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;Intergenic;Closest= yes chr4p15.2 chr4 22967181 52771714 DEL -0.251624971027325 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=RHOH,SLC34A2,PHOX2B,TEC,N4BP2;DisruptL=;DisruptR= no chr4p15.2-q12 chr4 52771742 57018941 DUP 0.629036371253031 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=FIP1L1,CHIC2,KIT,KDR,PDGFRA;DisruptL=;DisruptR=POLR2B yes chr4q12 chr4 57018942 59832663 DUP 0.869721161194789 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=POLR2B;DisruptR= yes chr4q12-q13.1 chr4 59832664 62845465 DEL -0.745599671506481 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chr4q13.1 chr4 62845466 65266704 DUP 1.03324061621762 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;COSMIC;DisruptL=;DisruptR= yes chr4q13.1 chr4 65266705 89015232 DEL -0.726209393975852 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=PTPN13,AFF1;DisruptL=;DisruptR=FAM13A no chr4q13.1-q22.1 chr4 89015233 91384037 DEL -0.551987312075293 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=FAM13A;DisruptR=CCSER1 yes chr4q22.1 chr4 91384038 91964419 DEL -7.61060032054407 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;COSMIC;DisruptL=CCSER1;DisruptR= yes chr4q22.1 chr4 91964420 190066290 DEL -0.718854782975871 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=IL2,FBXW7,CASP3,RAP1GDS1,TET2,LEF1,FAT4,FAT1;DisruptL=;DisruptR=DBET no chr4q22.1-q35.2 chr5 11484 11509602 DUP 0.790507268812484 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SDHA,TERT,CTNND2;DisruptL=;DisruptR=CTNND2 yes chr5p15.33-p15.2 chr5 11509603 12810903 DUP 0.635055955064469 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CTNND2;DisruptL=CTNND2;DisruptR= yes chr5p15.2 chr5 12810904 12820362 DEL -6.89606394026236 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=LINC01194 yes chr5p15.2 chr5 12820363 32366972 DUP 0.649559515575666 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CDH10,DROSHA;DisruptL=;DisruptR=ZFR yes chr5p15.2-p13.3 chr5 32366973 87038731 DUP 0.257831240812828 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=RAD17,IL7R,LIFR,MAP3K1,IL6ST,PIK3R1;DisruptL=ZFR;DisruptR=AC109492.1 no chr5p13.3-q14.3 chr5 87038732 87057656 DEL -7.07707722310885 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;DisruptL=AC109492.1;DisruptR=AC109492.1 yes chr5q14.3 chr5 87057657 140717308 DUP 0.251907548991506 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=APC,ACSL6,AFF4;DisruptL=AC109492.1;DisruptR= no chr5q14.3-q31.3 chr5 140717309 140724487 DEL -5.56457745234456 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;COSMIC;DisruptL=;DisruptR= yes chr5q31.3 chr5 140724488 164930824 DUP 0.282490619041053 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=PDGFRB,CD74,ITK,PWWP2A,ARHGAP26,CSF1R,EBF1;DisruptL=;DisruptR=AC109466.1 no chr5q31.3-q34 chr5 164930825 165579621 DUP 0.80306639767394 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC109466.1;DisruptR=AC008415.1 yes chr5q34 chr5 165579622 169123091 DUP 0.617436740974476 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AC008415.1;DisruptR=SLIT3 yes chr5q34-q35.1 chr5 169123092 171131351 DUP 0.813318514403991 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=SLIT3;DisruptR=RANBP17 yes chr5q35.1 chr5 171131352 179626939 DUP 0.62436696523282 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=NPM1,FGFR4,TLX3,NSD1;DisruptL=RANBP17;DisruptR=HNRNPH1 yes chr5q35.1-q35.3 chr5 179626940 179633919 DEL -6.06500048438441 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HNRNPH1;DisruptR=HNRNPH1 yes chr5q35.3 chr5 179633920 179641489 DUP 0.777012585923037 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HNRNPH1;DisruptR= yes chr5q35.3 chr5 179641490 179655238 DEL -4.37617618393532 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr5q35.3 chr5 179655239 180949083 DUP 0.623764894836641 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=FLT4;DisruptL=;DisruptR=BTNL8 yes chr5q35.3 chr5 180949084 181003477 DEL -7.64046287587683 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;COSMIC;DisruptL=BTNL8;DisruptR=BTNL3 yes chr5q35.3 chr5 181003478 181449255 DUP 0.611975452890166 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=BTNL3;DisruptR= yes chr5q35.3 chr6 89830 607294 NEU -0.149104129847277 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;COSMIC;Cancer_census=IRF4;DisruptL=;DisruptR=EXOC2 yes chr6p25.3 chr6 607295 882087 DEL -1.67119447611573 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;DisruptL=EXOC2;DisruptR= yes chr6p25.3 chr6 882088 24909915 NEU -0.0483511794820358 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=DEK;DisruptL=;DisruptR=RIPOR2 no chr6p25.3-p22.3 chr6 24909916 32487100 DEL -0.656539918067314 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=HIST1H3B,HIST1H4I,HLA-A,POU5F1,TRIM27;DisruptL=RIPOR2;DisruptR= yes chr6p22.3-p21.32 chr6 32487101 36092705 DUP 0.302850317905756 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=DAXX,HMGA1,FANCE;DisruptL=;DisruptR=MAPK14 yes chr6p21.32-p21.31 chr6 36092706 37947068 NEU -0.0967941136561111 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CDKN1A,PIM1,SRSF3;DisruptL=MAPK14;DisruptR=ZFAND3 yes chr6p21.31-p21.2 chr6 37947069 38141254 DUP 1.18477778601739 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ZFAND3;DisruptR=ZFAND3 yes chr6p21.2 chr6 38141255 41251884 DUP 0.548742429654972 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ZFAND3;DisruptR= yes chr6p21.2-p21.1 chr6 41251885 52220478 DUP 0.294201620341052 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=TFEB,CCND3,NFKBIE,HSP90AB1;DisruptL=;DisruptR= yes chr6p21.1-p12.2 chr6 52220479 52679253 DUP 0.67843249455974 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=TMEM14A yes chr6p12.2 chr6 52679254 54303355 NEU -0.113325332000409 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=TMEM14A;DisruptR= yes chr6p12.2-p12.1 chr6 54303356 54849666 DEL -0.671023969071796 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=FAM83B yes chr6p12.1 chr6 54849667 59823890 DEL -1.60083889719855 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=BMP5;DisruptL=FAM83B;DisruptR= yes chr6p12.1-q11.1 chr6 60241646 73882341 NEU 0.155972730605217 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chr6q11.1-q13 chr6 73882342 73892649 DEL -6.15092264656889 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest= yes chr6q13 chr6 73892650 76727613 NEU 0.176726184642895 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chr6q13-q14.1 chr6 76727614 76749424 DEL -4.9180964591244 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;DisruptL=;DisruptR=;Intergenic;Closest= yes chr6q14.1 chr6 76749425 78257462 NEU 0.150655062407039 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chr6q14.1 chr6 78257463 78326601 DEL -6.95185190177402 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest= yes chr6q14.1 chr6 78326602 129707604 NEU 0.148880515050009 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=PRDM1,CCNC,FOXO3,ROS1,GOPC,RSPO3,PTPRK,EPHA7;DisruptL=;DisruptR=ARHGAP18 no chr6q14.1-q22.33 chr6 129707605 130003966 DUP 1.13327467858457 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ARHGAP18;DisruptR= yes chr6q22.33-q23.1 chr6 130003967 165311198 NEU 0.138815536940189 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SGK1,MYB,BCLAF1,TNFAIP3,ECT2L,EZR,ARID1B,QKI,ESR1;DisruptL=;DisruptR= no chr6q23.1-q27 chr6 165311199 165318598 DEL -6.94088330093951 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=C6orf118 yes chr6q27 chr6 165318599 166890852 NEU 0.0317309960597826 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=AL159163.1,RPS6KA2 yes chr6q27 chr6 166890853 170740360 DUP 0.387777877169966 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=FGFR1OP,MLLT4;DisruptL=AL159163.1,RPS6KA2;DisruptR= yes chr6q27 chr7 16339 43477638 DEL -0.560709462972241 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=HOXA11,HOXA13,CARD11,PMS2,RAC1,ETV1,HNRNPA2B1,HOXA9,FKBP9,SFRP4,JAZF1;DisruptL=AC215522.3;DisruptR=HECW1 no chr7p22.3-p13 chr7 43477639 50144341 DUP 0.644196964607283 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=HECW1;DisruptR=SPATA48 yes chr7p13-p12.2 chr7 50144342 53753365 DUP 0.5488216251663 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=IKZF1;DisruptL=SPATA48;DisruptR=LINC01446 yes chr7p12.2-p12.1 chr7 53753366 57487363 DUP 0.684645492773396 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ZNF479,EGFR;DisruptL=LINC01446;DisruptR= yes chr7p12.1-p11.2 chr7 57497083 62116180 DUP 0.965485441878537 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr7p11.2-q11.21 chr7 62454737 62742671 DEL -0.245177623811479 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;Intergenic;Closest= yes chr7q11.21 chr7 62742672 69920123 DEL -0.794513457266777 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SBDS;DisruptL=;DisruptR=AUTS2 yes chr7q11.21-q11.22 chr7 69920124 70236679 DEL -1.79308786302776 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AUTS2;DisruptR=AUTS2 yes chr7q11.22 chr7 70236680 84167774 DEL -0.735553565593352 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ELN,HIP1;DisruptL=AUTS2;DisruptR=SEMA3A yes chr7q11.22-q21.11 chr7 84167775 84789192 NEU -0.0553300631948354 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=SEMA3A;DisruptR= yes chr7q21.11 chr7 84789193 92202778 DEL -0.725288941891063 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=GRM3,AKAP9;DisruptL=;DisruptR=AC000120.1,KRIT1 yes chr7q21.11-q21.2 chr7 92202779 92380602 DEL -1.63139151336501 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC000120.1,KRIT1;DisruptR=ANKIB1 yes chr7q21.2 chr7 92380603 116918672 DEL -0.727073979951145 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CDK6,TRRAP,CUX1,MET;DisruptL=ANKIB1;DisruptR=CAPZA2 no chr7q21.2-q31.2 chr7 116918673 125559131 NEU -0.158556659893076 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=POT1;DisruptL=CAPZA2;DisruptR= yes chr7q31.2-q31.33 chr7 125559132 137445253 DEL -0.746967472905017 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SMO,SND1;DisruptL=;DisruptR=DGKI yes chr7q31.33-q33 chr7 137445254 140911186 NEU -0.17448442199291 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=KIAA1549,CREB3L2,TRIM24,BRAF;DisruptL=DGKI;DisruptR=BRAF yes chr7q33-q34 chr7 140911187 141311252 NEU 0.198966737498963 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=BRAF;DisruptL=BRAF;DisruptR=TMEM178B yes chr7q34 chr7 141311253 144556795 NEU -0.222629027973291 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=FAM131B;DisruptL=TMEM178B;DisruptR=TPK1 yes chr7q34-q35 chr7 144556796 159335873 DEL -0.777732329037721 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=EZH2,MNX1,KMT2C,CNTNAP2;DisruptL=TPK1;DisruptR= yes chr7q35-q36.3 chr8 71162 36461420 DEL -0.744852641980785 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ARHGEF10,LEPROTL1,PCM1,WRN,NRG1;DisruptL=;DisruptR= no chr8p23.3-p12 chr8 36461421 43475932 NEU -0.152945090388919 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=WHSC1L1,FGFR1,IKBKB,ANK1,HOOK3;DisruptL=;DisruptR= yes chr8p12-p11.1 chr8 43475933 43646293 DUP 1.9227579309522 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr8p11.1 chr8 43646294 44903043 NEU -0.15415640042163 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr8p11.1 chr8 44968553 46943804 DUP 0.875025053883708 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr8p11.1-q11.1 chr8 46943805 60480053 DUP 0.704593074155982 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=TCEA1,PLAG1,CHCHD7;DisruptL=;DisruptR=LINC01301 yes chr8q11.1-q12.1 chr8 60480054 69408003 DUP 0.938592651750749 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=PREX2;DisruptL=LINC01301;DisruptR= yes chr8q12.1-q13.2 chr8 69408004 96324265 DUP 0.696724768887535 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=HEY1,NBN,CDH17,NCOA2,RUNX1T1,CNBD1;DisruptL=;DisruptR=PTDSS1 no chr8q13.2-q22.1 chr8 96324266 97238581 DUP 1.06725402591211 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=PTDSS1;DisruptR= yes chr8q22.1 chr8 97238582 101450536 DUP 0.712079735852209 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=COX6C,PABPC1;DisruptL=;DisruptR=AP001208.2 yes chr8q22.1-q22.3 chr8 101450537 111464795 DUP 1.4398482395071 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=EIF3E,UBR5,RSPO2;DisruptL=AP001208.2;DisruptR=LINC02237 yes chr8q22.3-q23.3 chr8 111464796 113801448 DUP 1.57135559465044 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CSMD3;DisruptL=LINC02237;DisruptR= yes chr8q23.3 chr8 113801449 114412277 DUP 0.714406250990239 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr8q23.3 chr8 114412278 121698090 DUP 1.13010244716529 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=RAD21,EXT1;DisruptL=;DisruptR=AC104233.1 yes chr8q23.3-q24.13 chr8 121698091 145078494 DUP 1.22646583953892 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MYC,RECQL4,NDRG1,FAM135B;DisruptL=AC104233.1;DisruptR= no chr8q24.13-q24.3 chr9 10000 28551864 DEL -1.48528028864086 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CD274,PDCD1LG2,PSIP1,CDKN2A,JAK2,NFIB,MLLT3,PTPRD;DisruptL=;DisruptR=LINGO2 no chr9p24.3-p21.1 chr9 28551865 30540068 DUP 0.702650028242232 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=LINGO2;DisruptR=LINC01242 yes chr9p21.1 chr9 30540069 45516998 NEU -0.0499425618406077 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=FANCG,PAX5;DisruptL=LINC01242;DisruptR= yes chr9p21.1-q12 chr9 60528185 63787540 DEL -1.36775168457111 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr9q12-q13 chr9 63825346 65079292 NEU -0.193030449787371 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr9q13-q21.11 chr9 65079293 65515654 DEL -1.86624047159657 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr9q21.11 chr9 65515655 113363791 NEU -0.144239721997054 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=OMD,KLF4,TAL2,SYK,PTCH1,XPA,NR4A3,GNAQ,WNK2,FANCC;DisruptL=;DisruptR=BSPRY no chr9q21.11-q32 chr9 113363792 113614612 DUP 0.228207644669989 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=BSPRY;DisruptR=AL162727.3 yes chr9q32 chr9 113614613 126950429 NEU -0.156838731723287 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=TNC,CNTRL,PPP6C;DisruptL=AL162727.3;DisruptR=RALGPS1 yes chr9q32-q33.3 chr9 126950430 127070381 DEL -0.689170587313099 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=RALGPS1;DisruptR=RALGPS1 yes chr9q33.3 chr9 127070382 138313848 NEU -0.187064819922902 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SET,ABL1,RALGDS,BRD3,NOTCH1,NUP214,TSC1,FNBP1;DisruptL=RALGPS1;DisruptR= yes chr9q33.3-q34.3 chr10 10287 3336245 DUP 0.364060580183314 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=LARP4B;DisruptL=;DisruptR= yes chr10p15.3-p15.2 chr10 3336246 23965103 DUP 0.665610949117923 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=KLF6,GATA3,MLLT10;DisruptL=;DisruptR=KIAA1217 no chr10p15.2-p12.2 chr10 23965104 27759513 DUP 0.965541744865292 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ABI1;DisruptL=KIAA1217;DisruptR=MKX-AS1 yes chr10p12.2-p12.1 chr10 27759514 29240315 DUP 0.690721488063426 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=MKX-AS1;DisruptR= yes chr10p12.1 chr10 29240316 37167257 DUP 0.245520390723314 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=KIF5B,ZEB1;DisruptL=;DisruptR=ANKRD30A yes chr10p12.1-p11.21 chr10 37167258 38483627 DUP 0.485955877582138 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ANKRD30A;DisruptR= yes chr10p11.21-p11.1 chr10 38581843 39340908 DUP 0.769506692694336 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr10p11.1 chr10 39340909 63904555 DUP 0.352414501394552 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=NCOA4,RET,A1CF,CCDC6;DisruptL=;DisruptR=AC022387.1 no chr10p11.1-q21.3 chr10 63904556 133787316 NEU -0.177469739844892 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=TLX1,PRF1,NUTM2B,NUTM2A,CYP2C8,NFKB2,TET1,KAT6B,BMPR1A,PTEN,FAS,CPEB3,SUFU,NT5C2,VTI1A,TCF7L2,KIAA1598,FGFR2,MGMT;DisruptL=AC022387.1;DisruptR= no chr10q21.3-q26.3 chr11 128355 4827727 NEU -0.227260020869506 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=HRAS,NUP98,CARS;DisruptL=LINC01001;DisruptR=MMP26 yes chr11p15.5-p15.4 chr11 4827728 6030161 DUP 0.518208644462701 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=MMP26;DisruptR=OR56A1 yes chr11p15.4 chr11 6030162 6378337 DUP 0.978243591681258 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=OR56A1;DisruptR= yes chr11p15.4 chr11 6378338 7289777 DUP 0.512029718142495 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=SYT9 yes chr11p15.4 chr11 7289778 7779072 DUP 0.990228853497327 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=SYT9;DisruptR=AC044810.3,AC044810.2 yes chr11p15.4 chr11 7779073 10522050 DUP 0.580653243856889 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=LMO1;DisruptL=AC044810.3,AC044810.2;DisruptR=RNF141 yes chr11p15.4 chr11 10522051 11283093 NEU -0.150333649248185 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=RNF141;DisruptR=GALNT18 yes chr11p15.4 chr11 11283094 12344015 DUP 0.566220364618513 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=GALNT18;DisruptR=MICAL2 yes chr11p15.4-p15.3 chr11 12344016 27802356 NEU -0.183767805167806 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MYOD1,FANCF;DisruptL=MICAL2;DisruptR=AC103796.1 yes chr11p15.3-p14.1 chr11 27802357 29804998 DUP 0.5928957735582 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AC103796.1;DisruptR=AC107973.1 yes chr11p14.1 chr11 29804999 36593149 NEU -0.159834122679093 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=WT1,LMO2;DisruptL=AC107973.1;DisruptR=RAG2,RAG1 yes chr11p14.1-p12 chr11 36593150 39290297 DUP 0.592723697279865 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=RAG2,RAG1;DisruptR= yes chr11p12 chr11 39290298 45539524 NEU -0.20627578692781 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=EXT2;DisruptL=;DisruptR=AC103855.2 yes chr11p12-p11.2 chr11 45539525 48243068 DUP 0.569882047787684 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CREB3L1,DDB2;DisruptL=AC103855.2;DisruptR= yes chr11p11.2 chr11 48243069 48425478 NEU -0.164435654785307 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr11p11.2 chr11 48425479 48860163 DUP 0.538161301475876 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;COSMIC;DisruptL=;DisruptR= yes chr11p11.2-p11.12 chr11 48860164 49740712 DUP 1.03221561208068 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;COSMIC;DisruptL=;DisruptR=AC136759.1 yes chr11p11.12 chr11 49740713 54537482 DUP 0.508779550055583 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC136759.1;DisruptR= yes chr11p11.12-q11 chr11 54537483 58828468 NEU 0.139096433637212 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CLP1,CTNND1;DisruptL=;DisruptR= yes chr11q11-q12.1 chr11 58828469 59869482 DUP 0.424954727545846 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chr11q12.1 chr11 59869483 60293095 DUP 0.853107095929642 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=MS4A4A yes chr11q12.1-q12.2 chr11 60293096 62369230 NEU -0.188640281448978 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=FEN1,SDHAF2;DisruptL=MS4A4A;DisruptR=ASRGL1 yes chr11q12.2-q12.3 chr11 62369231 62579533 DUP 0.42066972946544 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ASRGL1;DisruptR=AP002990.1,TUT1 yes chr11q12.3 chr11 62579534 65505249 NEU -0.170898147336137 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MEN1,MALAT1;DisruptL=AP002990.1,TUT1;DisruptR=MALAT1 yes chr11q12.3-q13.1 chr11 65505250 67782059 DUP 0.245405053000852 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=MALAT1;DisruptR= yes chr11q13.1-q13.2 chr11 67782060 69098161 NEU -0.181283218917646 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=TPCN2 yes chr11q13.2-q13.3 chr11 69098162 69356466 DUP 2.64528812586497 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TPCN2;DisruptR=MYEOV yes chr11q13.3 chr11 69356467 69779346 DUP 2.99653147357031 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CCND1;DisruptL=MYEOV;DisruptR= yes chr11q13.3 chr11 69779347 70550613 DUP 1.95284082114091 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=SHANK2 yes chr11q13.3-q13.4 chr11 70550614 72659717 NEU -0.211431030716356 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=NUMA1;DisruptL=SHANK2;DisruptR=PDE2A yes chr11q13.4 chr11 72659718 73060314 DUP 0.285254505546659 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=PDE2A;DisruptR=FCHSD2 yes chr11q13.4 chr11 73060315 74628478 NEU -0.0937088593073541 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=FCHSD2;DisruptR=POLD3 yes chr11q13.4 chr11 74628479 78640469 DUP 0.63154348327726 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=POLD3;DisruptR= yes chr11q13.4-q14.1 chr11 78640470 80765205 NEU -0.204390478605318 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chr11q14.1 chr11 80765206 121197406 DEL -0.743642959923248 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SDHD,FAT3,BIRC3,POU2AF1,PAFAH1B2,DDX6,BCL9L,FOXR1,EED,MAML2,ATM,DDX10,ZBTB16,CBL,ARHGEF12,PICALM,KMT2A;DisruptL=;DisruptR= no chr11q14.1-q23.3 chr11 121197407 121472902 NEU -0.192568437319585 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=SORL1 yes chr11q23.3-q24.1 chr11 121472903 133550952 DEL -0.793838060691559 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=KCNJ5,FLI1;DisruptL=SORL1;DisruptR= yes chr11q24.1-q25 chr11 133550953 135076522 DEL -1.86373066093716 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chr11q25 chr12 41087 11377302 NEU -0.176524390793408 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=PTPN6,KDM5A,CCND2,CHD4,ZNF384,ERC1;DisruptL=;DisruptR=PRB1 yes chr12p13.33-p13.2 chr12 11377303 11391409 DEL -6.34224245033427 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PRB1;DisruptR=PRB1 yes chr12p13.2 chr12 11391410 12378537 NEU -0.125552613032335 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ETV6;DisruptL=PRB1;DisruptR=BORCS5 yes chr12p13.2 chr12 12378538 12389537 DEL -5.95875302269849 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;COSMIC;DisruptL=BORCS5;DisruptR=BORCS5 yes chr12p13.2 chr12 12389538 56255706 NEU -0.15311469442555 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=CDKN1B,HOXC13,HOXC11,KRAS,COL2A1,KMT2D,PRPF40B,SMARCD1,ATF1,ETNK1,PPFIBP1,ARID2,ERBB3;DisruptL=BORCS5;DisruptR=ANKRD52 no chr12p13.2-q13.3 chr12 56255707 59542040 DUP 0.826929606848957 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=NAB2,GLI1,DDIT3,CDK4,NACA,STAT6,LRIG3;DisruptL=ANKRD52;DisruptR= yes chr12q13.3-q14.1 chr12 59542041 59552840 DEL -4.85912613384275 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=LINC02448 yes chr12q14.1 chr12 59552841 61144793 DUP 0.897506608055226 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chr12q14.1 chr12 61144794 65713849 NEU -0.137770498992205 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=WIF1;DisruptL=;DisruptR= yes chr12q14.1-q14.3 chr12 65713850 67923115 DUP 2.44010820245558 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=HMGA2;DisruptL=;DisruptR= yes chr12q14.3-q15 chr12 67923116 69782592 DUP 1.61938509627978 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MDM2;DisruptL=;DisruptR=RAB3IP yes chr12q15 chr12 69782593 69869146 NEU -0.145418345236653 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=RAB3IP;DisruptR=MYRFL yes chr12q15 chr12 69869147 71964313 DUP 1.48214864782128 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=PTPRB;DisruptL=MYRFL;DisruptR=TPH2 yes chr12q15-q21.1 chr12 71964314 72511836 DUP 2.09900360229418 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=TPH2;DisruptR=TRHDE yes chr12q21.1 chr12 72511837 101739241 NEU -0.148441349047853 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=BTG1,USP44;DisruptL=TRHDE;DisruptR=SYCP3,CHPT1 no chr12q21.1-q23.2 chr12 101739242 101984829 DUP 0.263184674882525 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=SYCP3,CHPT1;DisruptR=DRAM1 yes chr12q23.2 chr12 101984830 112325530 NEU -0.193508163017244 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SH2B3,CHST11,ALDH2;DisruptL=DRAM1;DisruptR=HECTD4 yes chr12q23.2-q24.13 chr12 112325531 112386380 DUP 2.5072245204425 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HECTD4;DisruptR= yes chr12q24.13 chr12 112386381 125881076 NEU -0.213500281355981 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=TBX3,SETD1B,ZCCHC8,PTPN11,HNF1A,BCL7A,CLIP1,NCOR2;DisruptL=;DisruptR= yes chr12q24.13-q24.32 chr12 125881077 133264924 NEU 0.137703196375541 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=POLE;DisruptL=;DisruptR= yes chr12q24.32-q24.33 chr13 16022426 18408580 DUP 0.469003811336288 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr13p11.2-q11 chr13 18408581 23788056 DEL -0.400935138724099 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ZNF198;DisruptL=;DisruptR=MIPEP yes chr13q11-q12.12 chr13 23788057 24369558 NEU 0.143747946818759 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=MIPEP;DisruptR= yes chr13q12.12 chr13 24369559 24952567 NEU -0.106397184447943 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=TPTE2P1 yes chr13q12.12-q12.13 chr13 24952568 28880401 DUP 0.306942489471456 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CDX2,FLT3;DisruptL=TPTE2P1;DisruptR=MTUS2 yes chr13q12.13-q12.3 chr13 28880402 68670604 DEL -0.739853591055848 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CYSLTR2,BRCA2,LHFP,FOXO1,RB1,NBEA,LCP1;DisruptL=MTUS2;DisruptR= no chr13q12.3-q21.33 chr13 68670605 68694604 DEL -7.3098691573477 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;DisruptL=;DisruptR= yes chr13q21.33 chr13 68694605 97331911 DEL -0.721697515283187 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SOX21,GPC5;DisruptL=;DisruptR=MBNL2 no chr13q21.33-q32.1 chr13 97331912 97689109 DEL -1.65215433382122 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=MBNL2;DisruptR= yes chr13q32.1-q32.2 chr13 97689110 98509394 DEL -0.731040005149365 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=STK24 yes chr13q32.2 chr13 98509395 102234406 DUP 0.319431259184923 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=STK24;DisruptR=FGF14 yes chr13q32.2-q33.1 chr13 102234407 103143846 DUP 0.549043915253632 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ERCC5;DisruptL=FGF14;DisruptR= yes chr13q33.1 chr13 103143847 107326194 DUP 0.33362658845687 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=FAM155A yes chr13q33.1-q33.3 chr13 107326195 108157040 DUP 0.61022666783353 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=FAM155A;DisruptR= yes chr13q33.3 chr13 108157041 108951935 DUP 0.33548920200196 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=MYO16 yes chr13q33.3 chr13 108951936 110418575 DUP 0.611834301726922 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=MYO16;DisruptR=COL4A2 yes chr13q33.3-q34 chr13 110418576 114354111 NEU -0.209364982817957 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=COL4A2;DisruptR= yes chr13q34 chr14 16140244 20575158 NEU 0.122457500971757 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=CCNB1IP1;DisruptL=;DisruptR= yes chr14p11.1-q11.2 chr14 20575159 21264197 DUP 0.678532614517522 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=HNRNPC yes chr14q11.2 chr14 21264198 32961967 NEU 0.0911053877627032 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ARHGAP5;DisruptL=HNRNPC;DisruptR=NPAS3 yes chr14q11.2-q13.1 chr14 32961968 32970857 DEL -7.05185013008174 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=NPAS3;DisruptR=NPAS3 yes chr14q13.1 chr14 32970858 41140316 NEU 0.107723629299309 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=NKX2-1,FOXA1,BAZ1A;DisruptL=NPAS3;DisruptR= yes chr14q13.1-q21.1 chr14 41140317 41200380 DEL -7.01134362203325 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest= yes chr14q21.1 chr14 41200381 91109906 NEU 0.0848015123819308 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SIX1,NIN,KTN1,MAX,HIF1A,TSHR,RAD51B,GPHN;DisruptL=;DisruptR=DGLUCY no chr14q21.1-q32.11 chr14 91109907 91493334 DUP 0.602372788118238 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=DGLUCY;DisruptR=PPP4R3A yes chr14q32.11-q32.12 chr14 91493335 104243063 NEU 0.0126125653298669 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=TCL1A,DICER1,TRIP11,GOLGA5,BCL11B,HSP90AA1;DisruptL=PPP4R3A;DisruptR=AL590079.1 yes chr14q32.12-q32.33 chr14 104243064 104326322 DUP 1.16737442494562 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;COSMIC;DisruptL=AL590079.1;DisruptR= yes chr14q32.33 chr14 104326323 105433357 DUP 1.86227814484237 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=AKT1;DisruptL=;DisruptR=TEX22,MTA1 yes chr14q32.33 chr14 105433358 106883618 DUP 1.20719014095817 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;COSMIC;DisruptL=TEX22,MTA1;DisruptR= yes chr14q32.33 chr15 17083473 56746778 NEU -0.128929760930902 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=NUTM1,BUB1B,KNSTRN,B2M,CASC5,USP8,MYO5A;DisruptL=;DisruptR=AC090517.4 no chr15p11.2-q21.3 chr15 56746779 65078251 DUP 0.604623642039819 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=TCF12;DisruptL=AC090517.4;DisruptR= yes chr15q21.3-q22.31 chr15 65078252 72000243 NEU 0.187372558177132 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MAP2K1,SMAD3;DisruptL=;DisruptR=AC022872.1,MYO9A yes chr15q22.31-q23 chr15 72000244 72362589 DUP 0.838200589180974 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AC022872.1,MYO9A;DisruptR=AC009690.1,HEXA yes chr15q23 chr15 72362590 101981087 NEU 0.141715468783762 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=FES,PML,POLG,IDH2,BLM,CRTC3,CHD2,NTRK3;DisruptL=AC009690.1,HEXA;DisruptR= no chr15q23-q26.3 chr16 10005 452824 DEL -0.42732386186204 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=AXIN1;DisruptL=;DisruptR=AL049542.1,RAB11FIP3 yes chr16p13.3 chr16 452830 13289377 NEU -0.0842553565494412 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=TRAF7,SOCS1,RMI2,TNFRSF17,TSC2,RUNDC2A,CREBBP,GRIN2A,CIITA,NTHL1;DisruptL=AL049542.1,RAB11FIP3;DisruptR=U91319.1 yes chr16p13.3-p13.12 chr16 13289378 24481285 DUP 0.328432616925288 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ERCC4,PALB2,MYH11,PRKCB;DisruptL=U91319.1;DisruptR=AC008938.1 yes chr16p13.12-p12.1 chr16 24481286 24513921 DEL -0.747596091630151 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC008938.1;DisruptR= yes chr16p12.1 chr16 24513922 34502581 DUP 0.299125150834721 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=FUS,IL21R;DisruptL=;DisruptR= yes chr16p12.1-p11.2 chr16 34596149 90226217 NEU -0.181781397356921 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=MAF,CYLD,HERPUD1,CDH11,CBFB,RFWD3,CBFA2T3,CTCF,CDH1,ZFHX3,FANCA;DisruptL=;DisruptR= no chr16p11.2-q24.3 chr17 168977 21968703 DUP 0.217563470658792 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=TP53,YWHAE,USP6,PER1,FLCN,RABEP1,GAS7,MAP2K4,NCOR1,SPECC1;DisruptL=DOC2B;DisruptR= no chr17p13.3-p11.2 chr17 22044138 34345357 DEL -0.256453140322619 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=NF1,SUZ12;DisruptL=;DisruptR= yes chr17p11.2-q12 chr17 34345358 36041470 DUP 0.249274005970333 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=TAF15;DisruptL=;DisruptR= yes chr17q12 chr17 36041471 39577425 DEL -0.704231834202628 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MLLT6,LASP1,CDK12;DisruptL=;DisruptR= yes chr17q12 chr17 39577426 39805109 DUP 0.256494424338889 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ERBB2;DisruptL=;DisruptR=IKZF3 yes chr17q12-q21.1 chr17 39805110 43351848 DEL -0.713851004856207 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CCR7,RARA,SMARCE1,STAT5B,STAT3,BRCA1;DisruptL=IKZF3;DisruptR= yes chr17q21.1-q21.31 chr17 43351849 44549195 NEU 0.166704247800543 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ETV4;DisruptL=;DisruptR= yes chr17q21.31 chr17 44549196 44627962 DEL -0.740932738065601 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr17q21.31 chr17 44627963 47874912 DUP 0.231437022893115 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chr17q21.31-q21.32 chr17 47874913 48072289 DUP 1.19863207025329 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=CBX1 yes chr17q21.32 chr17 48072290 55607901 DUP 0.202186303853969 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SPOP,KAT7,COL1A1,HLF;DisruptL=CBX1;DisruptR= yes chr17q21.32-q22 chr17 55607902 59518846 DUP 0.81383285865307 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=RNF43,MSI2;DisruptL=;DisruptR=LINC01476 yes chr17q22-q23.1 chr17 59518847 67102559 NEU -0.141052516020913 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=PPM1D,CD79B,DDX5,CLTC,BRIP1,AXIN2;DisruptL=LINC01476;DisruptR=HELZ yes chr17q23.1-q24.2 chr17 67102560 67148387 DUP 1.3583627761025 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HELZ;DisruptR=HELZ yes chr17q24.2 chr17 67148388 83247341 DUP 0.791047289051972 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=H3F3B,SRSF2,CANT1,PRKAR1A,ASPSCR1,SEPT9,RNF213;DisruptL=HELZ;DisruptR= yes chr17q24.2-q25.3 chr18 10010 276979 DUP 0.22074853918382 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;COSMIC;DisruptL=;DisruptR= yes chr18p11.32 chr18 276980 1091192 DUP 1.04813644038208 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=AP005328.1 yes chr18p11.32 chr18 1091193 1158563 DEL -0.322548060598207 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AP005328.1;DisruptR=AP005328.1 yes chr18p11.32 chr18 1158564 3047303 DUP 0.937345194362087 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AP005328.1;DisruptR= yes chr18p11.32-p11.31 chr18 3047304 7909753 DUP 1.14651333723066 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=PTPRM yes chr18p11.31-p11.23 chr18 7909754 8331767 DUP 1.36250549206999 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=PTPRM;DisruptR=PTPRM yes chr18p11.23 chr18 8331768 10125704 DUP 1.54829229064669 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=PTPRM;DisruptR=AP005271.1 yes chr18p11.23-p11.22 chr18 10125705 11294017 DUP 1.38310712575281 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AP005271.1;DisruptR= yes chr18p11.22-p11.21 chr18 11294018 11707457 DUP 1.07574876909463 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=GNAL yes chr18p11.21 chr18 11707458 20553041 NEU 0.151294110190065 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=GNAL;DisruptR= yes chr18p11.21-q11.1 chr18 20553042 23307595 DEL -0.26083117652766 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=TMEM241 yes chr18q11.1-q11.2 chr18 23307596 23971374 DUP 1.23048327950354 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=TMEM241;DisruptR=AC010754.1 yes chr18q11.2 chr18 23971375 24279287 DUP 0.562339268978641 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AC010754.1;DisruptR=OSBPL1A yes chr18q11.2 chr18 24279288 24684277 DEL -0.266592771554824 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=OSBPL1A;DisruptR= yes chr18q11.2 chr18 24684278 30126250 DEL -0.703256539061366 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SS18,ZNF521;DisruptL=;DisruptR= yes chr18q11.2-q12.1 chr18 30126251 40264437 DEL -0.896667200275399 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR= yes chr18q12.1-q12.3 chr18 40264438 49181919 DEL -0.289116574666235 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SMAD2,SETBP1;DisruptL=;DisruptR=DYM yes chr18q12.3-q21.1 chr18 49181920 57412429 DEL -0.932209022275792 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SMAD4,DCC;DisruptL=DYM;DisruptR= yes chr18q21.1-q21.31 chr18 57412430 59280627 DEL -0.487722296251774 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MALT1;DisruptL=;DisruptR=CPLX4 yes chr18q21.31-q21.32 chr18 59280628 60358650 DEL -0.947551266442059 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=CPLX4;DisruptR= yes chr18q21.32 chr18 60358651 60627050 DEL -0.479768614402234 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=AC010928.1 yes chr18q21.32 chr18 60627051 61626459 DEL -0.93571491638688 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AC010928.1;DisruptR=AC105094.2 yes chr18q21.32-q21.33 chr18 61626460 63805004 DUP 0.274081292808057 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=KDSR,BCL2;DisruptL=AC105094.2;DisruptR=SERPINB7 yes chr18q21.33 chr18 63805005 67194596 DUP 0.488054306127519 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;COSMIC;DisruptL=SERPINB7;DisruptR= yes chr18q21.33-q22.1 chr18 67194597 73989168 NEU 0.17843589477236 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=AC090125.1 yes chr18q22.1-q22.3 chr18 73989169 80263172 DUP 0.427946719450165 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AC090125.1;DisruptR= yes chr18q22.3-q23 chr19 90733 9163752 NEU -0.195339708194112 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=FSTL3,CD209,STK11,TCF3,GNA11,MAP2K2,SH3GL1,MLLT1,MUC16,VAV1;DisruptL=;DisruptR= yes chr19p13.3-p13.2 chr19 9163753 9173673 DEL -4.22049012507394 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV,1000G;DisruptL=;DisruptR=;Intergenic;Closest=ZNF317 yes chr19p13.2 chr19 9173674 12858860 NEU -0.141910244905219 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=KEAP1,DNM2,SMARCA4;DisruptL=;DisruptR=HOOK2,MAST1 yes chr19p13.2-p13.13 chr19 12858861 12880012 DEL -6.85279860001431 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HOOK2,MAST1;DisruptR=DNASE2 yes chr19p13.13 chr19 12880013 14687523 NEU -0.150710476454393 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=LYL1,CALR,PRKACA,DNAJB1;DisruptL=DNASE2;DisruptR=ADGRE3 yes chr19p13.13-p13.12 chr19 14687524 14707747 DUP 1.12164410347299 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ADGRE3;DisruptR=ZNF333 yes chr19p13.12 chr19 14707748 15684658 DUP 1.95077199050305 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=BRD4;DisruptL=ZNF333;DisruptR=CYP4F12 yes chr19p13.12 chr19 15684659 17134373 NEU 0.0710136359510683 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=TPM4;DisruptL=CYP4F12;DisruptR=MYO9B yes chr19p13.12-p13.11 chr19 17134374 20137237 NEU -0.0585006037191752 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=JAK3,ELL,CRTC1;DisruptL=MYO9B;DisruptR=AC011447.2,AC011447.3 yes chr19p13.11-p12 chr19 20137238 20501955 DUP 0.888068802013327 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;DisruptL=AC011447.2,AC011447.3;DisruptR=AC008554.1 yes chr19p12 chr19 20501956 23544292 NEU -0.187953211494779 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ZNF429;DisruptL=AC008554.1;DisruptR=ZNF675 yes chr19p12 chr19 23544293 24018595 DUP 0.345770546920996 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ZNF675;DisruptR= yes chr19p12 chr19 24018596 58607515 NEU -0.10464115433591 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CEBPA,BCL3,BCL2L12,KLK2,TFPT,CCNE1,CD79A,CIC,CBLC,ERCC2,BAX,POLD1,PPP2R1A,ZNF331,CNOT3,CEP89,LSM14A,AKT2;DisruptL=;DisruptR= no chr19p12-q13.43 chr20 67260 8764419 DUP 0.530902482769591 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SIRPA;DisruptL=;DisruptR=PLCB1 yes chr20p13-p12.3 chr20 8764420 22252838 DUP 0.784243387294541 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=CRNKL1;DisruptL=PLCB1;DisruptR= yes chr20p12.3-p11.22 chr20 22252839 28506070 DUP 0.948559652210414 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr20p11.22-q11.1 chr20 28791094 31001398 NEU 0.169081754698639 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr20q11.1-q11.21 chr20 31245066 31539638 DUP 1.20799932765185 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=HM13 yes chr20q11.21 chr20 31539639 34228084 DUP 1.85506238270643 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ASXL1;DisruptL=HM13;DisruptR=ASIP yes chr20q11.21-q11.22 chr20 34230621 36912930 DUP 1.25492600589821 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ASIP;DisruptR=SAMHD1 yes chr20q11.22-q11.23 chr20 36912931 39349450 DUP 1.00959936937571 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SRC;DisruptL=SAMHD1;DisruptR= yes chr20q11.23-q12 chr20 39349451 64334067 NEU 0.184135665239368 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MAFB,TOP1,SDC4,SALL4,GNAS,SS18L1,PTK6,PLCG1,NFATC2,PTPRT;DisruptL=;DisruptR= no chr20q12-q13.33 chr21 5030587 13507200 DUP 0.661047030338345 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FP565260.3;DisruptR= yes chr21p12-q11.2 chr21 13507201 14332448 DUP 1.14630682516936 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=DGV;COSMIC;DisruptL=;DisruptR=ABCC13 yes chr21q11.2 chr21 14332449 14697922 DUP 1.50274506763967 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ABCC13;DisruptR= yes chr21q11.2 chr21 14697923 14870793 DUP 1.90648531415764 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=LINC02246,AF127577.4 yes chr21q11.2 chr21 14870794 15873584 DUP 1.47303899324827 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=LINC02246,AF127577.4;DisruptR=USP25 yes chr21q11.2-q21.1 chr21 15873585 17474345 DUP 0.274407716800917 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=USP25;DisruptR= yes chr21q21.1 chr21 17474346 17986205 DUP 1.5982123096677 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=CHODL yes chr21q21.1 chr21 17986206 18481759 DUP 0.476968182141218 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=CHODL;DisruptR=TMPRSS15,AL109763.1 yes chr21q21.1 chr21 18481760 20113583 NEU 0.093394038792514 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=TMPRSS15,AL109763.1;DisruptR= yes chr21q21.1 chr21 20113584 21140907 DEL -0.328665966480949 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=NCAM2 yes chr21q21.1 chr21 21140908 26634790 NEU -0.118474984998303 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=NCAM2;DisruptR= yes chr21q21.1-q21.3 chr21 26634791 31947284 DEL -0.63416963082165 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=HUNK yes chr21q21.3-q22.11 chr21 31947285 32739134 DUP 0.734673373430006 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=HUNK;DisruptR=PAXBP1-AS1,PAXBP1 yes chr21q22.11 chr21 32739135 34714566 DUP 0.274661867627123 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=OLIG2;DisruptL=PAXBP1-AS1,PAXBP1;DisruptR=CLIC6 yes chr21q22.11-q22.12 chr21 34714567 34819639 DEL -1.21829154535324 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=RUNX1;DisruptL=CLIC6;DisruptR=RUNX1 yes chr21q22.12 chr21 34819640 34847754 DEL -7.81402264900858 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=RUNX1;DisruptL=RUNX1;DisruptR=RUNX1 yes chr21q22.12 chr21 34847755 40764259 DEL -0.47886272434819 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=RUNX1,ERG;DisruptL=RUNX1;DisruptR=DSCAM yes chr21q22.12-q22.2 chr21 40764260 41078298 DUP 1.13879206536824 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=DSCAM;DisruptR= yes chr21q22.2 chr21 41078299 41571036 DEL -0.502838720995289 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=TMPRSS2;DisruptL=;DisruptR= yes chr21q22.2-q22.3 chr21 41571037 41825925 NEU -0.0542522390372822 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=PRDM15 yes chr21q22.3 chr21 41825926 42103808 DUP 1.12683966496424 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=PRDM15;DisruptR=UMODL1-AS1,UMODL1 yes chr21q22.3 chr21 42103809 44064549 NEU -0.0760051576379108 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=U2AF1;DisruptL=UMODL1-AS1,UMODL1;DisruptR=TRAPPC10 yes chr21q22.3 chr21 44064550 46107841 DUP 1.22310508747388 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=TRAPPC10;DisruptR=COL6A2 yes chr21q22.3 chr21 46107842 46699872 NEU -0.0470192234921808 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=COL6A2;DisruptR= yes chr21q22.3 chr22 10514978 12187340 DEL -0.749751645009501 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR= yes chr22p11.2 chr22 12694064 23762693 DUP 0.876052567777724 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=SEPT5,DGCR8,LZTR1,MAPK1,CLTCL1,BCR;DisruptL=;DisruptR= yes chr22p11.2-q11.23 chr22 23762694 29285918 DUP 1.12574436708373 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SMARCB1,ZNRF3,EWSR1,MN1,CHEK2;DisruptL=;DisruptR=EWSR1 yes chr22q11.23-q12.2 chr22 29285919 46073918 DUP 0.706411015423026 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=APOBEC3B,EWSR1,ZNF278,ISX,PDGFB,MKL1,NF2,MYH9,EP300;DisruptL=EWSR1;DisruptR=MIRLET7BHG yes chr22q12.2-q13.31 chr22 46073919 46234133 DUP 1.2632891096072 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=MIRLET7BHG;DisruptR=PPARA yes chr22q13.31 chr22 46234134 50808368 DUP 0.634099868172225 bicseq2 HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=PPARA;DisruptR= yes chr22q13.31-q13.33