#INFO: PE => number of discordant paired end reads supporting the SV #INFO: SR => number of split reads supporting the SV #INFO: 1000G => 1000 Genomes Project call set #INFO: DGV => Database of Genomic Variants #INFO: GAP => UCSC gap regions #INFO: inHouse => In-house database of SVs called in germline genomes #INFO: COSMIC => COSMIC v86 #INFO: Cancer_census => Cancer Census COSMIC v86 #INFO: KnownFusion => Known list of fusions from NYGC and/or COSMIC #chr1 start1 end1 chr2 start2 end2 type score strand1 strand2 evidence tools tumor--normal info cnv_changepoint_1 cnv_changepoint_2 splazerS_tumor splazerS_normal chrX 44887191 44887192 chrX 47658825 47658826 DUP NA - + [Svaba_SR=29,Svaba_PE=25],[Manta_PE=20,Manta_SR=25],[Lumpy_PE=14,Lumpy_SR=21] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=ARAF|Tier2,KDM6A|Tier1,RBM10|Tier1;DisruptL=KDM6A;DisruptR=UXT;ClosestL=;ClosestR=UXT-AS1 44887175 47658809 20,44887191,47658826 0,0,0 chrX 45136456 45136457 chrX 45137951 45137952 DEL NA + - [Svaba_SR=35,Svaba_PE=44],[Manta_PE=45,Manta_SR=27],[Lumpy_PE=35,Lumpy_SR=14] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=CXorf36;ClosestR=CXorf36 44887175 44887175 15,45136456,45137951 0,0,0 chrX 57361939 57361940 chrX 57364610 57364611 INV NA - - [Svaba_SR=12,Svaba_PE=29],[Manta_PE=29,Manta_SR=10],[Lumpy_PE=24,Lumpy_SR=7] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=FAAH2;DisruptR=FAAH2;ClosestL=;ClosestR= 57361937 57361937 9,57361930,57364610 0,0,0 chrX 76242860 76242861 chrX 116501145 116501146 DUP NA - + [Svaba_SR=27,Svaba_PE=22],[Manta_PE=16,Manta_SR=26],[Lumpy_PE=15,Lumpy_SR=12] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=IRS4|Tier1,BTK|Tier1,ATRX|Tier1;DisruptL=;DisruptR=;ClosestL=RNU6-867P;ClosestR= 76245723 116456071 14,76242855,116501149 0,0,0 chrX 76244485 76244486 chrX 116500843 116500844 INV NA - - [Svaba_SR=24,Svaba_PE=22],[Manta_PE=25,Manta_SR=18],[Lumpy_PE=16,Lumpy_SR=11] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=IRS4|Tier1,BTK|Tier1,ATRX|Tier1;DisruptL=;DisruptR=;ClosestL=RNU6-867P;ClosestR= 76245723 116456071 17,76244484,116500843 0,0,0 chrX 79973209 79973210 chrX 79982346 79982347 DEL NA + - [Svaba_SR=18,Svaba_PE=23],[Manta_PE=22,Manta_SR=17],[Lumpy_PE=13,Lumpy_SR=5] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 76245724 76245724 0,0,0 0,0,0 chrX 80459951 80459952 chrX 80462152 80462153 DEL NA + - [Svaba_SR=8,Svaba_PE=92],[Manta_PE=75,Manta_SR=69],[Lumpy_PE=45,Lumpy_SR=60] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=TENT5D;ClosestR=TENT5D 84380545 84380545 45,80459950,80462152 0,0,0 chrX 84276246 84276247 chrX 84287224 84287225 INV NA - - [Svaba_SR=22,Svaba_PE=13],[Manta_PE=9,Manta_SR=21] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 84380545 84380545 0,0,0 0,0,0 chrX 84380522 84380523 chrX 84382004 84382005 INV NA + + [Svaba_SR=0,Svaba_PE=9],[Manta_PE=20,Manta_SR=26],[Lumpy_PE=17,Lumpy_SR=15] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=HDX;DisruptR=HDX;ClosestL=;ClosestR= 84380545 84380546 19,84380640,84382006 0,0,0 chrX 91727150 91727151 chrX 91796419 91796420 DUP NA - + [Svaba_SR=20,Svaba_PE=21],[Manta_PE=15,Manta_SR=19],[Lumpy_PE=14,Lumpy_SR=9] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=PCDH11X;ClosestL=;ClosestR=RNU2-26P 88321166 88321166 17,91727141,91796420 0,0,0 chrX 100877602 100877603 chrX 153586485 153586486 INV NA + + [Svaba_SR=38,Svaba_PE=50],[Manta_PE=47,Manta_SR=37],[Lumpy_PE=40,Lumpy_SR=29] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=IRS4|Tier1,DCAF12L2|Tier2,BTK|Tier1,STAG2|Tier1,ELF4|Tier1,PHF6|Tier1,ATP2B3|Tier1,SEPT6|Tier2,GPC3|Tier1,BCORL1|Tier1;DisruptL=;DisruptR=;ClosestL=NOX1;ClosestR=CCNQ 100877556 153586441 31,100877602,153586486 0,0,0 chrX 117971506 117971507 chrX 118882097 118882098 DUP NA - + [Svaba_SR=71,Svaba_PE=70],[Manta_PE=58,Manta_SR=71],[Lumpy_PE=52,Lumpy_SR=47] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=KLHL13;DisruptR=LINC01285;ClosestL=;ClosestR=AC006965.1 117971510 118882103 49,117971503,118882107 0,0,0 chrX 139747038 139747039 chrX 153271819 153271820 INV NA + + [Manta_PE=10,Manta_SR=37] manta HCC-1143_80--HCC-1143BL_40 known=;gap;DisruptL=ATP11C;DisruptR=;ClosestL=;ClosestR=AC236972.4 139747068 153149106 31,139747040,153271820 0,0,0 chr1 6465318 6465319 chr3 85183520 85183521 TRA NA + - [Svaba_SR=77,Svaba_PE=25],[Manta_PE=24,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TNFRSF25;DisruptR=CADM2;ClosestL=PLEKHG5;ClosestR= 6465257 85183423 0,0,0 0,0,0 chr1 6465318 6465319 chr3 85187355 85187356 TRA NA + + [Svaba_SR=43,Svaba_PE=0],[Manta_PE=26,Manta_SR=35],[Lumpy_PE=11,Lumpy_SR=24] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TNFRSF25;DisruptR=CADM2;Fusion=CADM2-TNFRSF25;ClosestL=PLEKHG5;ClosestR= 6465257 85183423 26,6465320,85187356 0,0,0 chr1 6509231 6509232 chr1 6510626 6510627 INV NA - - [Manta_PE=16,Manta_SR=18],[Lumpy_PE=12,Lumpy_SR=12] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PLEKHG5;DisruptR=PLEKHG5;ClosestL=NOL9;ClosestR=NOL9 6465257 6465257 10,6509237,6510621 0,0,0 chr1 6509232 6509233 chr21 34847762 34847763 TRA NA - - [Manta_PE=18,Manta_SR=18] manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=RUNX1|Tier1;DisruptL=PLEKHG5;DisruptR=RUNX1;ClosestL=NOL9;ClosestR= 6465257 34847755 0,0,0 0,0,0 chr1 6510727 6510728 chr21 34847762 34847763 TRA NA + - [Svaba_SR=26,Svaba_PE=10],[Manta_PE=2,Manta_SR=22] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=RUNX1|Tier1;DisruptL=PLEKHG5;DisruptR=RUNX1;Fusion=RUNX1-PLEKHG5;ClosestL=NOL9;ClosestR= 6465257 34847755 13,6510727,34847762 0,0,0 chr1 6623384 6623385 chr1 227866329 227866330 INV NA - - [Manta_PE=11,Manta_SR=31],[Lumpy_PE=3,Lumpy_SR=27] lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=ID3|Tier2,MDS2|Tier2,MYCL|Tier1,TAL1|Tier1,JUN|Tier1,BCL10|Tier1,RPL5|Tier1,RBM15|Tier1,NRAS|Tier1,FAM46C|Tier1,MLLT11|Tier1,S100A7|Tier2,SLC45A3|Tier1,CASP9|Tier2,PAX7|Tier1,LCK|Tier1,SFPQ|Tier1,THRAP3|Tier2,CSF3R|Tier1,MPL|Tier1,MUTYH|Tier1,STIL|Tier1,CDKN2C|Tier1,FUBP1|Tier1,BCL9|Tier1,TPM3|Tier1,LMNA|Tier1,PRCC|Tier1,NTRK1|Tier1,FCRL4|Tier1,FCGR2B|Tier1,DDR2|Tier1,PRRX1|Tier1,ABL2|Tier1,TPR|Tier1,ELF3|Tier2,MDM4|Tier1,ELK4|Tier1,H3F3A|Tier1,MTOR|Tier1,PRDM2|Tier2,SPEN|Tier1,SDHB|Tier1,ARHGEF10L|Tier2,ARID1A|Tier1,JAK1|Tier1,TRIM33|Tier1,NOTCH2|Tier1,ARNT|Tier1,SDHC|Tier1,CDC73|Tier1,PTPRC|Tier1,CAMTA1|Tier1,EPS15|Tier1,ATP1A1|Tier1,PDE4DIP|Tier1,MUC1|Tier1,PBX1|Tier1;DisruptL=PHF13;DisruptR=;ClosestL=THAP3;ClosestR=PRSS38 6465257 223431463 18,6623385,227866329 0,0,0 chr1 6623385 6623386 chr1 227866441 227866442 INV NA + + [Manta_PE=14,Manta_SR=27],[Lumpy_PE=3,Lumpy_SR=20] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=ID3|Tier2,MDS2|Tier2,MYCL|Tier1,TAL1|Tier1,JUN|Tier1,BCL10|Tier1,RPL5|Tier1,RBM15|Tier1,NRAS|Tier1,FAM46C|Tier1,MLLT11|Tier1,S100A7|Tier2,SLC45A3|Tier1,CASP9|Tier2,PAX7|Tier1,LCK|Tier1,SFPQ|Tier1,THRAP3|Tier2,CSF3R|Tier1,MPL|Tier1,MUTYH|Tier1,STIL|Tier1,CDKN2C|Tier1,FUBP1|Tier1,BCL9|Tier1,TPM3|Tier1,LMNA|Tier1,PRCC|Tier1,NTRK1|Tier1,FCRL4|Tier1,FCGR2B|Tier1,DDR2|Tier1,PRRX1|Tier1,ABL2|Tier1,TPR|Tier1,ELF3|Tier2,MDM4|Tier1,ELK4|Tier1,H3F3A|Tier1,MTOR|Tier1,PRDM2|Tier2,SPEN|Tier1,SDHB|Tier1,ARHGEF10L|Tier2,ARID1A|Tier1,JAK1|Tier1,TRIM33|Tier1,NOTCH2|Tier1,ARNT|Tier1,SDHC|Tier1,CDC73|Tier1,PTPRC|Tier1,CAMTA1|Tier1,EPS15|Tier1,ATP1A1|Tier1,PDE4DIP|Tier1,MUC1|Tier1,PBX1|Tier1;DisruptL=PHF13;DisruptR=;ClosestL=THAP3;ClosestR=PRSS38 6465257 223431463 19,6623387,227866442 0,0,0 chr1 8115745 8115746 chr1 8337706 8337707 DUP NA - + [Svaba_SR=0,Svaba_PE=11],[Manta_PE=8,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AL034417.2;DisruptR=SLC45A1;Fusion=SLC45A1+AL034417.2;ClosestL=;ClosestR=RF00019 8673995 8673995 6,8115746,8337582 0,0,0 chr1 8115746 8115747 chr1 8341045 8341046 INV NA - - [Svaba_SR=28,Svaba_PE=19],[Manta_PE=20,Manta_SR=16],[Lumpy_PE=15,Lumpy_SR=11] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AL034417.2;DisruptR=SLC45A1;ClosestL=;ClosestR=RERE 8673995 8673995 13,8115746,8341045 0,0,0 chr1 8337686 8337687 chr1 8341281 8341282 INV NA + + [Manta_PE=17,Manta_SR=21] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SLC45A1;DisruptR=SLC45A1;ClosestL=RF00019;ClosestR=RERE 8673995 8673995 11,8337688,8341282 0,0,0 chr1 8673961 8673962 chr1 8950735 8950736 DUP NA - + [Svaba_SR=48,Svaba_PE=55],[Manta_PE=45,Manta_SR=43],[Lumpy_PE=38,Lumpy_SR=35] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=RERE;DisruptR=CA6;ClosestL=;ClosestR= 8673995 8950766 28,8673963,8950736 0,0,0 chr1 19771904 19771905 chr1 23063404 23063405 DUP NA - + [Svaba_SR=20,Svaba_PE=16],[Manta_PE=17,Manta_SR=17],[Lumpy_PE=11,Lumpy_SR=8] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TMCO4;DisruptR=KDM1A,AL031428.1;Fusion=TMCO4+AL031428.1;ClosestL=;ClosestR=MIR4419A 19769881 23063291 14,19771904,23063409 0,0,0 chr1 40528747 40528748 chr16 187562 187563 TRA NA - - [Svaba_SR=21,Svaba_PE=11],[Manta_PE=10,Manta_SR=18],[Lumpy_PE=8,Lumpy_SR=16] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=ZNF684;ClosestR=Z69706.1 47818851 10005 17,40528747,187560 0,0,0 chr1 47818840 47818841 chr1 70293544 70293545 DUP NA - + [Svaba_SR=22,Svaba_PE=19],[Manta_PE=18,Manta_SR=15],[Lumpy_PE=15,Lumpy_SR=12] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=JUN|Tier1,CDKN2C|Tier1,JAK1|Tier1,EPS15|Tier1;DisruptL=AC096541.1,TRABD2B;DisruptR=ANKRD13C;Fusion=TRABD2B+ANKRD13C;ClosestL=;ClosestR= 47818851 83866422 12,47818841,70293545 0,0,0 chr1 51383095 51383096 chr1 70292967 70292968 DEL NA + - [Svaba_SR=22,Svaba_PE=21],[Manta_PE=22,Manta_SR=16],[Lumpy_PE=19,Lumpy_SR=5] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=JUN|Tier1,JAK1|Tier1,EPS15|Tier1;DisruptL=EPS15;DisruptR=ANKRD13C;Fusion=ANKRD13C+EPS15;ClosestL=RNU6-877P;ClosestR= 51383049 83866422 0,0,0 0,0,0 chr1 52860644 52860645 chr1 53006333 53006334 DEL NA + - [Svaba_SR=16,Svaba_PE=16],[Manta_PE=16,Manta_SR=13],[Lumpy_PE=13,Lumpy_SR=4] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=ZYG11A;DisruptR=SCP2;Fusion=ZYG11A+SCP2;ClosestL=;ClosestR=TUBBP10 51383049 51383049 11,52860642,53006333 0,0,0 chr1 54258679 54258680 chr1 54270175 54270176 DEL NA + - [Manta_PE=7,Manta_SR=3],[Lumpy_PE=6,Lumpy_SR=2] lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SSBP3;DisruptR=SSBP3;ClosestL=SSBP3-AS1;ClosestR=AL161644.1 51383049 51383049 2,54258681,54270176 0,0,0 chr1 58133514 58133515 chr1 58140197 58140198 DEL NA + - [Svaba_SR=26,Svaba_PE=28],[Manta_PE=27,Manta_SR=20],[Lumpy_PE=17,Lumpy_SR=15] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=DAB1;DisruptR=DAB1;ClosestL=;ClosestR= 51383049 51383049 18,58133514,58140197 0,0,0 chr1 68760869 68760870 chr6 158632522 158632523 TRA NA - - [Manta_PE=12,Manta_SR=20],[Lumpy_PE=4,Lumpy_SR=1] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AL033530.1;DisruptR=TMEM181;ClosestL=;ClosestR=DYNLT1 83866422 166891771 0,0,0 0,0,0 chr1 68761024 68761025 chr6 158632501 158632502 TRA NA + + [Svaba_SR=22,Svaba_PE=9],[Manta_PE=10,Manta_SR=17],[Lumpy_PE=7,Lumpy_SR=15] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AL033530.1;DisruptR=TMEM181;ClosestL=;ClosestR=DYNLT1 83866422 166891771 16,68761023,158632502 0,0,0 chr1 83866390 83866391 chr1 84289947 84289948 DUP NA - + [Svaba_SR=40,Svaba_PE=43],[Manta_PE=40,Manta_SR=36],[Lumpy_PE=35,Lumpy_SR=26] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=TTLL7;DisruptR=;ClosestL=LINC01725;ClosestR=SAMD13 83866422 84289902 30,83866393,84289948 0,0,0 chr1 94125559 94125560 chr1 94476963 94476964 DUP NA - + [Svaba_SR=41,Svaba_PE=52],[Manta_PE=44,Manta_SR=38],[Lumpy_PE=39,Lumpy_SR=23] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=;DisruptR=ABCD3;ClosestL=ABCA4;ClosestR= 94125587 94476856 32,94125555,94476964 0,0,0 chr1 101718078 101718079 chr20 29887491 29887492 TRA NA - - [Svaba_SR=0,Svaba_PE=25],[Manta_PE=24,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=3] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC01709;DisruptR=;ClosestL=RNU6-965P;ClosestR=DUX4L37 103478104 29339193 6,101718079,29887492 0,0,0 chr1 101718262 101718263 chr1 107356428 107356429 DEL NA + - [Svaba_SR=12,Svaba_PE=19],[Manta_PE=18,Manta_SR=11],[Lumpy_PE=15,Lumpy_SR=4] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC01709;DisruptR=NTNG1;Fusion=LINC01709+NTNG1;ClosestL=RNU6-965P;ClosestR= 103478104 107356413 10,101718263,107356428 0,0,0 chr1 103478736 103478737 chr7 86260442 86260443 TRA NA + + [Svaba_SR=23,Svaba_PE=15],[Manta_PE=17,Manta_SR=18],[Lumpy_PE=12,Lumpy_SR=14] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC095032.1;DisruptR=;ClosestL=;ClosestR= 103478105 84789193 16,103478737,86260443 0,0,0 chr1 124984581 124984582 chr21 15414727 15414728 TRA NA - - [Svaba_SR=7,Svaba_PE=9],[Manta_PE=7,Manta_SR=8] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=AJ009632.2;ClosestL=;ClosestR= 107356413 15873584 0,0,0 0,0,0 chr1 124984848 124984849 chr21 46035776 46035777 TRA NA + - [Svaba_SR=7,Svaba_PE=0],[Manta_PE=3,Manta_SR=7] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR=AP001476.1 107356413 46107841 5,124984850,46035776 0,0,0 chr1 143191333 143191334 chr6 32039557 32039558 TRA NA + + [Svaba_SR=16,Svaba_PE=3],[Lumpy_PE=2,Lumpy_SR=3] lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=CYP21A2;ClosestL=;ClosestR=TNXB 150474851 32487100 10,143191335,32039559 0,0,0 chr1 150474819 150474820 chr1 150749754 150749755 DUP NA - + [Svaba_SR=55,Svaba_PE=53],[Manta_PE=42,Manta_SR=42],[Lumpy_PE=30,Lumpy_SR=35] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=RPRD2;DisruptR=CTSS;ClosestL=TARS2;ClosestR= 150474851 150749712 36,150474821,150749755 0,0,0 chr1 155287407 155287408 chr1 155310603 155310604 DEL NA + - [Svaba_SR=17,Svaba_PE=23],[Manta_PE=21,Manta_SR=15],[Lumpy_PE=15,Lumpy_SR=11] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=HCN3;DisruptR=FDPS;Fusion=HCN3+FDPS;ClosestL=PKLR;ClosestR=RUSC1-AS1 150749712 150749712 14,155287407,155310603 0,0,0 chr1 156727473 156727474 chr1 156728410 156728411 DEL NA + - [Svaba_SR=5,Svaba_PE=0],[Manta_PE=4,Manta_SR=6] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=ISG20L2;DisruptR=ISG20L2;ClosestL=RRNAD1;ClosestR=RRNAD1 150749712 150749712 5,156727475,156728410 0,0,0 chr1 186672822 186672823 chr1 188617939 188617940 DUP NA - + [Svaba_SR=0,Svaba_PE=11],[Manta_PE=10,Manta_SR=0] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PTGS2;DisruptR=;ClosestL=PACERR;ClosestR= 186672517 186672517 0,0,0 0,0,0 chr1 186672823 186672824 chr12 67114875 67114876 TRA NA - + [Svaba_SR=25,Svaba_PE=16],[Manta_PE=16,Manta_SR=19],[Lumpy_PE=11,Lumpy_SR=16] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PTGS2;DisruptR=;ClosestL=PACERR;ClosestR=RAB11AP2 186672517 67923115 17,186672823,67114876 0,0,0 chr1 188617781 188617782 chr21 32343522 32343523 TRA NA - - [Svaba_SR=25,Svaba_PE=6],[Manta_PE=5,Manta_SR=24],[Lumpy_PE=3,Lumpy_SR=18] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=URB1;ClosestL=;ClosestR= 186672517 32739659 21,188617781,32343522 0,0,0 chr1 188617939 188617940 chr12 67114681 67114682 TRA NA + - [Manta_PE=2,Manta_SR=18] manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR=RAB11AP2 186672517 67923115 17,188617941,67114681 0,0,0 chr1 200900232 200900233 chr10 29373569 29373570 TRA NA + - [Svaba_SR=40,Svaba_PE=12],[Manta_PE=12,Manta_SR=41] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=INAVA;DisruptR=;ClosestL=MROH3P;ClosestR= 203360618 29240716 20,200900233,29373569 0,0,0 chr1 200900232 200900233 chr5 164930879 164930880 TRA NA + - [Svaba_SR=60,Svaba_PE=30],[Manta_PE=27,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=INAVA;DisruptR=AC109466.1;Fusion=INAVA-AC109466.1;ClosestL=MROH3P;ClosestR=RNU6-209P 203360618 164930825 0,0,0 0,0,0 chr1 200908919 200908920 chr20 8765271 8765272 TRA NA - - [Svaba_SR=16,Svaba_PE=21],[Manta_PE=21,Manta_SR=10],[Lumpy_PE=20,Lumpy_SR=6] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=INAVA;DisruptR=PLCB1;ClosestL=MROH3P;ClosestR= 203360618 8764420 9,200908920,8765271 0,0,0 chr1 200934816 200934817 chr10 29240543 29240544 TRA NA + + [Svaba_SR=29,Svaba_PE=17],[Manta_PE=19,Manta_SR=24],[Lumpy_PE=13,Lumpy_SR=16] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=MROH3P;DisruptR=;ClosestL=RNU6-704P;ClosestR= 203360618 29240715 18,200934818,29240547 0,0,0 chr1 202013942 202013943 chr1 202424227 202424228 DUP NA - + [Svaba_SR=29,Svaba_PE=33],[Manta_PE=29,Manta_SR=27],[Lumpy_PE=24,Lumpy_SR=16] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=ELF3|Tier2;DisruptL=ELF3,AL691482.3;DisruptR=PPP1R12B;Fusion=PPP1R12B+ELF3|PPP1R12B+AL691482.3;ClosestL=ELF3-AS1;ClosestR=RNU6-89P 203360618 203360618 21,202013942,202424228 0,0,0 chr1 202223003 202223004 chr1 202475925 202475926 DUP NA - + [Svaba_SR=20,Svaba_PE=24],[Manta_PE=26,Manta_SR=18],[Lumpy_PE=24,Lumpy_SR=9] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LGR6;DisruptR=PPP1R12B;Fusion=PPP1R12B+LGR6;ClosestL=;ClosestR=AC099336.2 203360618 203360618 6,202223006,202475926 0,0,0 chr1 203360676 203360677 chr1 223431545 223431546 DUP NA - + [Svaba_SR=82,Svaba_PE=106],[Manta_PE=101,Manta_SR=76],[Lumpy_PE=88,Lumpy_SR=57] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=SLC45A3|Tier1,MDM4|Tier1,ELK4|Tier1;DisruptL=;DisruptR=;ClosestL=AL359837.1;ClosestR= 203360619 223431463 53,203360677,223431549 0,0,0 chr1 203425428 203425429 chr1 203429109 203429110 INV NA + + [Svaba_SR=17,Svaba_PE=25],[Manta_PE=28,Manta_SR=14],[Lumpy_PE=26,Lumpy_SR=10] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 203360619 203360619 2,203425427,203429110 0,0,0 chr1 205097876 205097877 chr1 235138998 235138999 DEL NA + - [Svaba_SR=29,Svaba_PE=32],[Manta_PE=26,Manta_SR=29],[Lumpy_PE=17,Lumpy_SR=20] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=SLC45A3|Tier1,ELK4|Tier1,H3F3A|Tier1;DisruptL=RBBP5;DisruptR=RBM34,ARID4B;Fusion=RBM34+RBBP5|ARID4B+RBBP5;ClosestL=AL583832.1;ClosestR=TOMM20 205097487 234776418 16,205097891,235138998 0,0,0 chr1 209171311 209171312 chr13 108157081 108157082 TRA NA + + [Svaba_SR=28,Svaba_PE=23],[Manta_PE=23,Manta_SR=25],[Lumpy_PE=17,Lumpy_SR=16] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=AC092810.2;ClosestR= 212301736 107326495 22,209171312,108157082 0,0,0 chr1 209244791 209244792 chr1 212681433 212681434 DUP NA - + [Svaba_SR=15,Svaba_PE=26],[Manta_PE=25,Manta_SR=12],[Lumpy_PE=24,Lumpy_SR=6] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=;ClosestL=AC092810.1;ClosestR=BATF3 212301736 213004741 2,209244790,212681443 0,0,0 chr1 211388560 211388561 chr2 104320969 104320970 TRA NA - - [Svaba_SR=19,Svaba_PE=16],[Manta_PE=18,Manta_SR=20],[Lumpy_PE=10,Lumpy_SR=14] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC00467;DisruptR=;ClosestL=TRAF5;ClosestR= 212301736 105664599 17,211388547,104320969 0,0,0 chr1 211808734 211808735 chr19 14950825 14950826 TRA NA + + [Svaba_SR=17,Svaba_PE=23],[Manta_PE=21,Manta_SR=14],[Lumpy_PE=13,Lumpy_SR=13] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LPGAT1;DisruptR=SLC1A6;ClosestL=RF00019;ClosestR=OR7C2 212301736 14687524 12,211808735,14950826 0,0,0 chr1 212301721 212301722 chr6 30029837 30029838 TRA NA - - [Svaba_SR=70,Svaba_PE=83],[Manta_PE=91,Manta_SR=61],[Lumpy_PE=60,Lumpy_SR=48] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=AL360091.3,PPP2R5A;DisruptR=ZNRD1ASP;Fusion=ZNRD1ASP-PPP2R5A;ClosestL=AL360091.2;ClosestR=ETF1P1 212301736 32487100 45,212301724,30029837 0,0,0 chr1 213000165 213000166 chr8 121698470 121698471 TRA NA + - [Svaba_SR=15,Svaba_PE=14],[Manta_PE=14,Manta_SR=11],[Lumpy_PE=10,Lumpy_SR=8] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=ANGEL2;DisruptR=AC104233.1;ClosestL=VASH2;ClosestR=AC104233.2 213004741 121696691 11,213000167,121698468 0,0,0 chr1 217777448 217777449 chr11 29804982 29804983 TRA NA - + [Svaba_SR=34,Svaba_PE=36],[Manta_PE=31,Manta_SR=29],[Lumpy_PE=23,Lumpy_SR=23] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SPATA17;DisruptR=AC107973.1;Fusion=AC107973.1-SPATA17;ClosestL=SPATA17-AS1;ClosestR= 217777418 29804998 26,217777448,29804983 0,0,0 chr1 220803994 220803995 chrX 87103995 87103996 TRA NA - - [Svaba_SR=13,Svaba_PE=11],[Manta_PE=11,Manta_SR=12],[Lumpy_PE=5,Lumpy_SR=12] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=MARC1;DisruptR=;ClosestL=MARC2;ClosestR= 220805315 87101847 10,220803997,87103995 0,0,0 chr1 221676688 221676689 chr7 140930514 140930515 TRA NA - + [Svaba_SR=16,Svaba_PE=15],[Manta_PE=17,Manta_SR=11],[Lumpy_PE=15,Lumpy_SR=7] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR=AC006006.1 220805316 137445254 11,221676690,140930515 0,0,0 chr1 222787229 222787230 chr1 222795328 222795329 INV NA + + [Svaba_SR=25,Svaba_PE=25],[Manta_PE=23,Manta_SR=23],[Lumpy_PE=18,Lumpy_SR=21] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR=AL392172.1 223431462 223431462 20,222787229,222795329 0,0,0 chr1 222794716 222794717 chr18 73989233 73989234 TRA NA - - [Svaba_SR=23,Svaba_PE=25],[Manta_PE=29,Manta_SR=19],[Lumpy_PE=20,Lumpy_SR=15] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=AC090125.1;ClosestL=;ClosestR= 223431462 73989169 17,222794718,73989233 0,0,0 chr1 234957883 234957884 chr1 235095124 235095125 DUP NA - + [Svaba_SR=16,Svaba_PE=20],[Manta_PE=18,Manta_SR=14],[Lumpy_PE=15,Lumpy_SR=11] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AL391832.1,AL391832.2;DisruptR=;ClosestL=;ClosestR=AL732292.1 234776418 234776418 10,234957886,235095125 0,0,0 chr1 234972979 234972980 chr1 235146066 235146067 DUP NA - + [Svaba_SR=30,Svaba_PE=36],[Manta_PE=35,Manta_SR=26],[Lumpy_PE=25,Lumpy_SR=16] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=;DisruptR=RBM34,ARID4B;ClosestL=AL391832.2;ClosestR=TOMM20 234776418 234776418 2,234972981,235146066 0,0,0 chr1 246598539 246598540 chr1 246600082 246600083 DEL NA + - [Svaba_SR=20,Svaba_PE=22],[Manta_PE=23,Manta_SR=17],[Lumpy_PE=16,Lumpy_SR=15] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=CNST;DisruptR=CNST;ClosestL=AL591623.1;ClosestR=AL591623.1 248946322 248946322 12,246598539,246600082 0,0,0 chr2 2752746 2752747 chr6 52542329 52542330 TRA NA - - [Svaba_SR=23,Svaba_PE=15],[Manta_PE=9,Manta_SR=20],[Lumpy_PE=7,Lumpy_SR=14] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=TRAM2;ClosestL=;ClosestR=EFHC1 10005 52679253 16,2752747,52542329 0,0,0 chr2 2752961 2752962 chr14 102959581 102959582 TRA NA + + [Manta_PE=3,Manta_SR=20] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=CDC42BPB;ClosestL=;ClosestR= 10005 104243063 10,2752963,102959582 0,0,0 chr2 2752962 2752963 chr2 91414359 91414360 DEL NA + - [Svaba_SR=0,Svaba_PE=10],[Manta_PE=9,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=MYCN|Tier1,PCBP1|Tier2,C2orf44|Tier1,NCOA1|Tier1,ASXL2|Tier2,SIX2|Tier2,EPAS1|Tier1,MSH6|Tier1,FBXO11|Tier1,BCL11A|Tier1,REL|Tier1,XPO1|Tier1,DCTN1|Tier1,DNMT3A|Tier1,STRN|Tier1,EML4|Tier1,MSH2|Tier1,ALK|Tier1,BIRC6|Tier2;DisruptL=;DisruptR=;ClosestL=;ClosestR= 10005 94141931 0,0,0 0,0,0 chr2 20726878 20726879 chr2 20774844 20774845 DEL NA + - [Svaba_SR=11,Svaba_PE=12],[Manta_PE=11,Manta_SR=10],[Lumpy_PE=7,Lumpy_SR=7] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LDAH;DisruptR=LDAH;ClosestL=;ClosestR= 37825578 37825578 9,20726880,20774844 0,0,0 chr2 24579528 24579529 chr2 24695351 24695352 DUP NA - + [Svaba_SR=18,Svaba_PE=31],[Manta_PE=31,Manta_SR=13],[Lumpy_PE=23,Lumpy_SR=12] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;Cancer_census=NCOA1|Tier1;DisruptL=NCOA1;DisruptR=NCOA1;ClosestL=RNA5SP88;ClosestR=RNU6-936P 37825578 37825578 11,24579529,24695352 0,0,0 chr2 33705112 33705113 chr2 33705891 33705892 DEL NA + - [Svaba_SR=5,Svaba_PE=0],[Manta_PE=2,Manta_SR=5],[Lumpy_PE=4,Lumpy_SR=4] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=LINC01317;ClosestR=LINC01317 37825578 37825578 5,33705113,33705891 0,0,0 chr2 37825636 37825637 chr17 72487322 72487323 TRA NA - - [Svaba_SR=14,Svaba_PE=20],[Manta_PE=20,Manta_SR=12],[Lumpy_PE=14,Lumpy_SR=10] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=;DisruptR=LINC00511;ClosestL=LINC00211;ClosestR= 37825579 67102560 10,37825628,72487320 0,0,0 chr2 62620842 62620843 chr2 63261205 63261206 DUP NA - + [Svaba_SR=37,Svaba_PE=40],[Manta_PE=33,Manta_SR=27],[Lumpy_PE=31,Lumpy_SR=2] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=AC092155.1;DisruptR=WDPCP;Fusion=AC092155.1+WDPCP;ClosestL=;ClosestR= 62620851 63608437 0,0,0 0,0,0 chr2 63034488 63034489 chr13 16683888 16683889 TRA NA - + [Svaba_SR=12,Svaba_PE=14],[Manta_PE=8,Manta_SR=21],[Lumpy_PE=5,Lumpy_SR=2] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=EHBP1;DisruptR=;ClosestL=AC009501.1;ClosestR= 62620851 16000006 20,63034489,16683889 0,0,0 chr2 91414360 91414361 chr14 102959495 102959496 TRA NA - - [Manta_PE=0,Manta_SR=24] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=CDC42BPB;ClosestL=;ClosestR= 94141931 104243063 8,91414360,102959494 0,0,0 chr2 91414462 91414463 chr17 35740374 35740375 TRA NA + + [Svaba_SR=16,Svaba_PE=0],[Manta_PE=3,Manta_SR=18],[Lumpy_PE=3,Lumpy_SR=12] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=RASL10B,TAF15;ClosestL=;ClosestR=GAS2L2 94141931 36041470 11,91414462,35740375 0,0,0 chr2 96997335 96997336 chr11 73060366 73060367 TRA NA + + [Svaba_SR=19,Svaba_PE=18],[Manta_PE=19,Manta_SR=13],[Lumpy_PE=14,Lumpy_SR=9] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=;DisruptR=FCHSD2;ClosestL=AC079395.3;ClosestR= 95642457 73059915 13,96997336,73060367 0,0,0 chr2 99500341 99500342 chr2 101098846 101098847 DEL NA + - [Svaba_SR=5,Svaba_PE=5],[Manta_PE=5,Manta_SR=5],[Lumpy_PE=5,Lumpy_SR=2] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=AFF3|Tier1;DisruptL=;DisruptR=TBC1D8;ClosestL=REV1;ClosestR= 95642457 105664599 2,99500343,101098846 0,0,0 chr2 99677001 99677002 chr22 24803524 24803525 TRA NA - + [Svaba_SR=22,Svaba_PE=23],[Manta_PE=21,Manta_SR=20],[Lumpy_PE=8,Lumpy_SR=17] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=AFF3|Tier1;DisruptL=AFF3;DisruptR=;ClosestL=;ClosestR=SGSM1 95642457 24015969 17,99677001,24803525 0,0,0 chr2 99696052 99696053 chr2 99745352 99745353 INV NA + + [Svaba_SR=13,Svaba_PE=10],[Manta_PE=12,Manta_SR=13],[Lumpy_PE=10,Lumpy_SR=11] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=AFF3|Tier1;DisruptL=AFF3;DisruptR=AFF3;ClosestL=;ClosestR= 95642457 95642457 8,99696052,99745353 0,0,0 chr2 100094211 100094212 chr2 104093618 104093619 INV NA - - [Manta_PE=1,Manta_SR=9] manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=AFF3|Tier1;DisruptL=AFF3;DisruptR=;ClosestL=AC092667.1;ClosestR=LINC01965 95642457 105664599 8,100094213,104093617 0,0,0 chr2 101119638 101119639 chr10 38528505 38528506 TRA NA - - [Svaba_SR=21,Svaba_PE=28],[Lumpy_PE=19,Lumpy_SR=17] lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TBC1D8;DisruptR=;ClosestL=;ClosestR= 105664599 39580116 13,101119642,38528505 0,0,0 chr2 101119899 101119900 chr10 38527881 38527882 TRA NA + - [Svaba_SR=16,Svaba_PE=26],[Lumpy_PE=15,Lumpy_SR=8] svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TBC1D8;DisruptR=;ClosestL=;ClosestR= 105664599 39580116 5,101119900,38527881 0,0,0 chr2 101672710 101672711 chr10 38925624 38925625 TRA NA - + [Lumpy_PE=2,Lumpy_SR=2] lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 105664599 39580116 4,101672713,38925624 0,0,0 chr2 103110745 103110746 chr2 103111960 103111961 INV NA + + [Svaba_SR=19,Svaba_PE=16],[Manta_PE=21,Manta_SR=17],[Lumpy_PE=14,Lumpy_SR=16] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC073987.1;DisruptR=AC073987.1;ClosestL=;ClosestR= 105664599 105664599 12,103110745,103111961 0,0,0 chr2 103221167 103221168 chr2 103222714 103222715 DUP NA - + [Manta_PE=3,Manta_SR=4],[Lumpy_PE=3,Lumpy_SR=3] lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 105664599 105664599 3,103221169,103222717 0,0,0 chr2 103221390 103221391 chr2 103221966 103221967 INV NA + + [Manta_PE=6,Manta_SR=2],[Lumpy_PE=6,Lumpy_SR=2] lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 105664599 105664599 2,103221392,103221967 0,0,0 chr2 104061834 104061835 chr22 49964192 49964193 TRA NA - + [Svaba_SR=18,Svaba_PE=23],[Manta_PE=19,Manta_SR=12],[Lumpy_PE=17,Lumpy_SR=6] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC01965;DisruptR=;ClosestL=;ClosestR=PIM3 105664599 50808368 8,104061833,49964193 0,0,0 chr2 104063183 104063184 chr22 49963830 49963831 TRA NA - - [Svaba_SR=15,Svaba_PE=9],[Manta_PE=10,Manta_SR=10],[Lumpy_PE=7,Lumpy_SR=8] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC01965;DisruptR=PIM3;ClosestL=;ClosestR=MIR6821 105664599 50808368 10,104063183,49963830 0,0,0 chr2 104240194 104240195 chr16 465006 465007 TRA NA + - [Svaba_SR=35,Svaba_PE=42],[Manta_PE=39,Manta_SR=28],[Lumpy_PE=29,Lumpy_SR=20] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=RAB11FIP3;ClosestL=;ClosestR=AL049542.1 105664599 10005 26,104240194,465006 0,0,0 chr2 109290685 109290686 chr18 24684289 24684290 TRA NA - + [Svaba_SR=18,Svaba_PE=26],[Manta_PE=24,Manta_SR=14],[Lumpy_PE=16,Lumpy_SR=11] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SH3RF3;DisruptR=;ClosestL=;ClosestR=RAC1P1 109199785 24683978 12,109290684,24684291 0,0,0 chr2 114725269 114725270 chr18 63805018 63805019 TRA NA + - [Svaba_SR=19,Svaba_PE=16],[Manta_PE=15,Manta_SR=18],[Lumpy_PE=10,Lumpy_SR=13] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=DPP10;DisruptR=SERPINB7;Fusion=DPP10-SERPINB7;ClosestL=;ClosestR= 114973555 61626460 14,114725273,63805017 0,0,0 chr2 114974129 114974130 chr21 32740681 32740682 TRA NA + + [Svaba_SR=27,Svaba_PE=24],[Manta_PE=24,Manta_SR=23],[Lumpy_PE=17,Lumpy_SR=17] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=DPP10;DisruptR=PAXBP1-AS1,PAXBP1;Fusion=DPP10-PAXBP1;ClosestL=;ClosestR=SYNJ1 114973556 32739660 17,114974128,32740689 0,0,0 chr2 115753434 115753435 chr22 28670132 28670133 TRA NA - + [Svaba_SR=0,Svaba_PE=11],[Manta_PE=9,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=DPP10;DisruptR=TTC28;ClosestL=;ClosestR=CHEK2 114973556 29344638 0,0,0 0,0,0 chr2 115753450 115753451 chr22 28669982 28669983 TRA NA + - [Svaba_SR=13,Svaba_PE=0],[Manta_PE=4,Manta_SR=7] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=DPP10;DisruptR=TTC28;ClosestL=;ClosestR=CHEK2 114973556 29344638 6,115753450,28669982 0,0,0 chr2 135367225 135367226 chr2 135375203 135375204 DEL NA + - [Svaba_SR=43,Svaba_PE=50],[Manta_PE=46,Manta_SR=37],[Lumpy_PE=32,Lumpy_SR=31] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=ZRANB3;DisruptR=ZRANB3;ClosestL=;ClosestR= 114973556 114973556 29,135367224,135375203 0,0,0 chr2 142877181 142877182 chr2 142883247 142883248 DEL NA + - [Svaba_SR=19,Svaba_PE=24],[Manta_PE=23,Manta_SR=20],[Lumpy_PE=14,Lumpy_SR=10] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=KYNU;ClosestL=KYNU;ClosestR= 114973556 114973556 16,142877187,142883246 0,0,0 chr2 143042583 143042584 chr12 30577021 30577022 TRA NA - + [Lumpy_PE=4,Lumpy_SR=1] lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=KYNU;DisruptR=;ClosestL=;ClosestR= 114973556 56255606 3,143042582,30577008 0,0,0 chr2 152347817 152347818 chr2 152457171 152457172 DEL NA + - [Svaba_SR=20,Svaba_PE=31],[Manta_PE=26,Manta_SR=19],[Lumpy_PE=20,Lumpy_SR=16] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=FMNL2;DisruptR=FMNL2;ClosestL=;ClosestR= 114973556 114973556 16,152347818,152457171 0,0,0 chr2 165399970 165399971 chr2 166129437 166129438 DUP NA - + [Svaba_SR=36,Svaba_PE=33],[Manta_PE=34,Manta_SR=29],[Lumpy_PE=24,Lumpy_SR=21] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=;DisruptR=AC010127.1,SCN1A;ClosestL=SCN2A;ClosestR=RF00019 114973556 114973556 28,165399973,166129438 0,0,0 chr2 179388075 179388076 chrX 4728353 4728354 TRA NA + - [Svaba_SR=0,Svaba_PE=40],[Manta_PE=22,Manta_SR=25] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=AC068042.1;ClosestR= 242183395 10446 0,0,0 0,0,0 chr2 179388334 179388335 chrX 4728528 4728529 TRA NA - + [Svaba_SR=53,Svaba_PE=46],[Manta_PE=39,Manta_SR=45],[Lumpy_PE=27,Lumpy_SR=17] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=AC068042.1;ClosestR= 242183395 10446 33,179388337,4728529 0,0,0 chr2 187552041 187552042 chr2 187556879 187556880 DEL NA + - [Svaba_SR=11,Svaba_PE=17],[Manta_PE=12,Manta_SR=17],[Lumpy_PE=7,Lumpy_SR=8] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC007319.1,TFPI;DisruptR=TFPI;ClosestL=;ClosestR=AC007319.1 242183395 242183395 11,187552043,187556879 0,0,0 chr2 188399228 188399229 chr5 59193764 59193765 TRA NA + - [Svaba_SR=8,Svaba_PE=2],[Manta_PE=2,Manta_SR=8],[Lumpy_PE=2,Lumpy_SR=4] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=GULP1;DisruptR=PDE4D;ClosestL=LINC01090;ClosestR= 242183395 32366973 4,188399230,59193764 0,0,0 chr2 218087110 218087111 chr2 218098245 218098246 DEL NA + - [Svaba_SR=17,Svaba_PE=23],[Manta_PE=21,Manta_SR=14],[Lumpy_PE=13,Lumpy_SR=9] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=RUFY4;DisruptR=;ClosestL=;ClosestR=RUFY4 242183395 242183395 12,218087112,218098245 0,0,0 chr3 9307908 9307909 chr3 9404959 9404960 DUP NA - + [Svaba_SR=49,Svaba_PE=63],[Manta_PE=58,Manta_SR=48],[Lumpy_PE=55,Lumpy_SR=22] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SRGAP3,AC026191.1;DisruptR=SETD5;ClosestL=;ClosestR=THUMPD3-AS1 9676603 9676603 0,0,0 0,0,0 chr3 9676589 9676590 chr3 10083212 10083213 DUP NA - + [Svaba_SR=70,Svaba_PE=79],[Manta_PE=74,Manta_SR=60],[Lumpy_PE=66,Lumpy_SR=34] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=FANCD2|Tier1;DisruptL=MTMR14;DisruptR=FANCD2,FANCD2OS;Fusion=FANCD2+MTMR14;ClosestL=;ClosestR= 9676603 10083194 46,9676588,10083213 0,0,0 chr3 13545519 13545520 chr9 72457733 72457734 TRA NA - - [Svaba_SR=21,Svaba_PE=15],[Manta_PE=15,Manta_SR=20],[Lumpy_PE=11,Lumpy_SR=12] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=FBLN2;ClosestR=AL445646.1 10083194 66040022 14,13545512,72457733 0,0,0 chr3 13545970 13545971 chr21 32343657 32343658 TRA NA + + [Svaba_SR=30,Svaba_PE=11],[Manta_PE=10,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=URB1;ClosestL=FBLN2;ClosestR= 10083194 32739659 0,0,0 0,0,0 chr3 13545970 13545971 chr6 144660231 144660232 TRA NA + - [Svaba_SR=19,Svaba_PE=5],[Manta_PE=6,Manta_SR=15],[Lumpy_PE=2,Lumpy_SR=12] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=UTRN;ClosestL=FBLN2;ClosestR= 10083194 130003967 11,13545972,144660225 0,0,0 chr3 37547039 37547040 chr3 37719792 37719793 DUP NA - + [Svaba_SR=52,Svaba_PE=60],[Manta_PE=51,Manta_SR=47],[Lumpy_PE=44,Lumpy_SR=37] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=ITGA9;DisruptR=ITGA9;ClosestL=;ClosestR= 37547021 37719800 37,37547042,37719793 0,0,0 chr3 39770252 39770253 chr3 41312690 41312691 DUP NA - + [Svaba_SR=63,Svaba_PE=70],[Manta_PE=65,Manta_SR=51],[Lumpy_PE=60,Lumpy_SR=40] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=CTNNB1|Tier1;DisruptL=;DisruptR=ULK4;ClosestL=;ClosestR= 39770243 41312676 40,39770256,41312691 0,0,0 chr3 41158029 41158030 chr14 100903975 100903976 TRA NA + + [Svaba_SR=18,Svaba_PE=10],[Manta_PE=7,Manta_SR=20],[Lumpy_PE=3,Lumpy_SR=15] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=AL117190.1,MEG8;ClosestL=AC009743.1;ClosestR=RF02146 41312675 104243063 12,41158031,100903976 0,0,0 chr3 52565285 52565286 chr3 52629472 52629473 DEL NA + - [Svaba_SR=44,Svaba_PE=50],[Manta_PE=48,Manta_SR=36],[Lumpy_PE=37,Lumpy_SR=18] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=PBRM1|Tier1;DisruptL=SMIM4,PBRM1;DisruptR=PBRM1;ClosestL=RNU6ATAC16P;ClosestR= 52565238 52629454 17,52565284,52629472 0,0,0 chr3 85183520 85183521 chr3 85187151 85187152 INV NA - - [Svaba_SR=44,Svaba_PE=0],[Manta_PE=40,Manta_SR=44],[Lumpy_PE=29,Lumpy_SR=26] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=CADM2;DisruptR=CADM2;ClosestL=;ClosestR= 85183423 85183423 32,85183519,85187151 0,0,0 chr3 85660778 85660779 chr3 85663710 85663711 DEL NA + - [Svaba_SR=40,Svaba_PE=48],[Manta_PE=42,Manta_SR=33],[Lumpy_PE=29,Lumpy_SR=27] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=CADM2;DisruptR=CADM2;ClosestL=;ClosestR= 85183423 85183423 26,85660777,85663710 0,0,0 chr3 94678278 94678279 chr10 61749704 61749705 TRA NA - - [Manta_PE=4,Manta_SR=4] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=CABCOCO1;ClosestL=;ClosestR= 95005470 63904755 3,94678277,61749704 0,0,0 chr3 95900220 95900221 chr5 153304740 153304741 TRA NA + - [Manta_PE=4,Manta_SR=5] manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 95005471 164930824 4,95900222,153304739 0,0,0 chr3 117319407 117319408 chr3 117323182 117323183 DEL NA + - [Svaba_SR=24,Svaba_PE=17],[Manta_PE=13,Manta_SR=22],[Lumpy_PE=9,Lumpy_SR=17] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 95005471 95005471 19,117319408,117323182 0,0,0 chr3 126089031 126089032 chr3 126135677 126135678 DEL NA + - [Svaba_SR=24,Svaba_PE=19],[Manta_PE=17,Manta_SR=19],[Lumpy_PE=13,Lumpy_SR=12] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SLC41A3,AC079848.1;DisruptR=ALDH1L1;Fusion=ALDH1L1+SLC41A3;ClosestL=ALDH1L1;ClosestR= 95005471 95005471 15,126089033,126135677 0,0,0 chr3 132552072 132552073 chr21 16887338 16887339 TRA NA + - [Manta_PE=3,Manta_SR=5],[Lumpy_PE=2,Lumpy_SR=2] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=ACAD11;ClosestR=AF212831.1 95005471 17474345 4,132552074,16887338 0,0,0 chr3 141665762 141665763 chr17 73289754 73289755 TRA NA - + [Manta_PE=0,Manta_SR=22] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC092978.1;DisruptR=CDC42EP4;ClosestL=;ClosestR= 170316551 67102560 6,141665769,73289763 0,0,0 chr3 156596536 156596537 chr20 22251588 22251589 TRA NA - - [Svaba_SR=15,Svaba_PE=7],[Manta_PE=8,Manta_SR=15],[Lumpy_PE=8,Lumpy_SR=3] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR=LINC01427 170316551 21885645 15,156596535,22251588 0,0,0 chr3 156596713 156596714 chr20 22253039 22253040 TRA NA + - [Svaba_SR=14,Svaba_PE=8],[Manta_PE=5,Manta_SR=11],[Lumpy_PE=4,Lumpy_SR=5] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR=LINC01427 170316551 21885645 10,156596713,22253039 0,0,0 chr3 170317088 170317089 chr3 195524531 195524532 INV NA - - [Svaba_SR=24,Svaba_PE=29],[Manta_PE=28,Manta_SR=19],[Lumpy_PE=18,Lumpy_SR=16] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;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=;DisruptR=PPP1R2;ClosestL=PRKCI;ClosestR=RNU6ATAC24P 170316552 194248004 17,170317087,195524531 0,0,0 chr3 173507699 173507700 chr3 195524477 195524478 INV NA + + [Svaba_SR=25,Svaba_PE=27],[Manta_PE=25,Manta_SR=20],[Lumpy_PE=22,Lumpy_SR=12] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;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=PPP1R2;Fusion=NLGN1+PPP1R2;ClosestL=;ClosestR=RNU6ATAC24P 173659062 194248004 17,173507699,195524478 0,0,0 chr3 173507997 173507998 chr3 194247718 194247719 INV NA - - [Svaba_SR=22,Svaba_PE=23],[Manta_PE=23,Manta_SR=20],[Lumpy_PE=17,Lumpy_SR=9] lumpy,svaba,manta 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;Fusion=LINC02036+NLGN1;ClosestL=;ClosestR= 173659062 194248003 0,0,0 0,0,0 chr3 193906127 193906128 chr3 193912491 193912492 DEL NA + - [Svaba_SR=45,Svaba_PE=59],[Manta_PE=61,Manta_SR=34] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 194248003 194248003 23,193906127,193912491 0,0,0 chr4 7325452 7325453 chr10 51033383 51033384 TRA NA + - [Svaba_SR=0,Svaba_PE=13],[Manta_PE=9,Manta_SR=0] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SORCS2;DisruptR=PRKG1;Fusion=SORCS2-PRKG1;ClosestL=MIR4798;ClosestR= 10011 39580117 0,0,0 0,0,0 chr4 7325452 7325453 chr10 51269343 51269344 TRA NA + - [Svaba_SR=69,Svaba_PE=56],[Manta_PE=55,Manta_SR=58],[Lumpy_PE=37,Lumpy_SR=48] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SORCS2;DisruptR=PRKG1;Fusion=SORCS2-PRKG1;ClosestL=MIR4798;ClosestR= 10011 39580117 45,7325452,51269343 0,0,0 chr4 7334743 7334744 chr10 50991309 50991310 TRA NA - + [Svaba_SR=73,Svaba_PE=100],[Manta_PE=86,Manta_SR=63],[Lumpy_PE=60,Lumpy_SR=54] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SORCS2;DisruptR=PRKG1;Fusion=PRKG1-SORCS2;ClosestL=;ClosestR= 10011 39580117 44,7334745,50991310 0,0,0 chr4 13541213 13541214 chr4 13542655 13542656 DEL NA + - [Svaba_SR=14,Svaba_PE=19],[Manta_PE=18,Manta_SR=12],[Lumpy_PE=11,Lumpy_SR=10] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=NKX3-2;DisruptR=NKX3-2;ClosestL=LINC01096;ClosestR=LINC01096 14827697 14827697 10,13541212,13542655 0,0,0 chr4 14827425 14827426 chr4 15665086 15665087 DUP NA - + [Svaba_SR=30,Svaba_PE=33],[Manta_PE=31,Manta_SR=26],[Lumpy_PE=25,Lumpy_SR=20] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC00504;DisruptR=FBXL5;Fusion=LINC00504+FBXL5;ClosestL=;ClosestR=FAM200B 14827697 15664844 22,14827427,15665087 0,0,0 chr4 22959992 22959993 chr4 22967233 22967234 DEL NA + - [Svaba_SR=59,Svaba_PE=66],[Manta_PE=63,Manta_SR=48],[Lumpy_PE=45,Lumpy_SR=33] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;ClosestL=;ClosestR= 15664844 15664844 38,22959992,22967233 0,0,0 chr4 37747941 37747942 chr4 37749092 37749093 DEL NA + - [Svaba_SR=15,Svaba_PE=17],[Manta_PE=11,Manta_SR=14],[Lumpy_PE=10,Lumpy_SR=12] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 52771714 52771714 11,37747943,37749088 0,0,0 chr4 41713489 41713490 chr4 41722276 41722277 DEL NA + - [Svaba_SR=18,Svaba_PE=20],[Manta_PE=21,Manta_SR=20],[Lumpy_PE=16,Lumpy_SR=10] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=OR5M14P;ClosestR=OR5M14P 52771714 52771714 16,41713489,41722276 0,0,0 chr4 54132841 54132842 chr4 54134550 54134551 DEL NA + - [Svaba_SR=24,Svaba_PE=32],[Manta_PE=30,Manta_SR=18],[Lumpy_PE=21,Lumpy_SR=13] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC058822.1;DisruptR=AC058822.1;ClosestL=;ClosestR= 52771742 52771742 14,54132841,54134550 0,0,0 chr4 57019050 57019051 chr7 56443992 56443993 TRA NA - - [Svaba_SR=19,Svaba_PE=19],[Manta_PE=20,Manta_SR=18],[Lumpy_PE=16,Lumpy_SR=14] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=POLR2B;DisruptR=AC092447.7;Fusion=AC092447.7-POLR2B;ClosestL=IGFBP7;ClosestR=AC092447.10 57339073 57487363 18,57019050,56443992 0,0,0 chr4 59828040 59828041 chr4 59828615 59828616 DEL NA + - [Manta_PE=66,Manta_SR=82],[Lumpy_PE=60,Lumpy_SR=57] lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=RF00019;ClosestR=RF00019 59832563 59832563 55,59828042,59828616 0,0,0 chr4 59832640 59832641 chr9 28551943 28551944 TRA NA + - [Svaba_SR=85,Svaba_PE=93],[Manta_PE=82,Manta_SR=75],[Lumpy_PE=57,Lumpy_SR=57] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=;DisruptR=LINGO2;ClosestL=RF00019;ClosestR= 59832564 28551865 52,59832641,28551943 0,0,0 chr4 65266722 65266723 chr11 69365928 69365929 TRA NA + - [Svaba_SR=77,Svaba_PE=104],[Manta_PE=93,Manta_SR=71],[Lumpy_PE=70,Lumpy_SR=60] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=MYEOV;ClosestL=;ClosestR=AP005233.2 65266705 69098162 53,65266721,69365928 0,0,0 chr4 82823868 82823869 chr8 97238613 97238614 TRA NA - + [Svaba_SR=36,Svaba_PE=34],[Manta_PE=14,Manta_SR=30],[Lumpy_PE=6,Lumpy_SR=22] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=SEC31A;DisruptR=;ClosestL=;ClosestR=AP003115.1 89026738 97238582 20,82823867,97238614 0,0,0 chr4 82823983 82823984 chr8 96324292 96324293 TRA NA + - [Svaba_SR=33,Svaba_PE=0],[Manta_PE=14,Manta_SR=30],[Lumpy_PE=5,Lumpy_SR=16] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=SEC31A;DisruptR=PTDSS1;ClosestL=;ClosestR=RF00019 89026738 96324266 21,82823985,96324286 0,0,0 chr4 91384071 91384072 chr18 61626507 61626508 TRA NA + - [Svaba_SR=41,Svaba_PE=51],[Manta_PE=47,Manta_SR=34],[Lumpy_PE=39,Lumpy_SR=22] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=CCSER1;DisruptR=AC105094.2;ClosestL=;ClosestR=AC090409.1 91384038 61626460 30,91384073,61626506 0,0,0 chr4 91964436 91964437 chr4 91968879 91968880 INV NA - - [Svaba_SR=41,Svaba_PE=37],[Manta_PE=37,Manta_SR=37],[Lumpy_PE=22,Lumpy_SR=27] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;ClosestL=;ClosestR= 91964420 91964420 25,91964435,91968879 0,0,0 chr4 92714812 92714813 chr4 92741756 92741757 INV NA + + [Manta_PE=6,Manta_SR=7],[Lumpy_PE=5,Lumpy_SR=8] lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=GRID2;DisruptR=GRID2;ClosestL=MTND1P19;ClosestR= 91964420 91964420 7,92714814,92741757 0,0,0 chr4 92714815 92714816 chr4 92741711 92741712 INV NA - - [Manta_PE=3,Manta_SR=4],[Lumpy_PE=5,Lumpy_SR=8] lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=GRID2;DisruptR=GRID2;ClosestL=MTND1P19;ClosestR= 91964420 91964420 3,92714815,92741705 0,0,0 chr4 104438018 104438019 chr4 189036389 189036390 INV NA - - [Manta_PE=7,Manta_SR=0] manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=IL2|Tier1,FBXW7|Tier1,CASP3|Tier2,TET2|Tier1,LEF1|Tier1,FAT4|Tier1,FAT1|Tier1;DisruptL=;DisruptR=;ClosestL=;ClosestR= 91964420 190066290 3,104438194,189036344 0,0,0 chr4 168286143 168286144 chr20 14619539 14619540 TRA NA + - [Svaba_SR=0,Svaba_PE=13],[Lumpy_PE=4,Lumpy_SR=1] lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=DDX60;DisruptR=MACROD2-IT1,MACROD2;ClosestL=;ClosestR= 190066290 8764420 0,0,0 0,0,0 chr4 189021274 189021275 chr4 189022112 189022113 DUP NA - + [Svaba_SR=19,Svaba_PE=28],[Manta_PE=23,Manta_SR=15],[Lumpy_PE=23,Lumpy_SR=12] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=AC122138.1;ClosestR= 190066290 190066290 14,189021273,189022113 0,0,0 chr4 189022112 189022113 chr4 189024736 189024737 DEL NA + - [Svaba_SR=39,Svaba_PE=0],[Manta_PE=18,Manta_SR=16],[Lumpy_PE=11,Lumpy_SR=12] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;ClosestL=;ClosestR= 190066290 190066290 0,0,0 0,0,0 chr5 11509436 11509437 chr10 3336263 3336264 TRA NA + - [Svaba_SR=14,Svaba_PE=14],[Manta_PE=13,Manta_SR=10],[Lumpy_PE=10,Lumpy_SR=10] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=CTNND2|Tier2;DisruptL=CTNND2;DisruptR=;ClosestL=;ClosestR= 12810903 3411101 6,11509433,3336263 0,0,0 chr5 23767939 23767940 chr5 23769678 23769679 DEL NA + - [Svaba_SR=17,Svaba_PE=24],[Manta_PE=21,Manta_SR=15],[Lumpy_PE=18,Lumpy_SR=11] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 32366972 32366972 13,23767941,23769674 0,0,0 chr5 28710819 28710820 chr5 28711436 28711437 DEL NA + - [Svaba_SR=131,Svaba_PE=101],[Manta_PE=57,Manta_SR=86],[Lumpy_PE=57,Lumpy_SR=42] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 32366972 32366972 0,0,0 0,0,0 chr5 30463531 30463532 chr5 30475422 30475423 DEL NA + - [Svaba_SR=12,Svaba_PE=19],[Manta_PE=16,Manta_SR=13],[Lumpy_PE=14,Lumpy_SR=8] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;ClosestL=;ClosestR= 32366972 32366972 10,30463532,30475422 0,0,0 chr5 32366999 32367000 chr10 63904597 63904598 TRA NA + + [Svaba_SR=31,Svaba_PE=37],[Manta_PE=41,Manta_SR=25],[Lumpy_PE=31,Lumpy_SR=16] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=ZFR;DisruptR=AC022387.1;Fusion=AC022387.1-ZFR;ClosestL=;ClosestR=RPL7AP50 32366973 63904755 16,32367001,63904598 0,0,0 chr5 43171736 43171737 chr5 43188686 43188687 DEL NA + - [Svaba_SR=14,Svaba_PE=21],[Manta_PE=16,Manta_SR=8],[Lumpy_PE=12,Lumpy_SR=4] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=ZNF131;DisruptR=ZNF131;ClosestL=;ClosestR=NIM1K 32366973 32366973 8,43171736,43188686 0,0,0 chr5 59193924 59193925 chr10 61749857 61749858 TRA NA + + [Manta_PE=0,Manta_SR=7] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PDE4D;DisruptR=CABCOCO1;Fusion=CABCOCO1-PDE4D;ClosestL=;ClosestR= 32366973 63904755 5,59193926,61749858 0,0,0 chr5 59747085 59747086 chr5 59755805 59755806 DUP NA - + [Manta_PE=3,Manta_SR=5],[Lumpy_PE=2,Lumpy_SR=3] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PDE4D;DisruptR=PDE4D;ClosestL=;ClosestR= 32366973 32366973 4,59747085,59755806 0,0,0 chr5 76588049 76588050 chr10 12934286 12934287 TRA NA - + [Svaba_SR=23,Svaba_PE=10],[Manta_PE=10,Manta_SR=17],[Lumpy_PE=9,Lumpy_SR=8] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=IQGAP2;DisruptR=CCDC3;ClosestL=AC026725.1;ClosestR=RNA5SP300 32366973 3411102 15,76588048,12934287 0,0,0 chr5 76588341 76588342 chr7 43643802 43643803 TRA NA + + [Svaba_SR=25,Svaba_PE=9],[Manta_PE=9,Manta_SR=18],[Lumpy_PE=5,Lumpy_SR=16] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=IQGAP2;DisruptR=COA1;Fusion=IQGAP2-COA1;ClosestL=AC026725.1;ClosestR=STK17A 32366973 43477639 16,76588334,43643803 0,0,0 chr5 78710196 78710197 chr5 78727227 78727228 DEL NA + - [Svaba_SR=26,Svaba_PE=24],[Manta_PE=20,Manta_SR=19],[Lumpy_PE=17,Lumpy_SR=1] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC008802.1,LHFPL2;DisruptR=LHFPL2;Fusion=LHFPL2+AC008802.1;ClosestL=;ClosestR=AC008802.1 32366973 32366973 14,78710197,78727227 0,0,0 chr5 101330082 101330083 chr5 101342606 101342607 DEL NA + - [Svaba_SR=17,Svaba_PE=23],[Manta_PE=18,Manta_SR=14],[Lumpy_PE=14,Lumpy_SR=11] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 164930824 164930824 11,101330082,101342606 0,0,0 chr5 102801795 102801796 chr5 102874958 102874959 DEL NA + - [Svaba_SR=21,Svaba_PE=15],[Manta_PE=15,Manta_SR=15] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PAM;DisruptR=PAM;ClosestL=;ClosestR= 164930824 164930824 0,0,0 0,0,0 chr5 114587648 114587649 chr5 114630660 114630661 DEL NA + - [Svaba_SR=16,Svaba_PE=22],[Manta_PE=16,Manta_SR=13],[Lumpy_PE=15,Lumpy_SR=10] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC010230.1;DisruptR=AC010230.1;ClosestL=LINC01957;ClosestR= 164930824 164930824 11,114587649,114630650 0,0,0 chr5 120820992 120820993 chr5 120828971 120828972 INV NA + + [Manta_PE=4,Manta_SR=3],[Lumpy_PE=3,Lumpy_SR=2] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 164930824 164930824 3,120820994,120828977 0,0,0 chr5 139904402 139904403 chr21 41878046 41878047 TRA NA + + [Svaba_SR=51,Svaba_PE=23],[Manta_PE=15,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=NRG2;DisruptR=PRDM15;ClosestL=;ClosestR=AP001619.1 164930824 41825926 0,0,0 0,0,0 chr5 139904402 139904403 chr7 82672674 82672675 TRA NA + + [Svaba_SR=37,Svaba_PE=17],[Manta_PE=15,Manta_SR=33],[Lumpy_PE=10,Lumpy_SR=27] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=NRG2;DisruptR=;ClosestL=;ClosestR=AC004006.1 164930824 84167674 24,139904402,82672675 0,0,0 chr5 154695628 154695629 chr5 154762331 154762332 DEL NA + - [Svaba_SR=24,Svaba_PE=31],[Manta_PE=28,Manta_SR=23],[Lumpy_PE=16,Lumpy_SR=14] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=LARP1;ClosestL=MIR1303;ClosestR= 164930824 164930824 19,154695630,154762324 0,0,0 chr5 164930879 164930880 chr10 29373648 29373649 TRA NA - + [Svaba_SR=29,Svaba_PE=8],[Manta_PE=5,Manta_SR=29] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC109466.1;DisruptR=;ClosestL=RNU6-209P;ClosestR= 164930825 29240716 12,164930880,29373649 0,0,0 chr5 166229096 166229097 chr13 103143785 103143786 TRA NA + + [Svaba_SR=0,Svaba_PE=11],[Manta_PE=9,Manta_SR=0],[Lumpy_PE=5,Lumpy_SR=14] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 164930825 107326494 0,0,0 0,0,0 chr5 169123666 169123667 chr5 171131427 171131428 DUP NA - + [Svaba_SR=23,Svaba_PE=22],[Manta_PE=18,Manta_SR=21],[Lumpy_PE=12,Lumpy_SR=15] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SLIT3;DisruptR=RANBP17;ClosestL=;ClosestR= 164930825 164930825 19,169123666,171131428 0,0,0 chr5 170686418 170686419 chr13 104720019 104720020 TRA NA - - [Svaba_SR=13,Svaba_PE=8],[Manta_PE=12,Manta_SR=16],[Lumpy_PE=10,Lumpy_SR=1] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=KCNIP1;DisruptR=;ClosestL=AC027312.1;ClosestR= 164930825 107326494 0,0,0 0,0,0 chr5 170686434 170686435 chr13 104711356 104711357 TRA NA + + [Svaba_SR=23,Svaba_PE=14],[Manta_PE=17,Manta_SR=21] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=KCNIP1;DisruptR=;ClosestL=AC027312.1;ClosestR= 164930825 107326494 0,0,0 0,0,0 chr5 171130474 171130475 chr5 176905028 176905029 DUP NA - + [Svaba_SR=12,Svaba_PE=7],[Manta_PE=7,Manta_SR=9],[Lumpy_PE=7,Lumpy_SR=1] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=NPM1|Tier1,TLX3|Tier1;DisruptL=RANBP17;DisruptR=UIMC1;ClosestL=;ClosestR=HK3 164930825 180949083 0,0,0 0,0,0 chr5 172804771 172804772 chr13 104711184 104711185 TRA NA - - [Manta_PE=6,Manta_SR=10],[Lumpy_PE=3,Lumpy_SR=9] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=AC110011.1;ClosestR= 164930825 107326494 11,172804773,104711181 0,0,0 chr5 173535074 173535075 chr21 17229345 17229346 TRA NA + - [Svaba_SR=13,Svaba_PE=15],[Manta_PE=11,Manta_SR=12],[Lumpy_PE=7,Lumpy_SR=10] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR=NEK4P1 180949083 17474345 11,173535079,17229342 0,0,0 chr5 179626987 179626988 chr5 179641488 179641489 INV NA + + [Svaba_SR=84,Svaba_PE=86],[Manta_PE=87,Manta_SR=71],[Lumpy_PE=79,Lumpy_SR=29] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=HNRNPH1;DisruptR=;ClosestL=RF00017;ClosestR=C5orf60 180949083 180949083 45,179626986,179641489 0,0,0 chr6 5651670 5651671 chr7 137445350 137445351 TRA NA - - [Svaba_SR=0,Svaba_PE=9],[Manta_PE=6,Manta_SR=16],[Lumpy_PE=5,Lumpy_SR=15] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=FARS2;DisruptR=DGKI;Fusion=DGKI-FARS2;ClosestL=AL022097.1;ClosestR= 882088 137445254 10,5651672,137445274 0,0,0 chr6 5651755 5651756 chr10 37195842 37195843 TRA NA + - [Svaba_SR=0,Svaba_PE=16],[Manta_PE=7,Manta_SR=11],[Lumpy_PE=5,Lumpy_SR=7] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=FARS2;DisruptR=ANKRD30A;Fusion=FARS2-ANKRD30A;ClosestL=AL022097.1;ClosestR= 882088 37167258 7,5651754,37195765 0,0,0 chr6 10615715 10615716 chr6 10671380 10671381 INV NA - - [Manta_PE=7,Manta_SR=7],[Lumpy_PE=3,Lumpy_SR=6] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=GCNT2;DisruptR=;ClosestL=GCNT2P;ClosestR=C6orf52 882088 882088 7,10615718,10671378 0,0,0 chr6 24909910 24909911 chr13 23788151 23788152 TRA NA + - [Svaba_SR=26,Svaba_PE=29],[Manta_PE=29,Manta_SR=25],[Lumpy_PE=26,Lumpy_SR=13] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=RIPOR2;DisruptR=MIPEP;Fusion=MIPEP-RIPOR2;ClosestL=;ClosestR= 24909816 23788057 2,24909916,23788151 0,0,0 chr6 31282776 31282777 chr6 31676535 31676536 DUP NA - + [Svaba_SR=45,Svaba_PE=48],[Manta_PE=44,Manta_SR=38],[Lumpy_PE=36,Lumpy_SR=7] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=HLA-B;DisruptR=;ClosestL=RPL3P2;ClosestR=LY6G5C 32487100 32487100 30,31282778,31676536 0,0,0 chr6 36092690 36092691 chr11 72659713 72659714 TRA NA + - [Svaba_SR=31,Svaba_PE=29],[Manta_PE=24,Manta_SR=28],[Lumpy_PE=11,Lumpy_SR=26] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=MAPK14;DisruptR=PDE2A;ClosestL=Z95152.1;ClosestR=AP003065.1 36092606 72659618 22,36092689,72659713 0,0,0 chr6 37947053 37947054 chr6 37948416 37948417 INV NA - - [Svaba_SR=32,Svaba_PE=40],[Manta_PE=41,Manta_SR=34],[Lumpy_PE=32,Lumpy_SR=22] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=ZFAND3;DisruptR=ZFAND3;ClosestL=;ClosestR= 37947068 37947069 0,0,0 0,0,0 chr6 38119595 38119596 chr11 45539585 45539586 TRA NA - - [Svaba_SR=36,Svaba_PE=42],[Manta_PE=45,Manta_SR=26],[Lumpy_PE=30,Lumpy_SR=22] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=ZFAND3;DisruptR=AC103855.2;Fusion=AC103855.2-ZFAND3;ClosestL=;ClosestR= 38141254 45539525 21,38119596,45539585 0,0,0 chr6 38131029 38131030 chr6 38141273 38141274 INV NA + + [Svaba_SR=52,Svaba_PE=40],[Manta_PE=36,Manta_SR=45],[Lumpy_PE=32,Lumpy_SR=27] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=ZFAND3;DisruptR=ZFAND3;ClosestL=;ClosestR= 38141254 38141255 2,38131032,38141271 0,0,0 chr6 38475453 38475454 chr6 38488043 38488044 DEL NA + - [Svaba_SR=20,Svaba_PE=19],[Manta_PE=16,Manta_SR=15],[Lumpy_PE=12,Lumpy_SR=13] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=BTBD9;DisruptR=BTBD9;ClosestL=BTBD9-AS1;ClosestR=BTBD9-AS1 38141255 38141255 14,38475453,38488043 0,0,0 chr6 51934058 51934059 chr6 51937863 51937864 INV NA + + [Svaba_SR=16,Svaba_PE=26],[Manta_PE=28,Manta_SR=13],[Lumpy_PE=26,Lumpy_SR=8] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PKHD1;DisruptR=PKHD1;ClosestL=;ClosestR= 52221178 52221178 12,51934060,51937864 0,0,0 chr6 52220975 52220976 chr13 110468790 110468791 TRA NA - + [Svaba_SR=27,Svaba_PE=30],[Manta_PE=28,Manta_SR=23],[Lumpy_PE=17,Lumpy_SR=18] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=COL4A2;ClosestL=IL17F;ClosestR=COL4A2-AS2 52221178 110418576 21,52220974,110468791 0,0,0 chr6 52679254 52679255 chr18 23971471 23971472 TRA NA + + [Svaba_SR=59,Svaba_PE=61],[Manta_PE=70,Manta_SR=51],[Lumpy_PE=47,Lumpy_SR=24] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TMEM14A;DisruptR=AC010754.1;Fusion=TMEM14A-AC010754.1;ClosestL=GSTA8P;ClosestR=LAMA3 52679254 23971375 42,52679253,23971472 0,0,0 chr6 53892609 53892610 chr6 53893327 53893328 DEL NA + - [Manta_PE=24,Manta_SR=25],[Lumpy_PE=20,Lumpy_SR=19] lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LRRC1;DisruptR=LRRC1;ClosestL=;ClosestR= 54303155 54303155 22,53892611,53893328 0,0,0 chr6 54303391 54303392 chr15 76561854 76561855 TRA NA + - [Svaba_SR=19,Svaba_PE=0],[Manta_PE=7,Manta_SR=21],[Lumpy_PE=4,Lumpy_SR=17] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=SCAPER;ClosestL=TINAG;ClosestR= 54303156 72362590 16,54303392,76561854 0,0,0 chr6 54303442 54303443 chr16 67652158 67652159 TRA NA + + [Manta_PE=10,Manta_SR=0] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=CARMIL2;ClosestL=TINAG;ClosestR=ACD 54303156 90226217 0,0,0 0,0,0 chr6 58157667 58157668 chr13 110418585 110418586 TRA NA - + [Svaba_SR=54,Svaba_PE=74],[Manta_PE=26,Manta_SR=45],[Lumpy_PE=20,Lumpy_SR=7] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AL445250.1;DisruptR=COL4A2;Fusion=COL4A2-AL445250.1;ClosestL=;ClosestR=AL159153.1 59823890 110418576 39,58157667,110418586 0,0,0 chr6 58190428 58190429 chr11 78640457 78640458 TRA NA + + [Svaba_SR=50,Svaba_PE=50],[Manta_PE=49,Manta_SR=32] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AL445250.1;DisruptR=;ClosestL=;ClosestR=TENM4 59823890 78640370 28,58190430,78640458 0,0,0 chr6 82898488 82898489 chr6 82899849 82899850 DEL NA + - [Svaba_SR=14,Svaba_PE=17],[Manta_PE=16,Manta_SR=14],[Lumpy_PE=14,Lumpy_SR=7] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=UBE3D;DisruptR=UBE3D;ClosestL=;ClosestR= 78326602 78326602 10,82898490,82899849 0,0,0 chr6 85371209 85371210 chr11 69182921 69182922 TRA NA + + [Svaba_SR=0,Svaba_PE=20],[Manta_PE=7,Manta_SR=0] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=LINC02535;ClosestR=AP003071.2 78326602 69098162 0,0,0 0,0,0 chr6 108428792 108428793 chr6 108701375 108701376 DEL NA + - [Svaba_SR=20,Svaba_PE=25],[Manta_PE=21,Manta_SR=15],[Lumpy_PE=15,Lumpy_SR=12] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=FOXO3|Tier1;DisruptL=AFG1L;DisruptR=;ClosestL=;ClosestR=FOXO3 129707604 129707604 12,108428791,108701375 0,0,0 chr6 129707662 129707663 chr6 130004047 130004048 DUP NA - + [Svaba_SR=50,Svaba_PE=72],[Manta_PE=69,Manta_SR=40],[Lumpy_PE=59,Lumpy_SR=29] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=ARHGAP18;DisruptR=;ClosestL=;ClosestR=L3MBTL3 129707605 130003967 33,129707665,130004048 0,0,0 chr6 144660334 144660335 chr21 32343657 32343658 TRA NA + + [Manta_PE=2,Manta_SR=19],[Lumpy_PE=2,Lumpy_SR=12] lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=UTRN;DisruptR=URB1;Fusion=UTRN-URB1;ClosestL=;ClosestR= 130003967 32739659 10,144660336,32343658 0,0,0 chr6 166891543 166891544 chr16 13287330 13287331 TRA NA - - [Svaba_SR=21,Svaba_PE=28],[Manta_PE=27,Manta_SR=15],[Lumpy_PE=21,Lumpy_SR=13] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AL159163.1,RPS6KA2;DisruptR=U91319.1;Fusion=AL159163.1-U91319.1|RPS6KA2-U91319.1;ClosestL=RPS6KA2-AS1;ClosestR= 166891771 13284478 14,166891543,13287330 0,0,0 chr6 168164289 168164290 chr6 168191518 168191519 DUP NA - + [Svaba_SR=33,Svaba_PE=17],[Manta_PE=18,Manta_SR=0] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR=AL611929.1 166891772 166891772 0,0,0 0,0,0 chr7 29985175 29985176 chr22 28499903 28499904 TRA NA - + [Svaba_SR=32,Svaba_PE=0],[Manta_PE=8,Manta_SR=28],[Lumpy_PE=2,Lumpy_SR=15] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SCRN1;DisruptR=TTC28;Fusion=SCRN1-TTC28;ClosestL=AC007285.1;ClosestR= 43477638 29344638 19,29985176,28499904 0,0,0 chr7 29985277 29985278 chr21 14331478 14331479 TRA NA + - [Svaba_SR=0,Svaba_PE=12],[Manta_PE=10,Manta_SR=0] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SCRN1;DisruptR=ABCC13;ClosestL=AC007285.1;ClosestR= 43477638 13507201 0,0,0 0,0,0 chr7 43477683 43477684 chr17 67148382 67148383 TRA NA - + [Svaba_SR=66,Svaba_PE=86],[Manta_PE=76,Manta_SR=60],[Lumpy_PE=59,Lumpy_SR=40] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=HECW1;DisruptR=HELZ;ClosestL=;ClosestR= 43477639 67102560 43,43477682,67148383 0,0,0 chr7 44883007 44883008 chr7 44913973 44913974 DUP NA - + [Svaba_SR=70,Svaba_PE=59],[Manta_PE=71,Manta_SR=63],[Lumpy_PE=62,Lumpy_SR=39] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PURB;DisruptR=;ClosestL=MIR4657;ClosestR=AC004854.1 43477639 43477639 46,44883003,44913975 0,0,0 chr7 47787889 47787890 chr21 13481495 13481496 TRA NA - + [Svaba_SR=21,Svaba_PE=14],[Manta_PE=8,Manta_SR=13] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=HUS1,PKD1L1;DisruptR=GTF2IP2;Fusion=HUS1-GTF2IP2|PKD1L1-GTF2IP2;ClosestL=C7orf69;ClosestR=VN1R8P 43477639 13507200 13,47787891,13481496 0,0,0 chr7 47788066 47788067 chr7 57377873 57377874 DEL NA + - [Svaba_SR=19,Svaba_PE=17],[Manta_PE=11,Manta_SR=19],[Lumpy_PE=7,Lumpy_SR=12] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=ZNF479|Tier2,EGFR|Tier1,IKZF1|Tier1;DisruptL=HUS1,PKD1L1;DisruptR=;ClosestL=C7orf69;ClosestR= 43477639 57487363 15,47788066,57377873 0,0,0 chr7 53748552 53748553 chr7 53753362 53753363 DEL NA + - [Svaba_SR=65,Svaba_PE=79],[Manta_PE=74,Manta_SR=54],[Lumpy_PE=48,Lumpy_SR=43] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC01446;DisruptR=LINC01446;ClosestL=;ClosestR= 57487363 57487363 39,53748553,53753362 0,0,0 chr7 61041203 61041204 chr18 21481532 21481533 TRA NA - - [Lumpy_PE=3,Lumpy_SR=1] lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=GREB1L;ClosestL=;ClosestR= 62116180 20553042 3,61041202,21481531 0,0,0 chr7 62742736 62742737 chr7 87327162 87327163 DEL NA + - [Svaba_SR=0,Svaba_PE=8],[Manta_PE=8,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=SBDS|Tier1,ELN|Tier2,HIP1|Tier1,GRM3|Tier2;DisruptL=;DisruptR=TP53TG1;ClosestL=;ClosestR=RF02195 62742771 84789193 0,0,0 0,0,0 chr7 62742736 62742737 chr8 134414517 134414518 TRA NA + + [Svaba_SR=12,Svaba_PE=5],[Manta_PE=6,Manta_SR=10] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 62742771 145078494 9,62742738,134414518 0,0,0 chr7 69920183 69920184 chr7 70236713 70236714 DEL NA + - [Svaba_SR=12,Svaba_PE=18],[Manta_PE=17,Manta_SR=11],[Lumpy_PE=11,Lumpy_SR=10] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AUTS2;DisruptR=AUTS2;ClosestL=;ClosestR= 69920124 70236680 8,69920183,70236713 0,0,0 chr7 82613835 82613836 chr21 41878419 41878420 TRA NA - - [Svaba_SR=12,Svaba_PE=7],[Manta_PE=7,Manta_SR=10],[Lumpy_PE=4,Lumpy_SR=6] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=PRDM15;ClosestL=;ClosestR=AP001619.1 84167674 41825926 8,82613834,41878418 0,0,0 chr7 82616051 82616052 chr10 51349321 51349322 TRA NA + - [Svaba_SR=34,Svaba_PE=8],[Manta_PE=6,Manta_SR=29],[Lumpy_PE=4,Lumpy_SR=27] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=PRKG1;ClosestL=;ClosestR= 84167674 39580117 23,82616053,51349321 0,0,0 chr7 82616052 82616053 chr17 20111623 20111624 TRA NA + - [Svaba_SR=0,Svaba_PE=9],[Manta_PE=8,Manta_SR=0] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=SPECC1|Tier2;DisruptL=;DisruptR=SPECC1;ClosestL=;ClosestR=KCTD9P1 84167674 21658447 0,0,0 0,0,0 chr7 82672505 82672506 chr21 41878046 41878047 TRA NA - + [Svaba_SR=26,Svaba_PE=28],[Manta_PE=18,Manta_SR=21],[Lumpy_PE=13,Lumpy_SR=11] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=;DisruptR=PRDM15;ClosestL=AC004006.1;ClosestR=AP001619.1 84167674 41825926 14,82672505,41878047 0,0,0 chr7 86257760 86257761 chr21 26634844 26634845 TRA NA - + [Svaba_SR=23,Svaba_PE=23],[Manta_PE=20,Manta_SR=20],[Lumpy_PE=15,Lumpy_SR=14] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 84789193 26635290 20,86257759,26634845 0,0,0 chr7 87327163 87327164 chr8 134414383 134414384 TRA NA - - [Svaba_SR=18,Svaba_PE=0],[Manta_PE=0,Manta_SR=17] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TP53TG1;DisruptR=;ClosestL=RF02195;ClosestR= 84789193 145078494 15,87327163,134414383 0,0,0 chr7 89265302 89265303 chr7 89268691 89268692 DEL NA + - [Svaba_SR=22,Svaba_PE=16],[Manta_PE=17,Manta_SR=16],[Lumpy_PE=14,Lumpy_SR=1] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=ZNF804B;DisruptR=ZNF804B;ClosestL=;ClosestR= 92202778 92202778 0,0,0 0,0,0 chr7 92202777 92202778 chr7 92380664 92380665 DEL NA + - [Svaba_SR=24,Svaba_PE=24],[Manta_PE=15,Manta_SR=23],[Lumpy_PE=11,Lumpy_SR=16] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC000120.1,KRIT1;DisruptR=ANKIB1;ClosestL=RF00019;ClosestR= 92202778 92380732 18,92202778,92380664 0,0,0 chr7 116918744 116918745 chrX 57506628 57506629 TRA NA - + [Svaba_SR=21,Svaba_PE=21],[Manta_PE=15,Manta_SR=16] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=CAPZA2;DisruptR=;ClosestL=RF00019;ClosestR=FAAH2 116918673 57361937 13,116918745,57506629 0,0,0 chr7 137445279 137445280 chr10 37195765 37195766 TRA NA - - [Svaba_SR=32,Svaba_PE=15],[Manta_PE=8,Manta_SR=13] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=DGKI;DisruptR=ANKRD30A;Fusion=DGKI-ANKRD30A;ClosestL=;ClosestR= 137445254 37167258 0,0,0 0,0,0 chr7 140911265 140911266 chr7 140955783 140955784 INV NA - - [Svaba_SR=22,Svaba_PE=22],[Manta_PE=19,Manta_SR=19],[Lumpy_PE=12,Lumpy_SR=14] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=BRAF|Tier1;DisruptL=BRAF;DisruptR=;ClosestL=;ClosestR= 137445254 137445254 17,140911266,140955783 0,0,0 chr7 141230709 141230710 chr7 141238330 141238331 DEL NA + - [Svaba_SR=21,Svaba_PE=29],[Manta_PE=23,Manta_SR=17],[Lumpy_PE=17,Lumpy_SR=12] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TMEM178B;DisruptR=TMEM178B;ClosestL=;ClosestR= 144556595 144556595 15,141230711,141238330 0,0,0 chr7 141234566 141234567 chr7 141311291 141311292 INV NA + + [Svaba_SR=24,Svaba_PE=26],[Manta_PE=16,Manta_SR=0],[Lumpy_PE=14,Lumpy_SR=13] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TMEM178B;DisruptR=TMEM178B;ClosestL=;ClosestR= 144556595 144556595 6,141234568,141311292 0,0,0 chr8 10846875 10846876 chr20 47268863 47268864 TRA NA - - [Svaba_SR=18,Svaba_PE=0],[Manta_PE=13,Manta_SR=21],[Lumpy_PE=7,Lumpy_SR=15] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=ZMYND8;ClosestL=AC011008.1;ClosestR= 71162 39349551 20,10846878,47268863 0,0,0 chr8 10847021 10847022 chr20 47225235 47225236 TRA NA + + [Svaba_SR=26,Svaba_PE=21],[Manta_PE=19,Manta_SR=21],[Lumpy_PE=7,Lumpy_SR=14] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=ZMYND8;ClosestL=AC011008.1;ClosestR= 71162 39349551 17,10847023,47225236 0,0,0 chr8 38073703 38073704 chr8 38074256 38074257 DEL NA + - [Svaba_SR=43,Svaba_PE=57],[Manta_PE=44,Manta_SR=33],[Lumpy_PE=32,Lumpy_SR=14] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=AP006545.1;ClosestR=AP006545.1 36461421 36461421 20,38073700,38074256 0,0,0 chr8 43475992 43475993 chr11 70550642 70550643 TRA NA - + [Svaba_SR=201,Svaba_PE=240],[Manta_PE=202,Manta_SR=192],[Lumpy_PE=138,Lumpy_SR=143] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=SHANK2;ClosestL=AC134698.4;ClosestR= 43475933 70550614 90,43475994,70550643 0,0,0 chr8 43634263 43634264 chr8 43635536 43635537 INV NA + + [Manta_PE=51,Manta_SR=62],[Lumpy_PE=41,Lumpy_SR=15] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 43646293 43646293 26,43634275,43635537 0,0,0 chr8 43646325 43646326 chr14 104763654 104763655 TRA NA + + [Svaba_SR=133,Svaba_PE=136],[Manta_PE=126,Manta_SR=115],[Lumpy_PE=81,Lumpy_SR=81] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=SIVA1;ClosestL=;ClosestR=AL583722.2 43646294 104243064 65,43646326,104763655 0,0,0 chr8 46943846 46943847 chr8 60480162 60480163 DEL NA + - [Svaba_SR=22,Svaba_PE=22],[Manta_PE=15,Manta_SR=16] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=TCEA1|Tier1,PLAG1|Tier1,CHCHD7|Tier1;DisruptL=;DisruptR=LINC01301;ClosestL=AC091163.2;ClosestR= 45740171 60480054 16,46943847,60480162 0,0,0 chr8 47813737 47813738 chr11 58189360 58189361 TRA NA - - [Svaba_SR=42,Svaba_PE=43],[Manta_PE=40,Manta_SR=36],[Lumpy_PE=28,Lumpy_SR=24] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=PRKDC;DisruptR=OR9Q2;Fusion=PRKDC-OR9Q2;ClosestL=RF00019;ClosestR=OR9Q1 45740171 58828468 29,47813739,58189360 0,0,0 chr8 60642425 60642426 chr8 60724569 60724570 DEL NA + - [Svaba_SR=33,Svaba_PE=29],[Manta_PE=24,Manta_SR=0],[Lumpy_PE=19,Lumpy_SR=11] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=CHD7;ClosestL=AC068389.1;ClosestR= 60480054 60480054 16,60642425,60724569 0,0,0 chr8 80571008 80571009 chr16 22585150 22585151 TRA NA - - [Manta_PE=3,Manta_SR=15] manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=AC009812.2;ClosestR=AC106788.1 69392452 13284478 12,80571008,22585149 0,0,0 chr8 86159415 86159416 chr8 86201237 86201238 DEL NA + - [Svaba_SR=23,Svaba_PE=31],[Manta_PE=22,Manta_SR=24],[Lumpy_PE=16,Lumpy_SR=19] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=;DisruptR=AC084128.1;ClosestL=ATP6V0D2;ClosestR=SLC7A13 96324265 96324265 19,86159417,86201235 0,0,0 chr8 88879692 88879693 chr8 102821044 102821045 INV NA + + [Svaba_SR=19,Svaba_PE=0],[Manta_PE=4,Manta_SR=17] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=COX6C|Tier2,NBN|Tier1,CDH17|Tier2,PABPC1|Tier2,RUNX1T1|Tier1,UBR5|Tier1;DisruptL=;DisruptR=;ClosestL=;ClosestR=AZIN1 96324265 101450437 10,88879694,102821045 0,0,0 chr8 88879692 88879693 chr8 88884416 88884417 DEL NA + - [Svaba_SR=25,Svaba_PE=0],[Manta_PE=9,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 96324265 96324265 0,0,0 0,0,0 chr8 88884416 88884417 chr8 102820935 102820936 INV NA - - [Svaba_SR=15,Svaba_PE=6],[Manta_PE=6,Manta_SR=13] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=COX6C|Tier2,NBN|Tier1,CDH17|Tier2,PABPC1|Tier2,RUNX1T1|Tier1,UBR5|Tier1;DisruptL=;DisruptR=;ClosestL=;ClosestR=AZIN1 96324265 101450437 11,88884418,102820935 0,0,0 chr8 94880300 94880301 chr8 94902717 94902718 DEL NA + - [Svaba_SR=17,Svaba_PE=29],[Manta_PE=24,Manta_SR=15],[Lumpy_PE=20,Lumpy_SR=12] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=INTS8,CCNE2;DisruptR=NDUFAF6;Fusion=INTS8+NDUFAF6;ClosestL=AC087752.4;ClosestR=CCNE2 96324265 96324265 12,94880302,94902717 0,0,0 chr8 96324291 96324292 chr8 97238614 97238615 DUP NA - + [Svaba_SR=0,Svaba_PE=22],[Manta_PE=31,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PTDSS1;DisruptR=;ClosestL=RF00019;ClosestR=AP003115.1 96324266 97238582 0,0,0 0,0,0 chr8 101450517 101450518 chr11 69897840 69897841 TRA NA - + [Svaba_SR=36,Svaba_PE=41],[Manta_PE=40,Manta_SR=28],[Lumpy_PE=30,Lumpy_SR=23] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=AP001208.2;DisruptR=;ClosestL=AP001207.3;ClosestR=AP007216.1 101450437 69779347 23,101450517,69897841 0,0,0 chr8 101451844 101451845 chr11 69897285 69897286 TRA NA - - [Svaba_SR=0,Svaba_PE=30],[Manta_PE=26,Manta_SR=0] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AP001208.2;DisruptR=;ClosestL=AP001207.3;ClosestR=AP007216.1 101450437 69779347 0,0,0 0,0,0 chr8 101451845 101451846 chr8 113801324 113801325 INV NA - - [Svaba_SR=62,Svaba_PE=10],[Manta_PE=24,Manta_SR=0],[Lumpy_PE=5,Lumpy_SR=15] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=EIF3E|Tier1,UBR5|Tier1,RSPO2|Tier1,CSMD3|Tier2;DisruptL=AP001208.2;DisruptR=;ClosestL=AP001207.3;ClosestR= 101450437 113847102 5,101451839,113801145 0,0,0 chr8 102577650 102577651 chr8 102826797 102826798 DUP NA - + [Manta_PE=5,Manta_SR=4],[Lumpy_PE=3,Lumpy_SR=4] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=AZIN1;ClosestL=ODF1;ClosestR=GASAL1 101450437 101450437 4,102577656,102826804 0,0,0 chr8 112077674 112077675 chr8 112087837 112087838 DEL NA + - [Svaba_SR=16,Svaba_PE=22],[Manta_PE=21,Manta_SR=14],[Lumpy_PE=12,Lumpy_SR=9] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 113847102 113847102 13,112077673,112087837 0,0,0 chr8 113730713 113730714 chr8 113847230 113847231 INV NA + + [Svaba_SR=34,Svaba_PE=31],[Manta_PE=32,Manta_SR=27],[Lumpy_PE=29,Lumpy_SR=22] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 113847102 113847103 20,113730714,113847231 0,0,0 chr8 113801314 113801315 chr11 69780162 69780163 TRA NA + + [Svaba_SR=69,Svaba_PE=79],[Manta_PE=78,Manta_SR=58],[Lumpy_PE=51,Lumpy_SR=49] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR=FGF4 113847102 69779347 45,113801316,69780163 0,0,0 chr8 113801461 113801462 chr11 69897286 69897287 TRA NA + - [Svaba_SR=54,Svaba_PE=42],[Manta_PE=39,Manta_SR=50],[Lumpy_PE=24,Lumpy_SR=39] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR=AP007216.1 113847102 69779347 37,113801459,69897286 0,0,0 chr8 113817587 113817588 chr8 114411853 114411854 INV NA - - [Svaba_SR=52,Svaba_PE=42],[Manta_PE=45,Manta_SR=45],[Lumpy_PE=26,Lumpy_SR=31] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=;ClosestL=;ClosestR= 113847102 114412877 33,113817589,114411853 0,0,0 chr8 117297894 117297895 chr8 117323013 117323014 DEL NA + - [Svaba_SR=24,Svaba_PE=25],[Manta_PE=25,Manta_SR=18],[Lumpy_PE=17,Lumpy_SR=16] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=;ClosestL=RF00322;ClosestR=RF00322 114412878 114412878 20,117297889,117323013 0,0,0 chr8 118959452 118959453 chr16 67651851 67651852 TRA NA - - [Svaba_SR=17,Svaba_PE=4],[Manta_PE=4,Manta_SR=14],[Lumpy_PE=2,Lumpy_SR=10] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=CARMIL2;ClosestL=TNFRSF11B;ClosestR=ACD 121696690 90226217 14,118959451,67651851 0,0,0 chr8 118959598 118959599 chr9 131565190 131565191 TRA NA + + [Svaba_SR=24,Svaba_PE=8],[Manta_PE=8,Manta_SR=20],[Lumpy_PE=8,Lumpy_SR=12] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=TNFRSF11B;ClosestR=PRRT1B 121696690 138313848 16,118959600,131565191 0,0,0 chr8 122992392 122992393 chr8 123075947 123075948 DEL NA + - [Svaba_SR=59,Svaba_PE=64],[Manta_PE=52,Manta_SR=53],[Lumpy_PE=30,Lumpy_SR=41] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=TBC1D31;ClosestL=AC104316.2;ClosestR= 121696691 121696691 10,122992391,123075947 0,0,0 chr8 143023980 143023981 chr8 143042570 143042571 DEL NA + - [Svaba_SR=40,Svaba_PE=41],[Manta_PE=38,Manta_SR=29],[Lumpy_PE=30,Lumpy_SR=23] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=C8orf31;ClosestL=LY6E;ClosestR=AK3P2 145078494 145078494 24,143023978,143042570 0,0,0 chr8 144267751 144267752 chr8 144315558 144315559 DEL NA + - [Svaba_SR=18,Svaba_PE=31],[Manta_PE=29,Manta_SR=17],[Lumpy_PE=21,Lumpy_SR=13] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SCX,BOP1;DisruptR=DGAT1;Fusion=DGAT1+BOP1;ClosestL=MIR7112;ClosestR=AC233992.1 145078494 145078494 14,144267746,144315558 0,0,0 chr9 42783552 42783553 chr9 64784638 64784639 INV NA - - [Manta_PE=3,Manta_SR=7] manta HCC-1143_80--HCC-1143BL_40 known=;gap;DisruptL=;DisruptR=;ClosestL=ADGRF5P2;ClosestR=IGKV1OR-2 45516998 66040021 6,42783556,64784635 0,0,0 chr9 72457967 72457968 chr17 1788610 1788611 TRA NA + + [Svaba_SR=20,Svaba_PE=4],[Manta_PE=4,Manta_SR=20],[Lumpy_PE=3,Lumpy_SR=9] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=SMYD4;ClosestL=AL445646.1;ClosestR=SERPINF1 66040022 168977 14,72457969,1788612 0,0,0 chr9 72457967 72457968 chr17 35740200 35740201 TRA NA + - [Svaba_SR=0,Svaba_PE=12],[Manta_PE=12,Manta_SR=0] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=RASL10B,TAF15;ClosestL=AL445646.1;ClosestR=GAS2L2 66040022 36041470 0,0,0 0,0,0 chr9 94312707 94312708 chr9 94313512 94313513 DEL NA + - [Manta_PE=6,Manta_SR=24] manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;ClosestL=NUTM2F;ClosestR=NUTM2F 66040022 66040022 25,94312709,94313513 0,0,0 chr9 113363750 113363751 chr9 113614603 113614604 DUP NA - + [Svaba_SR=17,Svaba_PE=12],[Manta_PE=11,Manta_SR=16],[Lumpy_PE=10,Lumpy_SR=2] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=BSPRY;DisruptR=AL162727.3;ClosestL=HDHD3;ClosestR=AL162727.1 138313848 138313848 12,113363742,113614609 0,0,0 chr9 119084714 119084715 chr19 4778382 4778383 TRA NA + - [Manta_PE=4,Manta_SR=0] manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR=MIR7-3HG 138313848 90733 5,119084537,4778353 0,0,0 chr9 123290032 123290033 chr11 76901313 76901314 TRA NA + - [Svaba_SR=34,Svaba_PE=24],[Manta_PE=19,Manta_SR=28],[Lumpy_PE=10,Lumpy_SR=21] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=;DisruptR=ACER3;ClosestL=;ClosestR= 138313848 78640369 22,123290034,76901313 0,0,0 chr9 126949538 126949539 chr9 127070386 127070387 DEL NA + - [Svaba_SR=24,Svaba_PE=23],[Manta_PE=4,Manta_SR=18] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=RALGPS1;DisruptR=RALGPS1;ClosestL=;ClosestR=ANGPTL2 138313848 138313848 22,126949537,127070386 0,0,0 chr9 131564960 131564961 chr13 24968358 24968359 TRA NA - - [Svaba_SR=0,Svaba_PE=28],[Manta_PE=24,Manta_SR=22] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=TPTE2P1;ClosestL=PRRT1B;ClosestR= 138313848 24952906 20,131564960,24968358 0,0,0 chr10 73043 73044 chr12 68509747 68509748 TRA NA + + [Svaba_SR=18,Svaba_PE=13],[Manta_PE=16,Manta_SR=14],[Lumpy_PE=9,Lumpy_SR=9] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TUBB8;DisruptR=;ClosestL=IL9RP2;ClosestR= 10287 67923116 13,73044,68509748 0,0,0 chr10 6816583 6816584 chr17 67550458 67550459 TRA NA - - [Lumpy_PE=2,Lumpy_SR=2] lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC00707;DisruptR=PITPNC1;ClosestL=;ClosestR= 3411102 67102560 3,6816595,67550441 0,0,0 chr10 14933901 14933902 chr10 15104285 15104286 DEL NA + - [Manta_PE=2,Manta_SR=5] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=DCLRE1C;DisruptR=RPP38,NMT2;Fusion=NMT2+DCLRE1C;ClosestL=;ClosestR=C10orf111 23965103 23965103 4,14933903,15104285 0,0,0 chr10 23965110 23965111 chr10 27758065 27758066 DUP NA - + [Svaba_SR=26,Svaba_PE=23],[Manta_PE=17,Manta_SR=20],[Lumpy_PE=15,Lumpy_SR=17] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;Cancer_census=ABI1|Tier1;DisruptL=KIAA1217;DisruptR=MKX-AS1;Fusion=MKX-AS1+KIAA1217;ClosestL=;ClosestR=MKX 23965104 27758014 17,23965110,27758066 0,0,0 chr10 29469448 29469449 chr10 29471183 29471184 DEL NA + - [Svaba_SR=11,Svaba_PE=11],[Manta_PE=11,Manta_SR=10],[Lumpy_PE=7,Lumpy_SR=4] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SVIL-AS1,SVIL;DisruptR=SVIL-AS1,SVIL;ClosestL=;ClosestR= 29240716 29240716 9,29469450,29471177 0,0,0 chr10 38955179 38955180 chr22 25537608 25537609 TRA NA + + [Manta_PE=4,Manta_SR=5],[Lumpy_PE=2,Lumpy_SR=4] lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR=CRYBB2P1 39580116 24015969 4,38955181,25537609 0,0,0 chr10 50989426 50989427 chr10 51034007 51034008 DUP NA - + [Svaba_SR=0,Svaba_PE=23],[Manta_PE=20,Manta_SR=60],[Lumpy_PE=45,Lumpy_SR=46] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=PRKG1;ClosestL=PRKG1;ClosestR= 39580117 39580117 17,50989429,51034008 0,0,0 chr10 50989426 50989427 chr10 51269465 51269466 DUP NA - + [Svaba_SR=0,Svaba_PE=32],[Manta_PE=27,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=PRKG1;ClosestL=PRKG1;ClosestR= 39580117 39580117 0,0,0 0,0,0 chr10 51033383 51033384 chr10 51269492 51269493 DUP NA - + [Svaba_SR=0,Svaba_PE=28],[Manta_PE=13,Manta_SR=48],[Lumpy_PE=13,Lumpy_SR=16] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PRKG1;DisruptR=PRKG1;ClosestL=;ClosestR= 39580117 39580117 32,51033385,51269619 0,0,0 chr10 51349436 51349437 chr17 20111624 20111625 TRA NA + - [Manta_PE=0,Manta_SR=26],[Lumpy_PE=2,Lumpy_SR=17] lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=SPECC1|Tier2;DisruptL=PRKG1;DisruptR=SPECC1;Fusion=PRKG1-SPECC1;ClosestL=;ClosestR=KCTD9P1 39580117 21658447 4,51349438,20111624 0,0,0 chr10 52646823 52646824 chr10 52650698 52650699 DEL NA + - [Svaba_SR=31,Svaba_PE=27],[Manta_PE=22,Manta_SR=27],[Lumpy_PE=8,Lumpy_SR=19] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC074327.1;DisruptR=AC074327.1;ClosestL=;ClosestR= 63904755 63904755 20,52646827,52650698 0,0,0 chr10 54306934 54306935 chr10 54494396 54494397 DEL NA + - [Svaba_SR=25,Svaba_PE=25],[Manta_PE=22,Manta_SR=21],[Lumpy_PE=13,Lumpy_SR=18] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=PCDH15;DisruptR=PCDH15,AL353784.1;ClosestL=;ClosestR= 63904755 63904755 18,54306933,54494396 0,0,0 chr10 87097352 87097353 chr10 87201988 87201989 DEL NA + - [Svaba_SR=26,Svaba_PE=35],[Manta_PE=31,Manta_SR=24],[Lumpy_PE=22,Lumpy_SR=3] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SHLD2;DisruptR=;ClosestL=GLUD1;ClosestR=NUTM2A-AS1 63904756 63904756 21,87097352,87201988 0,0,0 chr10 102637238 102637239 chr10 102638085 102638086 DUP NA - + [Svaba_SR=19,Svaba_PE=20],[Manta_PE=4,Manta_SR=17],[Lumpy_PE=4,Lumpy_SR=11] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=SUFU;ClosestR=TRIM8 133787316 133787316 12,102637237,102638086 0,0,0 chr10 105020094 105020095 chr10 105041776 105041777 DEL NA + - [Svaba_SR=14,Svaba_PE=16],[Manta_PE=13,Manta_SR=12],[Lumpy_PE=11,Lumpy_SR=11] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=SORCS3;DisruptR=SORCS3;ClosestL=;ClosestR= 133787316 133787316 11,105020091,105041776 0,0,0 chr10 118059368 118059369 chr10 118078970 118078971 DEL NA + - [Svaba_SR=9,Svaba_PE=10],[Manta_PE=11,Manta_SR=9],[Lumpy_PE=7,Lumpy_SR=8] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=CASC2;DisruptR=CASC2;ClosestL=RAB11FIP2;ClosestR= 133787316 133787316 9,118059365,118078970 0,0,0 chr10 126525712 126525713 chr10 126567394 126567395 INV NA - - [Svaba_SR=19,Svaba_PE=21],[Manta_PE=19,Manta_SR=15],[Lumpy_PE=13,Lumpy_SR=12] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=C10orf90;DisruptR=C10orf90;ClosestL=;ClosestR= 133787316 133787316 11,126525711,126567394 0,0,0 chr10 126526972 126526973 chr10 126555979 126555980 DUP NA - + [Svaba_SR=21,Svaba_PE=24],[Manta_PE=20,Manta_SR=18],[Lumpy_PE=17,Lumpy_SR=13] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=C10orf90;DisruptR=C10orf90;ClosestL=;ClosestR= 133787316 133787316 16,126526971,126555981 0,0,0 chr11 6030233 6030234 chr11 7289788 7289789 INV NA - - [Svaba_SR=54,Svaba_PE=43],[Manta_PE=59,Manta_SR=53],[Lumpy_PE=36,Lumpy_SR=38] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=OR56A1;DisruptR=SYT9;Fusion=OR56A1+SYT9;ClosestL=RNA5SP329;ClosestR= 4827728 7289778 35,6030230,7289788 0,0,0 chr11 6378402 6378403 chr11 54541035 54541036 INV NA + + [Svaba_SR=0,Svaba_PE=43],[Manta_PE=45,Manta_SR=27],[Lumpy_PE=39,Lumpy_SR=16] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=MYOD1|Tier1,FANCF|Tier1,WT1|Tier1,LMO2|Tier1,CREB3L1|Tier1,DDB2|Tier1,LMO1|Tier1,EXT2|Tier1;DisruptL=;DisruptR=;ClosestL=SMPD1;ClosestR= 7289777 54537483 0,0,0 0,0,0 chr11 8415293 8415294 chr11 8417394 8417395 DEL NA + - [Svaba_SR=25,Svaba_PE=27],[Manta_PE=25,Manta_SR=24],[Lumpy_PE=20,Lumpy_SR=14] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=STK33;DisruptR=STK33;ClosestL=;ClosestR= 7844447 7844447 16,8415300,8417393 0,0,0 chr11 10522055 10522056 chr11 36593163 36593164 DEL NA + - [Svaba_SR=48,Svaba_PE=58],[Manta_PE=51,Manta_SR=46],[Lumpy_PE=35,Lumpy_SR=35] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=MYOD1|Tier1,FANCF|Tier1,WT1|Tier1,LMO2|Tier1;DisruptL=RNF141;DisruptR=RAG2;Fusion=RAG2+RNF141;ClosestL=MTRNR2L8;ClosestR=RAG1 10522051 36593150 34,10522054,36593163 0,0,0 chr11 11283180 11283181 chr11 39290286 39290287 DUP NA - + [Svaba_SR=48,Svaba_PE=58],[Manta_PE=55,Manta_SR=44],[Lumpy_PE=49,Lumpy_SR=30] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=MYOD1|Tier1,FANCF|Tier1,WT1|Tier1,LMO2|Tier1;DisruptL=GALNT18;DisruptR=;ClosestL=;ClosestR= 11283094 39290297 40,11283185,39290287 0,0,0 chr11 12343695 12343696 chr11 49740754 49740755 INV NA + + [Svaba_SR=40,Svaba_PE=42],[Manta_PE=43,Manta_SR=34],[Lumpy_PE=34,Lumpy_SR=26] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;Cancer_census=MYOD1|Tier1,FANCF|Tier1,WT1|Tier1,LMO2|Tier1,CREB3L1|Tier1,DDB2|Tier1,EXT2|Tier1;DisruptL=MICAL2;DisruptR=AC136759.1;ClosestL=;ClosestR= 12343416 49740713 27,12343696,49740765 0,0,0 chr11 18360996 18360997 chr11 18393125 18393126 DEL NA + - [Svaba_SR=18,Svaba_PE=22],[Manta_PE=22,Manta_SR=15],[Lumpy_PE=14,Lumpy_SR=10] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=GTF2H1;DisruptR=;ClosestL=;ClosestR=LDHA 12343416 12343416 15,18360997,18393125 0,0,0 chr11 47996838 47996839 chr11 51712926 51712927 INV NA - - [Manta_PE=3,Manta_SR=20] manta HCC-1143_80--HCC-1143BL_40 known=;gap;DisruptL=PTPRJ;DisruptR=;ClosestL=PTPRJ-AS1;ClosestR= 48860163 49740713 24,47996839,51712926 0,0,0 chr11 48037649 48037650 chr11 48243138 48243139 INV NA + + [Svaba_SR=37,Svaba_PE=51],[Manta_PE=58,Manta_SR=31],[Lumpy_PE=56,Lumpy_SR=17] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=PTPRJ;DisruptR=;ClosestL=;ClosestR=OR4X2 48860163 48860163 27,48037651,48243139 0,0,0 chr11 48423266 48423267 chr11 48845188 48845189 INV NA - - [Svaba_SR=30,Svaba_PE=27],[Manta_PE=36,Manta_SR=26],[Lumpy_PE=27,Lumpy_SR=12] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=;ClosestL=OR4C2P;ClosestR= 48860163 48860163 24,48423265,48845188 0,0,0 chr11 58190284 58190285 chr11 62369331 62369332 DEL NA + - [Svaba_SR=40,Svaba_PE=51],[Manta_PE=39,Manta_SR=36] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=FEN1|Tier2,SDHAF2|Tier1;DisruptL=OR9Q2;DisruptR=ASRGL1;Fusion=OR9Q2+ASRGL1;ClosestL=OR9Q1;ClosestR=RCC2P6 58828468 60292996 29,58190284,62369331 0,0,0 chr11 58902609 58902610 chrX 56991096 56991097 TRA NA - - [Svaba_SR=34,Svaba_PE=27],[Manta_PE=28,Manta_SR=30] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=GLYATL2;DisruptR=SPIN3;ClosestL=GLYATL1;ClosestR=AL139397.1 58828469 56991084 0,0,0 0,0,0 chr11 59869579 59869580 chr11 65511687 65511688 DUP NA - + [Svaba_SR=34,Svaba_PE=13],[Manta_PE=11,Manta_SR=0] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=FEN1|Tier2,MEN1|Tier1,MALAT1|Tier2,SDHAF2|Tier1;DisruptL=;DisruptR=;ClosestL=TCN1;ClosestR=SNRPGP19 59869483 65505150 0,0,0 0,0,0 chr11 59869579 59869580 chr11 68509921 68509922 DUP NA - + [Svaba_SR=30,Svaba_PE=7],[Manta_PE=7,Manta_SR=25] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=FEN1|Tier2,MEN1|Tier1,MALAT1|Tier2,SDHAF2|Tier1;DisruptL=;DisruptR=PPP6R3;ClosestL=TCN1;ClosestR= 59869483 69098161 0,0,0 0,0,0 chr11 60085406 60085407 chr13 110454732 110454733 TRA NA - - [Svaba_SR=22,Svaba_PE=22],[Manta_PE=24,Manta_SR=21],[Lumpy_PE=13,Lumpy_SR=12] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=COL4A2;ClosestL=MS4A2;ClosestR=COL4A2-AS2 60292995 110418576 14,60085405,110454726 0,0,0 chr11 60279269 60279270 chr11 62579531 62579532 INV NA + + [Svaba_SR=34,Svaba_PE=39],[Manta_PE=41,Manta_SR=30],[Lumpy_PE=37,Lumpy_SR=26] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;Cancer_census=FEN1|Tier2,SDHAF2|Tier1;DisruptL=;DisruptR=AP002990.1,TUT1;ClosestL=MS4A4A;ClosestR=EEF1G 60292995 60292996 28,60279270,62579532 0,0,0 chr11 60292660 60292661 chr11 60293218 60293219 INV NA + + [Svaba_SR=18,Svaba_PE=24],[Manta_PE=23,Manta_SR=14],[Lumpy_PE=19,Lumpy_SR=9] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=MS4A4A;DisruptR=MS4A4A;ClosestL=;ClosestR= 60292995 60292996 12,60292660,60293219 0,0,0 chr11 63930760 63930761 chr11 63934315 63934316 INV NA + + [Svaba_SR=36,Svaba_PE=24],[Manta_PE=25,Manta_SR=31] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=NAA40;ClosestR=NAA40 65505149 65505149 28,63930729,63934316 0,0,0 chr11 63930764 63930765 chr11 63935811 63935812 INV NA - - [Manta_PE=83,Manta_SR=60],[Lumpy_PE=52,Lumpy_SR=35] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;ClosestL=NAA40;ClosestR=NAA40 65505149 65505149 47,63930766,63935810 0,0,0 chr11 65505167 65505168 chr11 68509680 68509681 DUP NA - + [Svaba_SR=46,Svaba_PE=9],[Manta_PE=9,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=MALAT1;DisruptR=PPP6R3;Fusion=PPP6R3+MALAT1;ClosestL=RF01684;ClosestR= 65505150 69098161 0,0,0 0,0,0 chr11 65511293 65511294 chr12 33652636 33652637 TRA NA - - [Svaba_SR=24,Svaba_PE=0],[Manta_PE=20,Manta_SR=21],[Lumpy_PE=10,Lumpy_SR=21] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=SNRPGP19;ClosestR= 65505150 56255606 18,65511296,33652636 0,0,0 chr11 67780632 67780633 chr12 125881063 125881064 TRA NA + - [Svaba_SR=25,Svaba_PE=17],[Manta_PE=20,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=4] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=ALG1L8P;ClosestR=AC005252.1 67782749 125881976 0,0,0 0,0,0 chr11 67780880 67780881 chr12 33653292 33653293 TRA NA - + [Svaba_SR=0,Svaba_PE=11],[Manta_PE=11,Manta_SR=0] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=ALG1L8P;ClosestR= 67782749 56255606 0,0,0 0,0,0 chr11 68509503 68509504 chr12 33653292 33653293 TRA NA - + [Svaba_SR=16,Svaba_PE=14],[Manta_PE=15,Manta_SR=14],[Lumpy_PE=11,Lumpy_SR=10] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PPP6R3;DisruptR=;ClosestL=;ClosestR= 69098161 56255606 11,68509504,33653293 0,0,0 chr11 69098215 69098216 chr11 69099668 69099669 INV NA - - [Svaba_SR=113,Svaba_PE=106],[Manta_PE=197,Manta_SR=168],[Lumpy_PE=132,Lumpy_SR=128] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TPCN2;DisruptR=TPCN2;ClosestL=AP003071.1;ClosestR=AP003071.1 69098162 69098162 0,0,0 0,0,0 chr11 69189129 69189130 chr12 108227528 108227529 TRA NA - - [Manta_PE=10,Manta_SR=0] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=WSCD2;ClosestL=AP003071.2;ClosestR= 69098162 112325530 3,69189098,108227720 0,0,0 chr11 69757101 69757102 chr11 69769201 69769202 INV NA + + [Svaba_SR=0,Svaba_PE=86],[Manta_PE=108,Manta_SR=0] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=FGF4;ClosestR=FGF4 69779346 69779346 0,0,0 0,0,0 chr11 69757101 69757102 chr14 21263990 21263991 TRA NA + + [Svaba_SR=137,Svaba_PE=62],[Manta_PE=68,Manta_SR=142],[Lumpy_PE=17,Lumpy_SR=106] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=HNRNPC;ClosestL=FGF4;ClosestR= 69779346 21264197 71,69757103,21263991 0,0,0 chr11 69769200 69769201 chr14 21263862 21263863 TRA NA + - [Svaba_SR=133,Svaba_PE=49],[Manta_PE=56,Manta_SR=118],[Lumpy_PE=16,Lumpy_SR=101] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=;DisruptR=HNRNPC;ClosestL=FGF4;ClosestR= 69779346 21264197 68,69769197,21263862 0,0,0 chr11 73534605 73534606 chr11 73698866 73698867 DUP NA - + [Svaba_SR=8,Svaba_PE=23],[Manta_PE=23,Manta_SR=0],[Lumpy_PE=22,Lumpy_SR=1] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=FAM168A;DisruptR=RAB6A;Fusion=FAM168A+RAB6A;ClosestL=;ClosestR= 73059915 73059915 0,0,0 0,0,0 chr11 76901510 76901511 chr22 28499618 28499619 TRA NA + - [Svaba_SR=28,Svaba_PE=14],[Manta_PE=14,Manta_SR=28],[Lumpy_PE=11,Lumpy_SR=16] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=ACER3;DisruptR=TTC28;ClosestL=;ClosestR= 78640369 29344638 0,0,0 0,0,0 chr11 80765276 80765277 chrX 87668752 87668753 TRA NA + + [Manta_PE=7,Manta_SR=8],[Lumpy_PE=2,Lumpy_SR=7] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=KLHL4;ClosestL=AP002759.1;ClosestR= 80765305 87101847 7,80765278,87668753 0,0,0 chr11 121197469 121197470 chr11 121472976 121472977 DUP NA - + [Svaba_SR=20,Svaba_PE=13],[Manta_PE=14,Manta_SR=14],[Lumpy_PE=10,Lumpy_SR=3] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=SORL1;ClosestL=TECTA;ClosestR=AP000977.1 121197407 121473002 10,121197470,121472977 0,0,0 chr12 25346053 25346054 chr12 25347333 25347334 DUP NA - + [Svaba_SR=17,Svaba_PE=22],[Manta_PE=20,Manta_SR=17],[Lumpy_PE=17,Lumpy_SR=13] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 41087 41087 14,25346052,25347334 0,0,0 chr12 37654140 37654141 chr12 37658683 37658684 DUP NA - + [Svaba_SR=22,Svaba_PE=5],[Manta_PE=18,Manta_SR=21],[Lumpy_PE=24,Lumpy_SR=7] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 56255606 56255606 0,0,0 0,0,0 chr12 37654199 37654200 chr12 37658674 37658675 DEL NA + - [Svaba_SR=22,Svaba_PE=7],[Lumpy_PE=4,Lumpy_SR=8] svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 56255606 56255606 11,37654199,37658664 0,0,0 chr12 37654199 37654200 chr12 37658947 37658948 INV NA + + [Svaba_SR=34,Svaba_PE=11],[Manta_PE=6,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 56255606 56255606 0,0,0 0,0,0 chr12 37654605 37654606 chr12 37658765 37658766 INV NA - - [Svaba_SR=18,Svaba_PE=17],[Manta_PE=22,Manta_SR=13],[Lumpy_PE=23,Lumpy_SR=9] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 56255606 56255606 10,37654609,37658765 0,0,0 chr12 37654614 37654615 chr12 37658938 37658939 DEL NA + - [Svaba_SR=13,Svaba_PE=0],[Manta_PE=24,Manta_SR=16],[Lumpy_PE=13,Lumpy_SR=8] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 56255606 56255606 14,37654612,37658938 0,0,0 chr12 37656929 37656930 chr12 38268739 38268740 INV NA + + [Svaba_SR=31,Svaba_PE=19],[Manta_PE=21,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=RF00019 56255606 56255606 0,0,0 0,0,0 chr12 37657372 37657373 chr12 38301158 38301159 INV NA - - [Svaba_SR=23,Svaba_PE=21],[Manta_PE=23,Manta_SR=20],[Lumpy_PE=15,Lumpy_SR=15] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=ALG10B 56255606 56255606 18,37657369,38301158 0,0,0 chr12 49263676 49263677 chr12 49265087 49265088 DEL NA + - [Svaba_SR=20,Svaba_PE=29],[Manta_PE=27,Manta_SR=18],[Lumpy_PE=21,Lumpy_SR=12] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TUBA1C,AC010173.1;DisruptR=TUBA1C;ClosestL=AC125611.3;ClosestR=AC125611.3 56255606 56255606 14,49263672,49265087 0,0,0 chr12 56255681 56255682 chr12 61144864 61144865 DUP NA - + [Svaba_SR=60,Svaba_PE=71],[Manta_PE=63,Manta_SR=54],[Lumpy_PE=52,Lumpy_SR=39] svaba,lumpy,manta 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=;ClosestL=COQ10A;ClosestR= 56255607 61144794 37,56255678,61144868 0,0,0 chr12 65713913 65713914 chr12 112325570 112325571 INV NA - - [Svaba_SR=100,Svaba_PE=147],[Manta_PE=358,Manta_SR=343],[Lumpy_PE=203,Lumpy_SR=299] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=BTG1|Tier1,PTPRB|Tier1,USP44|Tier2,SH2B3|Tier1,HMGA2|Tier1,MDM2|Tier1,CHST11|Tier2,ALDH2|Tier2;DisruptL=;DisruptR=HECTD4;ClosestL=;ClosestR=AC004217.2 65713850 112325531 2,65713911,112325575 0,0,0 chr12 65856872 65856873 chr12 67766189 67766190 DEL NA + - [Svaba_SR=22,Svaba_PE=20],[Manta_PE=16,Manta_SR=20],[Lumpy_PE=8,Lumpy_SR=20] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=HMGA2|Tier1;DisruptL=AC090673.1,HMGA2;DisruptR=;ClosestL=;ClosestR=AC022513.1 65713850 67923115 18,65856873,67766189 0,0,0 chr12 66145833 66145834 chr12 66682452 66682453 DUP NA - + [Svaba_SR=30,Svaba_PE=40],[Manta_PE=34,Manta_SR=25],[Lumpy_PE=26,Lumpy_SR=23] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC078927.1,TMBIM4;DisruptR=GRIP1;Fusion=AC078927.1+GRIP1|TMBIM4+GRIP1;ClosestL=LLPH-DT;ClosestR= 65713850 65713850 22,66145834,66682453 0,0,0 chr12 66362648 66362649 chr12 68497810 68497811 DUP NA - + [Svaba_SR=51,Svaba_PE=65],[Manta_PE=58,Manta_SR=44],[Lumpy_PE=53,Lumpy_SR=31] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=GRIP1;DisruptR=;ClosestL=HELB;ClosestR=AC008033.2 65713850 67923116 32,66362649,68497811 0,0,0 chr12 66410668 66410669 chr12 69873475 69873476 DEL NA + - [Svaba_SR=12,Svaba_PE=22],[Manta_PE=28,Manta_SR=20],[Lumpy_PE=23,Lumpy_SR=14] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=MDM2|Tier1;DisruptL=GRIP1;DisruptR=MYRFL;ClosestL=;ClosestR=AC025263.2 65713850 69869147 19,66410665,69873475 0,0,0 chr12 66453482 66453483 chr12 68613971 68613972 DEL NA + - [Svaba_SR=65,Svaba_PE=61],[Manta_PE=54,Manta_SR=51],[Lumpy_PE=33,Lumpy_SR=39] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=GRIP1;DisruptR=RAP1B;ClosestL=;ClosestR=RPL10P12 65713850 67923116 40,66453484,68613971 0,0,0 chr12 67919941 67919942 chr12 67923109 67923110 INV NA + + [Svaba_SR=84,Svaba_PE=88],[Manta_PE=90,Manta_SR=78],[Lumpy_PE=76,Lumpy_SR=62] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;ClosestL=LINC01479;ClosestR=LINC01479 67923115 67923115 24,67919943,67923110 0,0,0 chr12 69782621 69782622 chr12 69869191 69869192 DEL NA + - [Svaba_SR=163,Svaba_PE=187],[Manta_PE=168,Manta_SR=149],[Lumpy_PE=105,Lumpy_SR=120] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=RAB3IP;DisruptR=MYRFL;Fusion=RAB3IP+MYRFL;ClosestL=AC025263.2;ClosestR=AC025263.2 69782593 69869147 80,69782622,69869191 0,0,0 chr12 69967248 69967249 chr12 70003771 70003772 INV NA + + [Svaba_SR=18,Svaba_PE=20],[Manta_PE=21,Manta_SR=11],[Lumpy_PE=18,Lumpy_SR=9] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC025159.1;DisruptR=AC025159.1;ClosestL=MYRFL;ClosestR= 69869147 69869147 11,69967248,70003772 0,0,0 chr12 71972105 71972106 chr12 71993496 71993497 DUP NA - + [Svaba_SR=23,Svaba_PE=22],[Manta_PE=18,Manta_SR=20],[Lumpy_PE=16,Lumpy_SR=12] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TPH2;DisruptR=TPH2;ClosestL=;ClosestR= 71964314 71964314 0,0,0 0,0,0 chr12 71975432 71975433 chr12 72007830 72007831 INV NA - - [Svaba_SR=64,Svaba_PE=66],[Manta_PE=63,Manta_SR=52],[Lumpy_PE=43,Lumpy_SR=36] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=TPH2;DisruptR=TPH2;ClosestL=;ClosestR= 71964314 71964314 39,71975433,72007830 0,0,0 chr12 72510655 72510656 chr12 72511895 72511896 INV NA + + [Svaba_SR=118,Svaba_PE=139],[Manta_PE=144,Manta_SR=113],[Lumpy_PE=120,Lumpy_SR=87] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=TRHDE;DisruptR=TRHDE;ClosestL=;ClosestR= 72511936 72511936 71,72510657,72511896 0,0,0 chr12 72534503 72534504 chr12 72535081 72535082 DUP NA - + [Svaba_SR=15,Svaba_PE=16],[Manta_PE=14,Manta_SR=14],[Lumpy_PE=12,Lumpy_SR=11] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TRHDE;DisruptR=TRHDE;ClosestL=;ClosestR= 72511937 72511937 12,72534504,72535082 0,0,0 chr12 96149120 96149121 chr12 96166173 96166174 DEL NA + - [Svaba_SR=25,Svaba_PE=25],[Manta_PE=22,Manta_SR=23],[Lumpy_PE=16,Lumpy_SR=17] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=LINC02452;ClosestL=LINC02452;ClosestR= 112325530 112325530 20,96149120,96166173 0,0,0 chr12 101739295 101739296 chr12 101984856 101984857 DUP NA - + [Svaba_SR=24,Svaba_PE=25],[Manta_PE=21,Manta_SR=15],[Lumpy_PE=18,Lumpy_SR=10] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SYCP3,CHPT1;DisruptR=DRAM1;Fusion=DRAM1+CHPT1;ClosestL=GNPTAB;ClosestR= 112325530 112325530 12,101739295,101984857 0,0,0 chr12 112316935 112316936 chr12 112384855 112384856 DUP NA - + [Svaba_SR=160,Svaba_PE=194],[Manta_PE=171,Manta_SR=145],[Lumpy_PE=151,Lumpy_SR=56] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=HECTD4;DisruptR=;ClosestL=AC004217.2;ClosestR=HECTD4 112325530 112386380 75,112316936,112384856 0,0,0 chr12 112317527 112317528 chr12 112386389 112386390 INV NA + + [Svaba_SR=154,Svaba_PE=128],[Manta_PE=178,Manta_SR=156],[Lumpy_PE=155,Lumpy_SR=129] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=HECTD4;DisruptR=;ClosestL=AC004217.2;ClosestR=HECTD4 112325530 112386381 82,112317526,112386390 0,0,0 chr13 25024466 25024467 chr13 25030471 25030472 DEL NA + - [Svaba_SR=21,Svaba_PE=22],[Manta_PE=23,Manta_SR=21],[Lumpy_PE=17,Lumpy_SR=9] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;ClosestL=AL590099.1;ClosestR=AL590099.1 24952906 24952906 18,25024465,25030471 0,0,0 chr13 28880457 28880458 chr13 98509424 98509425 DEL NA + - [Svaba_SR=47,Svaba_PE=66],[Manta_PE=58,Manta_SR=43],[Lumpy_PE=38,Lumpy_SR=36] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;gap;Cancer_census=CYSLTR2|Tier2,SOX21|Tier2,BRCA2|Tier1,LHFP|Tier2,FOXO1|Tier1,RB1|Tier1,NBEA|Tier2,LCP1|Tier2,GPC5|Tier2;DisruptL=MTUS2;DisruptR=STK24;ClosestL=;ClosestR= 28880402 98509395 37,28880457,98509424 0,0,0 chr13 97331894 97331895 chr13 97689069 97689070 DEL NA + - [Svaba_SR=31,Svaba_PE=28],[Manta_PE=19,Manta_SR=24],[Lumpy_PE=16,Lumpy_SR=15] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=MBNL2;DisruptR=;ClosestL=;ClosestR=AL359502.1 97331911 97689209 18,97331894,97689069 0,0,0 chr13 101085680 101085681 chr13 101107648 101107649 DEL NA + - [Svaba_SR=11,Svaba_PE=23],[Manta_PE=25,Manta_SR=9],[Lumpy_PE=19,Lumpy_SR=7] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=NALCN;DisruptR=NALCN;ClosestL=;ClosestR= 98509395 98509395 9,101085680,101107648 0,0,0 chr13 102238357 102238358 chr21 18481781 18481782 TRA NA - + [Svaba_SR=4,Svaba_PE=8],[Manta_PE=10,Manta_SR=5],[Lumpy_PE=9,Lumpy_SR=3] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=FGF14;DisruptR=TMPRSS15,AL109763.1;Fusion=FGF14-TMPRSS15|FGF14-AL109763.1;ClosestL=;ClosestR= 98509395 18484759 4,102238356,18481782 0,0,0 chr13 104720020 104720021 chr21 17226145 17226146 TRA NA - + [Lumpy_PE=2,Lumpy_SR=3] lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR=NEK4P1 107326494 17474345 3,104720018,17226145 0,0,0 chr13 107327055 107327056 chr18 3047589 3047590 TRA NA - - [Manta_PE=20,Manta_SR=0] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=FAM155A;DisruptR=;ClosestL=SNORD31B;ClosestR=MYOM1 107326495 3047603 0,0,0 0,0,0 chr13 107559859 107559860 chr13 108859484 108859485 DUP NA - + [Lumpy_PE=9,Lumpy_SR=4] lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=FAM155A;DisruptR=MYO16;ClosestL=;ClosestR= 107326495 107326495 5,107559859,108859484 0,0,0 chr13 107560030 107560031 chr13 108859489 108859490 INV NA - - [Svaba_SR=21,Svaba_PE=19],[Manta_PE=20,Manta_SR=18],[Lumpy_PE=3,Lumpy_SR=16] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=FAM155A;DisruptR=MYO16;Fusion=FAM155A+MYO16;ClosestL=;ClosestR= 107326495 107326495 17,107560032,108859489 0,0,0 chr13 107560301 107560302 chr13 108954298 108954299 DEL NA + - [Svaba_SR=24,Svaba_PE=27],[Manta_PE=23,Manta_SR=17],[Lumpy_PE=17,Lumpy_SR=13] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=FAM155A;DisruptR=MYO16;ClosestL=;ClosestR= 107326495 110418575 16,107560301,108954298 0,0,0 chr13 108859285 108859286 chr13 108952396 108952397 DEL NA + - [Svaba_SR=26,Svaba_PE=0],[Manta_PE=15,Manta_SR=20] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR= 107326495 110418575 3,108859287,108952275 0,0,0 chr13 108859328 108859329 chr13 108952203 108952204 DUP NA - + [Svaba_SR=24,Svaba_PE=0],[Manta_PE=10,Manta_SR=19] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR= 107326495 110418575 13,108859329,108952204 0,0,0 chr14 20575192 20575193 chr14 21264283 21264284 DUP NA - + [Svaba_SR=35,Svaba_PE=44],[Manta_PE=34,Manta_SR=30],[Lumpy_PE=31,Lumpy_SR=24] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=;DisruptR=HNRNPC;ClosestL=AL163195.3;ClosestR= 20575059 21264198 25,20575195,21264284 0,0,0 chr14 28611660 28611661 chr22 28669767 28669768 TRA NA - + [Svaba_SR=0,Svaba_PE=20],[Lumpy_PE=2,Lumpy_SR=28] lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC02300,TTC28;DisruptR=TTC28;Fusion=LINC02300-TTC28;ClosestL=EIF4A1P12;ClosestR=CHEK2 21264198 29344638 10,28611556,28669768 0,0,0 chr14 32961999 32962000 chr14 32970923 32970924 DEL NA + - [Svaba_SR=80,Svaba_PE=86],[Manta_PE=83,Manta_SR=68],[Lumpy_PE=59,Lumpy_SR=44] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=NPAS3;DisruptR=NPAS3;ClosestL=;ClosestR= 41140316 41140316 44,32961999,32970923 0,0,0 chr14 41463251 41463252 chr14 41474102 41474103 DEL NA + - [Svaba_SR=17,Svaba_PE=18],[Manta_PE=17,Manta_SR=17],[Lumpy_PE=15,Lumpy_SR=2] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 41200381 41200381 0,0,0 0,0,0 chr14 81201605 81201606 chr14 81202852 81202853 DUP NA - + [Svaba_SR=11,Svaba_PE=19],[Manta_PE=19,Manta_SR=0],[Lumpy_PE=15,Lumpy_SR=8] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=GTF2A1;DisruptR=GTF2A1;ClosestL=SNORA79;ClosestR=SNORA79 91109906 91109906 9,81201605,81202853 0,0,0 chr14 91109951 91109952 chr14 91493414 91493415 DUP NA - + [Svaba_SR=49,Svaba_PE=54],[Manta_PE=49,Manta_SR=40],[Lumpy_PE=46,Lumpy_SR=32] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=DGLUCY;DisruptR=PPP4R3A;ClosestL=SNORA11B;ClosestR= 91109907 91493434 28,91109952,91493415 0,0,0 chr14 100903884 100903885 chrX 87668584 87668585 TRA NA - - [Svaba_SR=17,Svaba_PE=3],[Manta_PE=2,Manta_SR=14] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AL117190.1,MEG8;DisruptR=KLHL4;ClosestL=RF02146;ClosestR= 104243063 87101847 8,100903895,87668584 0,0,0 chr14 104243055 104243056 chr14 104326293 104326294 INV NA - - [Svaba_SR=106,Svaba_PE=124],[Manta_PE=123,Manta_SR=88],[Lumpy_PE=86,Lumpy_SR=73] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AL590079.1;DisruptR=;ClosestL=;ClosestR= 104243063 104243064 57,104243056,104326293 0,0,0 chr14 104704163 104704164 chr14 105433354 105433355 DUP NA - + [Svaba_SR=89,Svaba_PE=96],[Manta_PE=82,Manta_SR=82],[Lumpy_PE=68,Lumpy_SR=55] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=AKT1|Tier1;DisruptL=INF2;DisruptR=TEX22,MTA1;Fusion=TEX22+INF2|MTA1+INF2;ClosestL=AL583722.4;ClosestR=AL928654.1 104243064 105433357 54,104704159,105433355 0,0,0 chr14 105117762 105117763 chr14 105352505 105352506 DUP NA - + [Svaba_SR=43,Svaba_PE=61],[Manta_PE=53,Manta_SR=40],[Lumpy_PE=45,Lumpy_SR=35] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=PACS2;ClosestL=AL512356.2;ClosestR=AL928654.4 105433357 105433357 29,105117762,105352506 0,0,0 chr14 105893557 105893558 chr14 105902666 105902667 DUP NA - + [Manta_PE=4,Manta_SR=82] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC246787.2,IGHD5-18;DisruptR=IGHD5-12;Fusion=IGHD5-18+IGHD5-12;ClosestL=IGHD4-17;ClosestR=IGHD4-11 105433358 105433358 5,105893572,105902683 0,0,0 chr15 56746798 56746799 chr15 56751379 56751380 INV NA - - [Svaba_SR=41,Svaba_PE=45],[Manta_PE=49,Manta_SR=31],[Lumpy_PE=36,Lumpy_SR=24] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=AC090517.4;DisruptR=AC090517.4;ClosestL=ZNF280D;ClosestR=ZNF280D 56746779 56746779 27,56746800,56751379 0,0,0 chr15 65803608 65803609 chr18 11294088 11294089 TRA NA - + [Svaba_SR=29,Svaba_PE=29],[Manta_PE=24,Manta_SR=25],[Lumpy_PE=18,Lumpy_SR=17] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=RAB11A;DisruptR=;ClosestL=DENND4A;ClosestR= 65078752 11293418 22,65803604,11294089 0,0,0 chr15 72000221 72000222 chr15 72362565 72362566 DUP NA - + [Svaba_SR=55,Svaba_PE=71],[Manta_PE=70,Manta_SR=44],[Lumpy_PE=66,Lumpy_SR=32] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC022872.1,MYO9A;DisruptR=AC009690.1,HEXA;Fusion=MYO9A+AC009690.1|MYO9A+HEXA;ClosestL=;ClosestR=AC009690.2 72000144 72362589 32,72000222,72362566 0,0,0 chr15 76561965 76561966 chr16 67651996 67651997 TRA NA + + [Manta_PE=1,Manta_SR=18],[Lumpy_PE=5,Lumpy_SR=11] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SCAPER;DisruptR=CARMIL2;Fusion=CARMIL2-SCAPER;ClosestL=;ClosestR=ACD 72362590 90226217 11,76561967,67651997 0,0,0 chr15 84047235 84047236 chr15 84047818 84047819 DEL NA + - [Svaba_SR=47,Svaba_PE=42],[Manta_PE=30,Manta_SR=41],[Lumpy_PE=21,Lumpy_SR=28] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=AC027807.1;ClosestR=AC027807.1 72362590 72362590 33,84047237,84047817 0,0,0 chr16 515531 515532 chr17 22058252 22058253 TRA NA + + [Svaba_SR=12,Svaba_PE=13],[Manta_PE=12,Manta_SR=9] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=RAB11FIP3;DisruptR=;ClosestL=LINC00235;ClosestR=ABBA01006766.1 10005 22044138 6,515530,22058253 0,0,0 chr16 3191703 3191704 chr16 3228907 3228908 DEL NA + - [Svaba_SR=26,Svaba_PE=28],[Manta_PE=28,Manta_SR=22],[Lumpy_PE=19,Lumpy_SR=10] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AJ003147.2;DisruptR=ZNF200;ClosestL=AJ003147.1;ClosestR=AJ003147.2 10005 10005 0,0,0 0,0,0 chr16 24481252 24481253 chr16 24513939 24513940 DEL NA + - [Svaba_SR=48,Svaba_PE=68],[Manta_PE=64,Manta_SR=45],[Lumpy_PE=49,Lumpy_SR=21] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=AC008938.1;DisruptR=;ClosestL=;ClosestR=AC008938.1 34502581 34502581 34,24481254,24513934 0,0,0 chr16 70232878 70232879 chr16 70281139 70281140 DEL NA + - [Svaba_SR=20,Svaba_PE=23],[Manta_PE=4,Manta_SR=19] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SMG1P7;DisruptR=AARS;Fusion=AARS+SMG1P7;ClosestL=EXOSC6;ClosestR=RN7SL279P 90226217 90226217 18,70232878,70281139 0,0,0 chr16 74657089 74657090 chr16 74659685 74659686 DEL NA + - [Manta_PE=4,Manta_SR=5],[Lumpy_PE=3,Lumpy_SR=4] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=RFWD3|Tier2;DisruptL=RFWD3;DisruptR=RFWD3;ClosestL=TMPOP2;ClosestR=TMPOP2 90226217 90226217 5,74657091,74659686 0,0,0 chr16 76745602 76745603 chr16 76759438 76759439 DEL NA + - [Svaba_SR=26,Svaba_PE=20],[Manta_PE=21,Manta_SR=23],[Lumpy_PE=13,Lumpy_SR=18] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC104151.1,AC106729.1;DisruptR=AC104151.1,AC106729.1;Fusion=AC104151.1+AC106729.1|AC106729.1+AC104151.1;ClosestL=;ClosestR= 90226217 90226217 21,76745604,76759438 0,0,0 chr16 89517377 89517378 chr16 89597850 89597851 DUP NA - + [Svaba_SR=13,Svaba_PE=0],[Manta_PE=20,Manta_SR=0],[Lumpy_PE=20,Lumpy_SR=4] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SPG7;DisruptR=;ClosestL=AC092123.1;ClosestR=CPNE7 90226217 90226217 6,89517378,89597851 0,0,0 chr17 1788505 1788506 chr17 35740201 35740202 INV NA - - [Svaba_SR=9,Svaba_PE=0],[Manta_PE=2,Manta_SR=16],[Lumpy_PE=2,Lumpy_SR=3] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=TP53|Tier1,USP6|Tier1,PER1|Tier1,FLCN|Tier1,RABEP1|Tier1,GAS7|Tier1,MAP2K4|Tier1,NCOR1|Tier1,SPECC1|Tier2,NF1|Tier1,SUZ12|Tier1;DisruptL=SMYD4;DisruptR=RASL10B,TAF15;Fusion=SMYD4+RASL10B|SMYD4+TAF15;ClosestL=SERPINF1;ClosestR=GAS2L2 168977 36041470 10,1788505,35740201 0,0,0 chr17 26663483 26663484 chr20 31572794 31572795 TRA NA + + [Manta_PE=4,Manta_SR=3],[Lumpy_PE=2,Lumpy_SR=2] manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=HM13,HM13-AS1;ClosestL=;ClosestR=AL110115.2 22044138 31539739 3,26663485,31572795 0,0,0 chr17 34007794 34007795 chr17 34345231 34345232 INV NA - - [Svaba_SR=33,Svaba_PE=44],[Manta_PE=42,Manta_SR=28],[Lumpy_PE=29,Lumpy_SR=24] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC024610.2,AC004147.4,ASIC2;DisruptR=;ClosestL=AC123769.1;ClosestR=CCL13 34345057 34345058 24,34007794,34345231 0,0,0 chr17 34019945 34019946 chr17 43351893 43351894 DEL NA + - [Svaba_SR=43,Svaba_PE=48],[Manta_PE=43,Manta_SR=36],[Lumpy_PE=29,Lumpy_SR=28] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=CCR7|Tier2,TAF15|Tier1,MLLT6|Tier1,LASP1|Tier1,CDK12|Tier1,RARA|Tier1,ERBB2|Tier1,SMARCE1|Tier1,STAT5B|Tier1,STAT3|Tier1,BRCA1|Tier1;DisruptL=AC024610.2,AC004147.4,ASIC2;DisruptR=;ClosestL=AC123769.1;ClosestR=AC109326.1 34345057 43301597 27,34019945,43351893 0,0,0 chr17 35981786 35981787 chr17 35985681 35985682 INV NA - - [Svaba_SR=30,Svaba_PE=27],[Manta_PE=24,Manta_SR=25],[Lumpy_PE=15,Lumpy_SR=15] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=CCL14,AC244100.2,CCL15-CCL14;ClosestL=CCL16;ClosestR=CCL16 36041470 36041470 21,35981786,35985676 0,0,0 chr17 36183293 36183294 chr17 36184037 36184038 INV NA + + [Svaba_SR=39,Svaba_PE=45],[Manta_PE=37,Manta_SR=32],[Lumpy_PE=32,Lumpy_SR=25] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC243829.1;DisruptR=AC243829.1;ClosestL=AC243829.2;ClosestR=AC243829.2 36041471 36041471 15,36183291,36184038 0,0,0 chr17 39577411 39577412 chr17 39805140 39805141 DUP NA - + [Svaba_SR=41,Svaba_PE=56],[Manta_PE=56,Manta_SR=28],[Lumpy_PE=56,Lumpy_SR=3] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=ERBB2|Tier1;DisruptL=;DisruptR=IKZF3;ClosestL=AC009283.1;ClosestR= 39577425 39805110 28,39577413,39805141 0,0,0 chr17 44549222 44549223 chr17 44628027 44628028 DEL NA + - [Svaba_SR=42,Svaba_PE=46],[Manta_PE=45,Manta_SR=34],[Lumpy_PE=24,Lumpy_SR=22] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=;ClosestL=FZD2;ClosestR=SMCO4P1 43301597 43301597 27,44549223,44628027 0,0,0 chr17 47874904 47874905 chr17 48072313 48072314 DUP NA - + [Svaba_SR=43,Svaba_PE=127],[Manta_PE=114,Manta_SR=82],[Lumpy_PE=95,Lumpy_SR=39] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=CBX1;ClosestL=AC018521.7;ClosestR=AC004477.3 47874813 48072290 2,47874899,48072313 0,0,0 chr17 55526546 55526547 chr17 55537682 55537683 INV NA - - [Svaba_SR=32,Svaba_PE=20],[Manta_PE=13,Manta_SR=26],[Lumpy_PE=9,Lumpy_SR=21] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=AC105021.1;ClosestL=AC105021.1;ClosestR=GARSP1 55607901 55607901 24,55526545,55537682 0,0,0 chr17 55526721 55526722 chr21 41571013 41571014 TRA NA + - [Svaba_SR=28,Svaba_PE=27],[Manta_PE=22,Manta_SR=21],[Lumpy_PE=17,Lumpy_SR=17] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=AC105021.1;ClosestR=AP006748.1 55607901 41825925 20,55526722,41571013 0,0,0 chr17 55527606 55527607 chr17 55538276 55538277 INV NA + + [Svaba_SR=19,Svaba_PE=15],[Manta_PE=15,Manta_SR=16],[Lumpy_PE=12,Lumpy_SR=14] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC105021.1;DisruptR=AC105021.1;ClosestL=SMIM36;ClosestR=GARSP1 55607901 55607901 14,55527605,55538277 0,0,0 chr17 55537681 55537682 chr21 41571012 41571013 TRA NA - - [Svaba_SR=0,Svaba_PE=20],[Manta_PE=16,Manta_SR=0] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC105021.1;DisruptR=;ClosestL=GARSP1;ClosestR=AP006748.1 55607901 41825925 0,0,0 0,0,0 chr17 55607904 55607905 chr17 59518907 59518908 DUP NA - + [Svaba_SR=72,Svaba_PE=97],[Manta_PE=78,Manta_SR=62],[Lumpy_PE=71,Lumpy_SR=21] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=RNF43|Tier1,MSI2|Tier1;DisruptL=;DisruptR=LINC01476;ClosestL=;ClosestR=RNU4-13P 55607902 59518847 47,55607906,59518908 0,0,0 chr17 67102576 67102577 chr17 67113691 67113692 INV NA - - [Svaba_SR=71,Svaba_PE=58],[Manta_PE=62,Manta_SR=59],[Lumpy_PE=43,Lumpy_SR=43] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=HELZ;DisruptR=HELZ;ClosestL=;ClosestR= 67102560 67102560 44,67102576,67113691 0,0,0 chr17 71544176 71544177 chr17 71545941 71545942 DEL NA + - [Svaba_SR=30,Svaba_PE=30],[Manta_PE=27,Manta_SR=30],[Lumpy_PE=20,Lumpy_SR=13] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 67102560 67102560 0,0,0 0,0,0 chr17 72463523 72463524 chr17 72475017 72475018 DEL NA + - [Svaba_SR=21,Svaba_PE=14],[Manta_PE=14,Manta_SR=19],[Lumpy_PE=10,Lumpy_SR=16] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR= 67102560 67102560 16,72463525,72475016 0,0,0 chr17 72466028 72466029 chr17 72472943 72472944 DEL NA + - [Svaba_SR=22,Svaba_PE=19],[Manta_PE=18,Manta_SR=18],[Lumpy_PE=12,Lumpy_SR=15] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR= 67102560 67102560 19,72466023,72472943 0,0,0 chr17 72474704 72474705 chr17 72485602 72485603 DEL NA + - [Svaba_SR=24,Svaba_PE=29],[Manta_PE=27,Manta_SR=21],[Lumpy_PE=20,Lumpy_SR=15] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR= 67102560 67102560 15,72474708,72485598 0,0,0 chr17 72475233 72475234 chr17 72534012 72534013 DEL NA + - [Svaba_SR=22,Svaba_PE=20],[Manta_PE=18,Manta_SR=16],[Lumpy_PE=9,Lumpy_SR=12] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR= 67102560 67102560 13,72475229,72534012 0,0,0 chr17 72487296 72487297 chrX 116501145 116501146 TRA NA + + [Svaba_SR=49,Svaba_PE=20],[Manta_PE=13,Manta_SR=0] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC00511;DisruptR=;ClosestL=;ClosestR= 67102560 116456071 0,0,0 0,0,0 chr17 72487296 72487297 chrX 76243013 76243014 TRA NA + + [Svaba_SR=28,Svaba_PE=14],[Manta_PE=16,Manta_SR=23],[Lumpy_PE=12,Lumpy_SR=16] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=LINC00511;DisruptR=;ClosestL=;ClosestR=RNU6-867P 67102560 76245723 21,72487298,76243018 0,0,0 chr17 81921915 81921916 chr21 14696103 14696104 TRA NA - - [Manta_PE=30,Manta_SR=47] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=MAFG;DisruptR=;ClosestL=SIRT7;ClosestR= 83247341 15873584 35,81921917,14696100 0,0,0 chr17 81922131 81922132 chr21 14696028 14696029 TRA NA + - [Svaba_SR=45,Svaba_PE=31],[Manta_PE=5,Manta_SR=39],[Lumpy_PE=29,Lumpy_SR=27] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=MAFG;DisruptR=;ClosestL=AC145207.8;ClosestR= 83247341 15873584 18,81922133,14696028 0,0,0 chr17 81922131 81922132 chr21 14696627 14696628 TRA NA + - [Svaba_SR=68,Svaba_PE=0],[Manta_PE=29,Manta_SR=40] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=MAFG;DisruptR=;ClosestL=AC145207.8;ClosestR= 83247341 15873584 0,0,0 0,0,0 chr17 81996893 81996894 chr17 81997849 81997850 DEL NA + - [Svaba_SR=2,Svaba_PE=5],[Lumpy_PE=3,Lumpy_SR=2] lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=ASPSCR1|Tier1;DisruptL=ASPSCR1;DisruptR=ASPSCR1;ClosestL=;ClosestR= 83247341 83247341 3,81996896,81997852 0,0,0 chr18 1091199 1091200 chr18 1158740 1158741 DEL NA + - [Svaba_SR=76,Svaba_PE=105],[Manta_PE=97,Manta_SR=62],[Lumpy_PE=76,Lumpy_SR=23] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=AP005328.1;DisruptR=AP005328.1;ClosestL=;ClosestR=AP005265.1 1091193 1158564 47,1091196,1158740 0,0,0 chr18 1442130 1442131 chr18 1517728 1517729 DEL NA + - [Manta_PE=8,Manta_SR=8] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=AC008109.1;ClosestL=;ClosestR= 1158564 1158564 10,1442132,1517729 0,0,0 chr18 1792586 1792587 chr18 30132066 30132067 DUP NA - + [Svaba_SR=4,Svaba_PE=7],[Manta_PE=5,Manta_SR=3],[Lumpy_PE=5,Lumpy_SR=3] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=SS18|Tier1,ZNF521|Tier1;DisruptL=;DisruptR=;ClosestL=AP005057.1;ClosestR= 1158564 30129851 3,1792587,30132067 0,0,0 chr18 2056157 2056158 chr18 2057225 2057226 INV NA + + [Svaba_SR=4,Svaba_PE=5],[Lumpy_PE=6,Lumpy_SR=3] svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AP005230.1;DisruptR=AP005230.1;ClosestL=;ClosestR= 1158564 1158564 4,2056154,2057226 0,0,0 chr18 5693420 5693421 chr18 10125703 10125704 DUP NA - + [Svaba_SR=23,Svaba_PE=20],[Manta_PE=19,Manta_SR=22],[Lumpy_PE=17,Lumpy_SR=7] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=AP005271.1;ClosestL=;ClosestR= 7909753 11293417 21,5693420,10125704 0,0,0 chr18 8331815 8331816 chr18 8670390 8670391 INV NA - - [Svaba_SR=20,Svaba_PE=19],[Manta_PE=20,Manta_SR=18],[Lumpy_PE=16,Lumpy_SR=10] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PTPRM;DisruptR=;ClosestL=;ClosestR=TOMM20P3 7909754 7909754 13,8331814,8670390 0,0,0 chr18 9792146 9792147 chr18 9856621 9856622 DEL NA + - [Svaba_SR=22,Svaba_PE=15],[Manta_PE=17,Manta_SR=19],[Lumpy_PE=12,Lumpy_SR=15] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=RAB31;DisruptR=RAB31;ClosestL=ZNF415P1;ClosestR=RNA5SP449 11293417 11293417 17,9792147,9856621 0,0,0 chr18 11707495 11707496 chr21 9022992 9022993 TRA NA + - [Svaba_SR=38,Svaba_PE=63],[Manta_PE=48,Manta_SR=55] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=GNAL;DisruptR=;ClosestL=;ClosestR=CR392039.2 11707458 13282812 34,11707494,9022992 0,0,0 chr18 14810726 14810727 chr18 14817612 14817613 DEL NA + - [Svaba_SR=16,Svaba_PE=25],[Manta_PE=19,Manta_SR=13],[Lumpy_PE=18,Lumpy_SR=1] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=ANKRD30B;DisruptR=AP006565.1,ANKRD30B;ClosestL=AP006565.1;ClosestR=MIR3156-2 11707458 11707458 12,14810731,14817612 0,0,0 chr18 23307636 23307637 chr20 31539702 31539703 TRA NA - - [Svaba_SR=96,Svaba_PE=114],[Manta_PE=104,Manta_SR=83],[Lumpy_PE=74,Lumpy_SR=48] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=TMEM241;DisruptR=HM13;Fusion=TMEM241-HM13;ClosestL=;ClosestR=AL110115.1 23307596 31539738 52,23307637,31539702 0,0,0 chr18 24278556 24278557 chr18 24279392 24279393 INV NA + + [Svaba_SR=20,Svaba_PE=22],[Manta_PE=20,Manta_SR=17],[Lumpy_PE=16,Lumpy_SR=14] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=OSBPL1A;DisruptR=OSBPL1A;ClosestL=;ClosestR= 24279287 24279288 13,24278557,24279393 0,0,0 chr18 59214242 59214243 chr18 59217204 59217205 DUP NA - + [Svaba_SR=26,Svaba_PE=26],[Manta_PE=25,Manta_SR=25],[Lumpy_PE=20,Lumpy_SR=20] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=GRP;ClosestR=GRP 59280927 59280927 23,59214241,59217205 0,0,0 chr18 59281023 59281024 chr18 60359158 60359159 DEL NA + - [Svaba_SR=14,Svaba_PE=14],[Manta_PE=16,Manta_SR=13],[Lumpy_PE=12,Lumpy_SR=11] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=CPLX4;DisruptR=;ClosestL=RAX;ClosestR=MC4R 59280928 59280928 12,59281019,60359158 0,0,0 chr19 8257771 8257772 chr22 24989957 24989958 TRA NA - - [Svaba_SR=7,Svaba_PE=3],[Manta_PE=4,Manta_SR=6],[Lumpy_PE=2,Lumpy_SR=4] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=CERS4;DisruptR=KIAA1671;ClosestL=AC022146.2;ClosestR=AL022323.3 12858860 24015969 6,8257772,24989957 0,0,0 chr19 8258007 8258008 chr22 24987321 24987322 TRA NA + - [Svaba_SR=4,Svaba_PE=4],[Manta_PE=5,Manta_SR=4],[Lumpy_PE=3,Lumpy_SR=1] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=CERS4;DisruptR=KIAA1671;Fusion=CERS4-KIAA1671;ClosestL=AC022146.2;ClosestR= 12858860 24015969 3,8258009,24987321 0,0,0 chr19 12858913 12858914 chr19 12880038 12880039 DEL NA + - [Svaba_SR=55,Svaba_PE=63],[Manta_PE=48,Manta_SR=49],[Lumpy_PE=33,Lumpy_SR=41] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=HOOK2,MAST1;DisruptR=DNASE2;Fusion=DNASE2+HOOK2;ClosestL=MIR6794;ClosestR=AC020934.2 12858861 12880013 29,12858913,12880038 0,0,0 chr19 14687538 14687539 chr19 14928275 14928276 INV NA - - [Svaba_SR=78,Svaba_PE=59],[Manta_PE=46,Manta_SR=72] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=ADGRE3;DisruptR=;ClosestL=ZNF333;ClosestR=OR7A15P 14687524 14687524 10,14687533,14928269 0,0,0 chr19 14707786 14707787 chr19 14913582 14913583 DUP NA - + [Svaba_SR=107,Svaba_PE=84],[Manta_PE=105,Manta_SR=82],[Lumpy_PE=105,Lumpy_SR=9] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=ZNF333;DisruptR=;ClosestL=ADGRE3;ClosestR=OR7A11P 14687524 14687524 0,0,0 0,0,0 chr19 14928300 14928301 chr19 15379943 15379944 INV NA - - [Svaba_SR=34,Svaba_PE=42],[Manta_PE=44,Manta_SR=31],[Lumpy_PE=35,Lumpy_SR=11] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=BRD4|Tier1;DisruptL=;DisruptR=AC005785.1;ClosestL=OR7A15P;ClosestR=AKAP8L 14687524 15684658 20,14928302,15379943 0,0,0 chr19 15195290 15195291 chr19 15634158 15634159 DUP NA - + [Svaba_SR=0,Svaba_PE=12],[Manta_PE=11,Manta_SR=10],[Lumpy_PE=11,Lumpy_SR=10] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=BRD4|Tier1;DisruptL=NOTCH3;DisruptR=;ClosestL=MIR6795;ClosestR=CYP4F8 15684658 15684658 0,0,0 0,0,0 chr19 15329197 15329198 chr19 20490430 20490431 INV NA + + [Svaba_SR=39,Svaba_PE=42],[Manta_PE=42,Manta_SR=34],[Lumpy_PE=39,Lumpy_SR=13] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=TPM4|Tier1,JAK3|Tier1,ELL|Tier1,CRTC1|Tier1;DisruptL=BRD4;DisruptR=AC008554.1;Fusion=AC008554.1+BRD4;ClosestL=AC005776.1;ClosestR= 15684658 20490395 25,15329201,20490431 0,0,0 chr19 15384118 15384119 chr19 15506506 15506507 DEL NA + - [Svaba_SR=21,Svaba_PE=22],[Manta_PE=19,Manta_SR=15],[Lumpy_PE=14,Lumpy_SR=8] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AKAP8L;DisruptR=;ClosestL=AC005785.2;ClosestR=CYP4F22 15684658 15684658 13,15384120,15506506 0,0,0 chr19 15523081 15523082 chr19 15546350 15546351 INV NA - - [Svaba_SR=87,Svaba_PE=65],[Manta_PE=59,Manta_SR=71],[Lumpy_PE=58,Lumpy_SR=1] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=CYP4F22;DisruptR=CYP4F22;ClosestL=AC011492.1;ClosestR=CYP4F23P 15684658 15684658 56,15523081,15546350 0,0,0 chr19 15533868 15533869 chr19 15684645 15684646 INV NA + + [Svaba_SR=178,Svaba_PE=88],[Manta_PE=194,Manta_SR=169] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=CYP4F22;DisruptR=CYP4F12;ClosestL=AC011492.1;ClosestR=CYP4F10P 15684658 15684658 77,15533870,15684646 0,0,0 chr19 15588870 15588871 chr19 15589780 15589781 DEL NA + - [Svaba_SR=97,Svaba_PE=151],[Manta_PE=126,Manta_SR=115],[Lumpy_PE=136,Lumpy_SR=91] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=CYP4F23P;ClosestR=CYP4F23P 15684658 15684658 69,15588872,15589780 0,0,0 chr19 15632140 15632141 chr19 20137691 20137692 DEL NA + - [Svaba_SR=71,Svaba_PE=65],[Manta_PE=63,Manta_SR=48],[Lumpy_PE=61,Lumpy_SR=3] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=TPM4|Tier1,JAK3|Tier1,ELL|Tier1,CRTC1|Tier1;DisruptL=;DisruptR=AC011447.2,AC011447.3;ClosestL=CYP4F8;ClosestR=BNIP3P15 15684658 20137238 41,15632139,20137687 0,0,0 chr19 17316666 17316667 chr19 17362636 17362637 DEL NA + - [Svaba_SR=6,Svaba_PE=14],[Manta_PE=14,Manta_SR=5],[Lumpy_PE=13,Lumpy_SR=2] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=DDA1;DisruptR=AC010463.2,PLVAP;Fusion=DDA1+AC010463.2;ClosestL=ABHD8;ClosestR=GTPBP3 15684659 15684659 4,17316668,17362635 0,0,0 chr19 20300586 20300587 chr19 20303756 20303757 DEL NA + - [Svaba_SR=21,Svaba_PE=33],[Manta_PE=31,Manta_SR=15],[Lumpy_PE=21,Lumpy_SR=10] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC078899.4,AC011447.3;DisruptR=AC078899.4,AC011447.3;ClosestL=;ClosestR= 20137238 20137238 12,20300585,20303756 0,0,0 chr19 20441327 20441328 chr19 20443259 20443260 DEL NA + - [Svaba_SR=67,Svaba_PE=85],[Manta_PE=73,Manta_SR=51],[Lumpy_PE=57,Lumpy_SR=7] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC008554.1;DisruptR=BNIP3P23,AC008554.1;ClosestL=BNIP3P23;ClosestR=ZNF826P 20490394 20490394 44,20441329,20443255 0,0,0 chr19 20497266 20497267 chr19 20498447 20498448 INV NA + + [Svaba_SR=23,Svaba_PE=25],[Manta_PE=26,Manta_SR=20],[Lumpy_PE=17,Lumpy_SR=15] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;COSMIC;DisruptL=AC008554.1;DisruptR=AC008554.1;ClosestL=;ClosestR= 20490395 20490395 16,20497268,20498448 0,0,0 chr19 20497437 20497438 chr19 20501960 20501961 DUP NA - + [Svaba_SR=33,Svaba_PE=36],[Manta_PE=31,Manta_SR=34],[Lumpy_PE=29,Lumpy_SR=13] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC008554.1;DisruptR=AC008554.1;ClosestL=;ClosestR= 20490395 20490395 28,20497438,20501961 0,0,0 chr19 20498993 20498994 chr19 20507532 20507533 DUP NA - + [Svaba_SR=28,Svaba_PE=0],[Manta_PE=33,Manta_SR=27],[Lumpy_PE=28,Lumpy_SR=24] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=AC008554.1;DisruptR=AC008554.1;ClosestL=;ClosestR= 20490395 20490395 23,20498993,20507533 0,0,0 chr19 20506933 20506934 chr19 24352249 24352250 DUP NA - + [Svaba_SR=36,Svaba_PE=29],[Manta_PE=33,Manta_SR=32],[Lumpy_PE=22,Lumpy_SR=10] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=ZNF429|Tier2;DisruptL=AC008554.1;DisruptR=;ClosestL=;ClosestR= 20490395 24018596 14,20506933,24352271 0,0,0 chr19 23544106 23544107 chr19 23692932 23692933 INV NA - - [Manta_PE=4,Manta_SR=10] manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=ZNF675;DisruptR=;ClosestL=;ClosestR=ZNF675 23544109 23544110 0,0,0 0,0,0 chr19 24348141 24348142 chr19 24353031 24353032 INV NA - - [Svaba_SR=37,Svaba_PE=31],[Manta_PE=31,Manta_SR=31],[Lumpy_PE=19,Lumpy_SR=22] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 24018596 24018596 25,24348141,24353031 0,0,0 chr19 24373673 24373674 chr19 24375338 24375339 DEL NA + - [Svaba_SR=25,Svaba_PE=29],[Manta_PE=32,Manta_SR=30] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 24018596 24018596 19,24373656,24375338 0,0,0 chr20 15067580 15067581 chr20 15078347 15078348 DUP NA - + [Svaba_SR=8,Svaba_PE=5],[Manta_PE=5,Manta_SR=7],[Lumpy_PE=3,Lumpy_SR=2] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=MACROD2;DisruptR=MACROD2;ClosestL=;ClosestR= 8764420 8764420 3,15067585,15078348 0,0,0 chr20 18763090 18763091 chr20 18763944 18763945 INV NA - - [Svaba_SR=3,Svaba_PE=8],[Lumpy_PE=5,Lumpy_SR=3] lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=DTD1;DisruptR=DTD1;ClosestL=AL121900.2;ClosestR=EEF1A1P34 21885644 21885644 3,18763090,18763944 0,0,0 chr20 22251586 22251587 chr20 22253038 22253039 INV NA - - [Svaba_SR=0,Svaba_PE=10],[Manta_PE=13,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;ClosestL=LINC01427;ClosestR=LINC01427 21885645 21885645 0,0,0 0,0,0 chr20 26330213 26330214 chr20 26331691 26331692 DEL NA + - [Svaba_SR=11,Svaba_PE=23],[Manta_PE=23,Manta_SR=12] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 28506070 28506070 4,26330156,26331691 0,0,0 chr20 31360012 31360013 chr20 31377616 31377617 DUP NA - + [Lumpy_PE=3,Lumpy_SR=2] lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=DEFB119;ClosestL=DEFB117;ClosestR=RF00561 31245066 31245066 4,31360011,31377616 0,0,0 chr20 36914523 36914524 chr20 36933537 36933538 INV NA + + [Svaba_SR=15,Svaba_PE=22],[Manta_PE=26,Manta_SR=12],[Lumpy_PE=24,Lumpy_SR=5] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=SAMHD1;DisruptR=SAMHD1;ClosestL=;ClosestR= 36912831 36912831 11,36914523,36933538 0,0,0 chr20 47103302 47103303 chr20 47104389 47104390 DEL NA + - [Svaba_SR=29,Svaba_PE=19],[Manta_PE=17,Manta_SR=18] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=EYA2;DisruptR=EYA2;ClosestL=;ClosestR= 39349551 39349551 0,0,0 0,0,0 chr20 47104471 47104472 chr20 47225242 47225243 DUP NA - + [Svaba_SR=0,Svaba_PE=8],[Lumpy_PE=3,Lumpy_SR=2] lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=EYA2;DisruptR=ZMYND8;ClosestL=;ClosestR= 39349551 39349551 3,47104393,47225243 0,0,0 chr20 47225235 47225236 chr20 47268863 47268864 DEL NA + - [Svaba_SR=42,Svaba_PE=13],[Manta_PE=10,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=ZMYND8;DisruptR=ZMYND8;ClosestL=;ClosestR= 39349551 39349551 0,0,0 0,0,0 chr20 48179659 48179660 chr20 48180192 48180193 DEL NA + - [Svaba_SR=24,Svaba_PE=0],[Manta_PE=18,Manta_SR=19],[Lumpy_PE=11,Lumpy_SR=16] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=;ClosestR= 39349551 39349551 19,48179660,48180192 0,0,0 chr21 13283045 13283046 chr21 13506275 13506276 DEL NA + - [Svaba_SR=42,Svaba_PE=52],[Manta_PE=48,Manta_SR=44] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=GTF2IP2 13282812 13507200 36,13283046,13506275 0,0,0 chr21 15873590 15873591 chr21 16679496 16679497 INV NA + + [Svaba_SR=126,Svaba_PE=125],[Manta_PE=135,Manta_SR=105],[Lumpy_PE=104,Lumpy_SR=83] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=USP25;DisruptR=;ClosestL=;ClosestR= 15873585 17474345 65,15873592,16679497 0,0,0 chr21 16672953 16672954 chr21 17986177 17986178 DUP NA - + [Svaba_SR=117,Svaba_PE=127],[Manta_PE=105,Manta_SR=93],[Lumpy_PE=85,Lumpy_SR=76] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=CHODL;ClosestL=;ClosestR= 15873585 17986205 64,16672958,17986178 0,0,0 chr21 17474427 17474428 chr21 41078325 41078326 DUP NA - + [Svaba_SR=124,Svaba_PE=153],[Manta_PE=131,Manta_SR=116],[Lumpy_PE=109,Lumpy_SR=87] manta,lumpy,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=OLIG2|Tier1,RUNX1|Tier1,ERG|Tier1;DisruptL=;DisruptR=;ClosestL=;ClosestR= 17474346 41078299 70,17474426,41078326 0,0,0 chr21 17592650 17592651 chr21 17621842 17621843 DUP NA - + [Svaba_SR=20,Svaba_PE=30],[Manta_PE=29,Manta_SR=15],[Lumpy_PE=27,Lumpy_SR=11] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=CXADR;DisruptR=BTG3-AS1;Fusion=BTG3-AS1+CXADR;ClosestL=BTG3;ClosestR=BTG3 17474346 17474346 13,17592651,17621843 0,0,0 chr21 31947365 31947366 chr21 45927270 45927271 INV NA - - [Svaba_SR=0,Svaba_PE=68],[Manta_PE=61,Manta_SR=0] manta,svaba HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=OLIG2|Tier1,TMPRSS2|Tier1,U2AF1|Tier1,RUNX1|Tier1,ERG|Tier1;DisruptL=HUNK;DisruptR=PCBP3;ClosestL=;ClosestR=AJ239328.1 31947285 46107841 2,31947365,45927258 0,0,0 chr21 34819613 34819614 chr21 34850895 34850896 DEL NA + - [Svaba_SR=22,Svaba_PE=27],[Manta_PE=26,Manta_SR=16],[Lumpy_PE=20,Lumpy_SR=14] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=RUNX1|Tier1;DisruptL=RUNX1;DisruptR=RUNX1;ClosestL=;ClosestR= 34819639 34847755 13,34819611,34850895 0,0,0 chr21 40764330 40764331 chr21 44064618 44064619 INV NA - - [Svaba_SR=111,Svaba_PE=133],[Manta_PE=145,Manta_SR=106],[Lumpy_PE=103,Lumpy_SR=56] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=TMPRSS2|Tier1,U2AF1|Tier1;DisruptL=DSCAM;DisruptR=TRAPPC10;Fusion=DSCAM+TRAPPC10;ClosestL=;ClosestR=H2AFZP1 40764260 44064550 5,40764317,44064618 0,0,0 chr21 41822940 41822941 chr21 42103805 42103806 DUP NA - + [Svaba_SR=42,Svaba_PE=94],[Manta_PE=79,Manta_SR=62],[Lumpy_PE=73,Lumpy_SR=43] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PRDM15;DisruptR=UMODL1-AS1,UMODL1;Fusion=PRDM15+UMODL1-AS1;ClosestL=;ClosestR= 41825925 42103908 39,41822941,42103806 0,0,0 chr21 41823975 41823976 chr21 46107855 46107856 INV NA + + [Svaba_SR=78,Svaba_PE=89],[Manta_PE=102,Manta_SR=75],[Lumpy_PE=90,Lumpy_SR=39] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=U2AF1|Tier1;DisruptL=PRDM15;DisruptR=COL6A2;Fusion=COL6A2+PRDM15;ClosestL=;ClosestR=AP001471.1 41825925 46107842 49,41823975,46107856 0,0,0 chr21 41825929 41825930 chr21 45927312 45927313 DUP NA - + [Svaba_SR=30,Svaba_PE=133],[Manta_PE=139,Manta_SR=60],[Lumpy_PE=136,Lumpy_SR=36] manta,svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=U2AF1|Tier1;DisruptL=PRDM15;DisruptR=PCBP3;ClosestL=;ClosestR=AJ239328.1 41825926 46107841 30,41825930,45927313 0,0,0 chr21 41831216 41831217 chr21 41833962 41833963 DEL NA + - [Svaba_SR=109,Svaba_PE=140],[Manta_PE=119,Manta_SR=91],[Lumpy_PE=94,Lumpy_SR=65] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;DisruptL=PRDM15;DisruptR=PRDM15;ClosestL=;ClosestR= 41825926 41825926 59,41831218,41833962 0,0,0 chr21 42948646 42948647 chr21 42950135 42950136 DEL NA + - [Svaba_SR=68,Svaba_PE=53],[Manta_PE=62,Manta_SR=60],[Lumpy_PE=43,Lumpy_SR=25] svaba,manta,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=MIR5692B;ClosestR=MIR5692B 42103909 42103909 39,42948644,42950135 0,0,0 chr22 16812440 16812441 chr22 27132898 27132899 INV NA - - [Manta_PE=3,Manta_SR=6],[Lumpy_PE=2,Lumpy_SR=4] lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;gap;Cancer_census=SEPT5|Tier2,DGCR8|Tier2,LZTR1|Tier1,MAPK1|Tier1,SMARCB1|Tier1,CLTCL1|Tier1,BCR|Tier1;DisruptL=XKR3;DisruptR=;ClosestL=HSFY1P1;ClosestR=AL008638.1 10514978 29344638 6,16812445,27132894 0,0,0 chr22 20476966 20476967 chr22 20591962 20591963 DEL NA + - [Svaba_SR=20,Svaba_PE=25],[Manta_PE=23,Manta_SR=15],[Lumpy_PE=16,Lumpy_SR=12] svaba,lumpy,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=KLHL22;DisruptR=CCDC74BP1;Fusion=CCDC74BP1+KLHL22;ClosestL=RNY1P9;ClosestR=MED15 24015968 24015968 12,20476962,20591962 0,0,0 chr22 23936453 23936454 chr22 23946301 23946302 INV NA - - [Svaba_SR=24,Svaba_PE=21],[Manta_PE=9,Manta_SR=22] svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=;DisruptR=;ClosestL=AP000350.1;ClosestR=AP000350.1 24015968 24015968 18,23936454,23946301 0,0,0 chr22 25536845 25536846 chr22 25555999 25556000 DEL NA + - [Svaba_SR=4,Svaba_PE=2],[Lumpy_PE=3,Lumpy_SR=2] svaba,lumpy HCC-1143_80--HCC-1143BL_40 known=;ClosestL=CRYBB2P1;ClosestR=AL022329.1 24015969 24015969 3,25536846,25555999 0,0,0 chr22 29187777 29187778 chr22 29344659 29344660 DUP NA - + [Svaba_SR=38,Svaba_PE=49],[Manta_PE=44,Manta_SR=39],[Lumpy_PE=37,Lumpy_SR=17] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=EWSR1|Tier1;DisruptL=;DisruptR=AP1B1;ClosestL=RNU6-1219P;ClosestR=MIR3653 29344638 29344639 27,29187768,29344660 0,0,0 chr22 29285161 29285162 chr22 29286804 29286805 INV NA + + [Svaba_SR=15,Svaba_PE=26],[Manta_PE=25,Manta_SR=18],[Lumpy_PE=23,Lumpy_SR=5] lumpy,manta,svaba HCC-1143_80--HCC-1143BL_40 known=;Cancer_census=EWSR1|Tier1;DisruptL=EWSR1;DisruptR=EWSR1;ClosestL=RHBDD3;ClosestR=RHBDD3 29344638 29344638 8,29285160,29286805 0,0,0 chr22 46073953 46073954 chr22 46234169 46234170 DUP NA - + [Svaba_SR=68,Svaba_PE=62],[Manta_PE=52,Manta_SR=57],[Lumpy_PE=45,Lumpy_SR=52] lumpy,svaba,manta HCC-1143_80--HCC-1143BL_40 known=;DisruptL=MIRLET7BHG;DisruptR=PPARA;Fusion=PPARA+MIRLET7BHG;ClosestL=AL121672.2;ClosestR=CDPF1 46073919 46234134 44,46073952,46234170 0,0,0