#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=79,Svaba_PE=100],[Manta_PE=82,Manta_SR=71],[Lumpy_PE=68,Lumpy_SR=50] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=ARAF,KDM6A,RBM10;DisruptL=KDM6A;DisruptR=UXT;ClosestL=;ClosestR=UXT-AS1 44887175 47658809 52,44887191,47658827 0,0,0 chrX 45136456 45136457 chrX 45137951 45137952 DEL NA + - [Svaba_SR=116,Svaba_PE=124],[Manta_PE=119,Manta_SR=103],[Lumpy_PE=87,Lumpy_SR=42] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=CXorf36;ClosestR=CXorf36 44887175 44887175 51,45136456,45137950 0,0,0 chrX 57361939 57361940 chrX 57364610 57364611 INV NA - - [Svaba_SR=66,Svaba_PE=65],[Manta_PE=61,Manta_SR=59],[Lumpy_PE=43,Lumpy_SR=46] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=FAAH2;DisruptR=FAAH2;ClosestL=;ClosestR= 57361937 57361937 44,57361930,57364609 0,0,0 chrX 76242859 76242860 chrX 76244484 76244485 INV NA - - [Svaba_SR=0,Svaba_PE=12] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=RNU6-867P;ClosestR=RNU6-867P 76244723 76244723 0,0,0 0,0,0 chrX 76242860 76242861 chrX 116501145 116501146 DUP NA - + [Svaba_SR=64,Svaba_PE=32],[Manta_PE=30,Manta_SR=70],[Lumpy_PE=26,Lumpy_SR=43] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=IRS4,BTK,ATRX;DisruptL=;DisruptR=;ClosestL=RNU6-867P;ClosestR= 76244723 116456787 48,76242855,116501150 0,0,0 chrX 76244485 76244486 chrX 116500843 116500844 INV NA - - [Svaba_SR=68,Svaba_PE=58],[Manta_PE=60,Manta_SR=62],[Lumpy_PE=36,Lumpy_SR=29] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=IRS4,BTK,ATRX;DisruptL=;DisruptR=;ClosestL=RNU6-867P;ClosestR= 76244723 116456787 41,76244484,116500842 0,0,0 chrX 77209157 77209158 chrX 77304273 77304274 DUP NA - + [Lumpy_PE=4,Lumpy_SR=2] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 76244724 76244724 2,77209158,77304274 0,0,0 chrX 79973209 79973210 chrX 79982346 79982347 DEL NA + - [Svaba_SR=75,Svaba_PE=59],[Manta_PE=52,Manta_SR=77],[Lumpy_PE=37,Lumpy_SR=13] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 76244724 76244724 0,0,0 0,0,0 chrX 80459951 80459952 chrX 80462152 80462153 DEL NA + - [Svaba_SR=134,Svaba_PE=168],[Manta_PE=231,Manta_SR=163],[Lumpy_PE=161,Lumpy_SR=138] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=TENT5D;ClosestR=TENT5D 84380645 84380645 86,80459950,80462151 0,0,0 chrX 84276233 84276234 chrX 84287223 84287224 INV NA - - [Manta_PE=24,Manta_SR=47],[Lumpy_PE=14,Lumpy_SR=1] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 84380645 84380645 0,0,0 0,0,0 chrX 84380638 84380639 chrX 84382004 84382005 INV NA + + [Svaba_SR=70,Svaba_PE=75],[Manta_PE=75,Manta_SR=60],[Lumpy_PE=64,Lumpy_SR=44] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HDX;DisruptR=HDX;ClosestL=;ClosestR= 84380645 84380646 44,84380640,84382007 0,0,0 chrX 89287531 89287532 chrX 89298078 89298079 DUP NA - + [Svaba_SR=67,Svaba_PE=29] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 88322773 88322773 42,89287531,89298080 0,0,0 chrX 89754735 89754736 chrX 89755514 89755515 DEL NA + - [Svaba_SR=24,Svaba_PE=19],[Manta_PE=9,Manta_SR=18],[Lumpy_PE=9,Lumpy_SR=8] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 88322773 88322773 17,89754737,89755513 0,0,0 chrX 91727150 91727151 chrX 91796419 91796420 DUP NA - + [Svaba_SR=95,Svaba_PE=85],[Manta_PE=61,Manta_SR=83],[Lumpy_PE=39,Lumpy_SR=57] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=PCDH11X;ClosestL=;ClosestR=RNU2-26P 88322773 88322773 58,91727141,91796421 0,0,0 chrX 100877604 100877605 chrX 153586247 153586248 INV NA + + [Svaba_SR=0,Svaba_PE=87],[Manta_PE=167,Manta_SR=146],[Lumpy_PE=131,Lumpy_SR=112] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=IRS4,DCAF12L2,BTK,STAG2,ELF4,PHF6,ATP2B3,SEPT6,GPC3,BCORL1;DisruptL=;DisruptR=;ClosestL=NOX1;ClosestR=CCNQ 100877556 153586440 80,100877602,153586487 0,0,0 chrX 117971506 117971507 chrX 118882097 118882098 DUP NA - + [Svaba_SR=194,Svaba_PE=252],[Manta_PE=219,Manta_SR=203] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=KLHL13;DisruptR=LINC01285;ClosestL=;ClosestR=AC006965.1 117971411 118882103 75,117971503,118882108 0,0,0 chrX 118481848 118481849 chrX 118482368 118482369 DEL NA + - [Svaba_SR=8,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=DOCK11;ClosestR=DOCK11 118882103 118882103 4,118481824,118482367 0,0,0 chrX 119675465 119675466 chrX 119676381 119676382 INV NA - - [Svaba_SR=0,Svaba_PE=8] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=SEPT6;DisruptL=SEPT6;DisruptR=SEPT6;ClosestL=AC005052.1;ClosestR=AC005052.1 118882104 118882104 0,0,0 0,0,0 chrX 139747038 139747039 chrX 153271819 153271820 INV NA + + [Manta_PE=44,Manta_SR=162] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;DisruptL=ATP11C;DisruptR=;ClosestL=;ClosestR=AC236972.4 139747068 153149106 92,139747040,153271821 0,0,0 chr1 6039119 6039120 chr1 6039638 6039639 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=KCNAB2;DisruptR=KCNAB2;ClosestL=;ClosestR= 6465256 6465256 0,0,0 2,6039108,6039637 chr1 6465293 6465294 chr3 85183519 85183520 TRA NA + - [Svaba_SR=0,Svaba_PE=18],[Manta_PE=42,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TNFRSF25;DisruptR=CADM2;ClosestL=PLEKHG5;ClosestR= 6465257 85183522 0,0,0 0,0,0 chr1 6465318 6465319 chr3 85187355 85187356 TRA NA + + [Svaba_SR=139,Svaba_PE=88],[Manta_PE=121,Manta_SR=120] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TNFRSF25;DisruptR=CADM2;Fusion=CADM2-TNFRSF25;ClosestL=PLEKHG5;ClosestR= 6465257 85183523 66,6465320,85187357 0,0,0 chr1 6509217 6509218 chr21 34847707 34847708 TRA NA - - [Manta_PE=73,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=RUNX1;DisruptL=PLEKHG5;DisruptR=RUNX1;ClosestL=NOL9;ClosestR= 6465257 34847754 0,0,0 0,0,0 chr1 6509232 6509233 chr1 6510621 6510622 INV NA - - [Svaba_SR=90,Svaba_PE=43],[Manta_PE=45,Manta_SR=70],[Lumpy_PE=24,Lumpy_SR=59] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PLEKHG5;DisruptR=PLEKHG5;ClosestL=NOL9;ClosestR=NOL9 6465257 6465257 39,6509237,6510620 0,0,0 chr1 6510727 6510728 chr21 34847762 34847763 TRA NA + - [Svaba_SR=91,Svaba_PE=53],[Manta_PE=26,Manta_SR=74],[Lumpy_PE=3,Lumpy_SR=58] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=RUNX1;DisruptL=PLEKHG5;DisruptR=RUNX1;Fusion=RUNX1-PLEKHG5;ClosestL=NOL9;ClosestR= 6465257 34847755 43,6510727,34847761 0,0,0 chr1 6623385 6623386 chr1 227866329 227866330 INV NA - - [Svaba_SR=149,Svaba_PE=47],[Manta_PE=76,Manta_SR=144],[Lumpy_PE=13,Lumpy_SR=115] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=ID3,MDS2,MYCL,TAL1,JUN,BCL10,RPL5,RBM15,NRAS,FAM46C,MLLT11,S100A7,SLC45A3,CASP9,PAX7,LCK,SFPQ,THRAP3,CSF3R,MPL,MUTYH,STIL,CDKN2C,FUBP1,BCL9,TPM3,LMNA,PRCC,NTRK1,FCRL4,FCGR2B,DDR2,PRRX1,ABL2,TPR,ELF3,MDM4,ELK4,H3F3A,MTOR,PRDM2,SPEN,SDHB,ARHGEF10L,ARID1A,JAK1,TRIM33,NOTCH2,ARNT,SDHC,CDC73,PTPRC,CAMTA1,EPS15,ATP1A1,PDE4DIP,MUC1,PBX1;DisruptL=PHF13;DisruptR=;ClosestL=THAP3;ClosestR=PRSS38 6465257 223431563 69,6623385,227866328 0,0,0 chr1 6623386 6623387 chr1 227866441 227866442 INV NA + + [Svaba_SR=158,Svaba_PE=50],[Manta_PE=54,Manta_SR=158],[Lumpy_PE=11,Lumpy_SR=127] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=ID3,MDS2,MYCL,TAL1,JUN,BCL10,RPL5,RBM15,NRAS,FAM46C,MLLT11,S100A7,SLC45A3,CASP9,PAX7,LCK,SFPQ,THRAP3,CSF3R,MPL,MUTYH,STIL,CDKN2C,FUBP1,BCL9,TPM3,LMNA,PRCC,NTRK1,FCRL4,FCGR2B,DDR2,PRRX1,ABL2,TPR,ELF3,MDM4,ELK4,H3F3A,MTOR,PRDM2,SPEN,SDHB,ARHGEF10L,ARID1A,JAK1,TRIM33,NOTCH2,ARNT,SDHC,CDC73,PTPRC,CAMTA1,EPS15,ATP1A1,PDE4DIP,MUC1,PBX1;DisruptL=PHF13;DisruptR=;ClosestL=THAP3;ClosestR=PRSS38 6465257 223431563 70,6623387,227866443 0,0,0 chr1 8115745 8115746 chr1 8337706 8337707 DUP NA - + [Svaba_SR=0,Svaba_PE=30] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL034417.2;DisruptR=SLC45A1;Fusion=SLC45A1+AL034417.2;ClosestL=;ClosestR=RF00019 8115685 8115685 15,8115746,8337583 0,0,0 chr1 8115746 8115747 chr1 8341045 8341046 INV NA - - [Svaba_SR=56,Svaba_PE=61],[Manta_PE=66,Manta_SR=71],[Lumpy_PE=47,Lumpy_SR=44] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL034417.2;DisruptR=SLC45A1;ClosestL=;ClosestR=RERE 8115685 8115685 49,8115746,8341044 0,0,0 chr1 8337686 8337687 chr1 8341281 8341282 INV NA + + [Manta_PE=49,Manta_SR=67] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SLC45A1;DisruptR=SLC45A1;ClosestL=RF00019;ClosestR=RERE 8115685 8115685 40,8337688,8341283 0,0,0 chr1 8673961 8673962 chr1 8950735 8950736 DUP NA - + [Svaba_SR=138,Svaba_PE=158],[Manta_PE=128,Manta_SR=122],[Lumpy_PE=108,Lumpy_SR=104] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=RERE;DisruptR=CA6;ClosestL=;ClosestR= 8673896 8950367 74,8673963,8950737 0,0,0 chr1 19771904 19771905 chr1 23063404 23063405 DUP NA - + [Svaba_SR=43,Svaba_PE=50],[Manta_PE=46,Manta_SR=50],[Lumpy_PE=36,Lumpy_SR=22] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TMCO4;DisruptR=KDM1A,AL031428.1;Fusion=TMCO4+AL031428.1;ClosestL=;ClosestR=MIR4419A 19771881 23063091 37,19771904,23063410 0,0,0 chr1 28454412 28454413 chr1 28454960 28454961 DEL NA + - [Svaba_SR=2,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PHACTR4;DisruptR=PHACTR4;ClosestL=CR391992.1;ClosestR=CR391992.1 23063091 23063091 2,28454415,28454996 0,0,0 chr1 40528747 40528748 chr16 187562 187563 TRA NA - - [Svaba_SR=67,Svaba_PE=28],[Manta_PE=29,Manta_SR=55],[Lumpy_PE=17,Lumpy_SR=43] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=ZNF684;ClosestR=Z69706.1 47818851 10005 43,40528747,187559 0,0,0 chr1 40529024 40529025 chrY 56870831 56870832 TRA NA + - [Svaba_SR=48,Svaba_PE=59] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=ZNF684;ClosestR=CTBP2P1 47818851 -1 41,40529026,56870830 0,0,0 chr1 43628365 43628366 chr1 43628935 43628936 DEL NA + - [Svaba_SR=3,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=PTPRF;ClosestR=PTPRF 47818851 47818851 2,43628274,43628863 0,0,0 chr1 47818840 47818841 chr1 70293544 70293545 DUP NA - + [Svaba_SR=59,Svaba_PE=77],[Manta_PE=75,Manta_SR=52],[Lumpy_PE=63,Lumpy_SR=38] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=JUN,CDKN2C,JAK1,EPS15;DisruptL=AC096541.1,TRABD2B;DisruptR=ANKRD13C;Fusion=TRABD2B+ANKRD13C;ClosestL=;ClosestR= 47818851 83866322 40,47818841,70293546 0,0,0 chr1 50547171 50547172 chr1 50547677 50547678 DEL NA + - [Svaba_SR=7,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAF1;DisruptR=FAF1;ClosestL=;ClosestR= 51383048 51383048 2,50547157,50547676 0,0,0 chr1 51383095 51383096 chr1 70292967 70292968 DEL NA + - [Svaba_SR=92,Svaba_PE=79],[Manta_PE=75,Manta_SR=61],[Lumpy_PE=68,Lumpy_SR=9] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=JUN,JAK1,EPS15;DisruptL=EPS15;DisruptR=ANKRD13C;Fusion=ANKRD13C+EPS15;ClosestL=RNU6-877P;ClosestR= 51383049 83866322 0,0,0 0,0,0 chr1 52125152 52125153 chr1 52125708 52125709 DEL NA + - [Svaba_SR=2,Svaba_PE=5] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=ZFYVE9;ClosestR=ZFYVE9 52861923 52861923 0,0,0 0,0,0 chr1 52382263 52382264 chr1 52382817 52382818 DEL NA + - [Svaba_SR=2,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ORC1;DisruptR=ORC1;ClosestL=PLA2G12AP1;ClosestR=PLA2G12AP1 52861923 52861923 2,52382231,52382830 0,0,0 chr1 52860644 52860645 chr1 53006333 53006334 DEL NA + - [Svaba_SR=57,Svaba_PE=97],[Manta_PE=63,Manta_SR=45],[Lumpy_PE=49,Lumpy_SR=26] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ZYG11A;DisruptR=SCP2;Fusion=ZYG11A+SCP2;ClosestL=;ClosestR=TUBBP10 52861923 53005833 40,52860642,53006332 0,0,0 chr1 54258682 54258683 chr1 54270176 54270177 DEL NA + - [Svaba_SR=13,Svaba_PE=9],[Manta_PE=11,Manta_SR=7],[Lumpy_PE=8,Lumpy_SR=6] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SSBP3;DisruptR=SSBP3;ClosestL=SSBP3-AS1;ClosestR=AL161644.1 53005833 53005833 7,54258681,54270175 0,0,0 chr1 58133514 58133515 chr1 58140197 58140198 DEL NA + - [Svaba_SR=61,Svaba_PE=73],[Manta_PE=63,Manta_SR=54],[Lumpy_PE=44,Lumpy_SR=41] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=DAB1;DisruptR=DAB1;ClosestL=;ClosestR= 53005833 53005833 42,58133514,58140196 0,0,0 chr1 68760869 68760870 chr6 158632522 158632523 TRA NA - - [Manta_PE=41,Manta_SR=61],[Lumpy_PE=16,Lumpy_SR=16] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL033530.1;DisruptR=TMEM181;ClosestL=;ClosestR=DYNLT1 83866322 165311198 7,68760871,158632518 0,0,0 chr1 68761024 68761025 chr6 158632501 158632502 TRA NA + + [Svaba_SR=81,Svaba_PE=32],[Manta_PE=32,Manta_SR=66],[Lumpy_PE=15,Lumpy_SR=46] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL033530.1;DisruptR=TMEM181;ClosestL=;ClosestR=DYNLT1 83866322 165311198 49,68761023,158632503 0,0,0 chr1 83866390 83866391 chr1 84289947 84289948 DUP NA - + [Svaba_SR=155,Svaba_PE=186],[Manta_PE=166,Manta_SR=134],[Lumpy_PE=134,Lumpy_SR=115] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=TTLL7;DisruptR=;ClosestL=LINC01725;ClosestR=SAMD13 83866323 84289902 74,83866393,84289949 0,0,0 chr1 90378420 90378421 chr1 90380090 90380091 DUP NA - + [Lumpy_PE=3,Lumpy_SR=1] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;ClosestL=;ClosestR= 94125487 94125487 0,0,0 0,0,0 chr1 94125559 94125560 chr1 94476963 94476964 DUP NA - + [Svaba_SR=168,Svaba_PE=222],[Manta_PE=198,Manta_SR=171] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=ABCD3;ClosestL=ABCA4;ClosestR= 94125488 94476956 82,94125555,94476965 0,0,0 chr1 101718033 101718034 chr20 29887513 29887514 TRA NA - - [Manta_PE=84,Manta_SR=0],[Lumpy_PE=69,Lumpy_SR=17] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC01709;DisruptR=;ClosestL=RNU6-965P;ClosestR=DUX4L37 103478704 28791094 11,101718079,29887491 0,0,0 chr1 101718262 101718263 chr1 107356428 107356429 DEL NA + - [Svaba_SR=61,Svaba_PE=87],[Manta_PE=86,Manta_SR=57],[Lumpy_PE=61,Lumpy_SR=29] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC01709;DisruptR=NTNG1;Fusion=LINC01709+NTNG1;ClosestL=RNU6-965P;ClosestR= 103478704 107356812 43,101718263,107356427 0,0,0 chr1 103478736 103478737 chr7 86260442 86260443 TRA NA + + [Svaba_SR=75,Svaba_PE=75],[Manta_PE=74,Manta_SR=60],[Lumpy_PE=45,Lumpy_SR=48] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC095032.1;DisruptR=;ClosestL=;ClosestR= 103478705 84789193 48,103478737,86260444 0,0,0 chr1 124984581 124984582 chr21 15414727 15414728 TRA NA - - [Svaba_SR=31,Svaba_PE=20],[Manta_PE=20,Manta_SR=26] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=AJ009632.2;ClosestL=;ClosestR= 124752057 15873584 0,0,0 0,0,0 chr1 124984622 124984623 chr21 15415107 15415108 TRA NA + + [Manta_PE=13,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=AJ009632.2;ClosestL=;ClosestR= 124752057 15873584 0,0,0 0,0,0 chr1 124984848 124984849 chr21 46035776 46035777 TRA NA + - [Svaba_SR=16,Svaba_PE=17],[Manta_PE=16,Manta_SR=13],[Lumpy_PE=11,Lumpy_SR=10] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=AP001476.1 124752057 46107841 12,124984850,46035775 0,0,0 chr1 143191334 143191335 chr6 32039558 32039559 TRA NA + + [Lumpy_PE=2,Lumpy_SR=15] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=CYP21A2;ClosestL=;ClosestR=TNXB 150474751 32487100 36,143191335,32039560 0,0,0 chr1 150474819 150474820 chr1 150749754 150749755 DUP NA - + [Svaba_SR=159,Svaba_PE=174],[Manta_PE=150,Manta_SR=138],[Lumpy_PE=116,Lumpy_SR=88] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=RPRD2;DisruptR=CTSS;ClosestL=TARS2;ClosestR= 150474752 150749712 2,150474817,150749752 0,0,0 chr1 150980878 150980879 chr1 151012024 151012025 DEL NA + - [Svaba_SR=12,Svaba_PE=15],[Manta_PE=15,Manta_SR=13] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=PRUNE1;ClosestL=ANXA9;ClosestR=MINDY1 150749712 150749712 11,150980860,151012056 0,0,0 chr1 155287407 155287408 chr1 155310603 155310604 DEL NA + - [Svaba_SR=72,Svaba_PE=97],[Manta_PE=88,Manta_SR=65],[Lumpy_PE=63,Lumpy_SR=53] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HCN3;DisruptR=FDPS;Fusion=HCN3+FDPS;ClosestL=PKLR;ClosestR=RUSC1-AS1 150749712 150749712 47,155287407,155310602 0,0,0 chr1 156727473 156727474 chr1 156728410 156728411 DEL NA + - [Svaba_SR=19,Svaba_PE=23],[Manta_PE=17,Manta_SR=14],[Lumpy_PE=14,Lumpy_SR=11] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ISG20L2;DisruptR=ISG20L2;ClosestL=RRNAD1;ClosestR=RRNAD1 150749712 150749712 13,156727475,156728409 0,0,0 chr1 179768684 179768685 chr1 179769216 179769217 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAM163A;DisruptR=FAM163A;ClosestL=;ClosestR= 186672816 186672816 0,0,0 0,0,0 chr1 179890893 179890894 chr1 179891472 179891473 DEL NA + - [Svaba_SR=3,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TOR1AIP1;DisruptR=TOR1AIP1;ClosestL=AL353708.3;ClosestR=RN7SL230P 186672816 186672816 0,0,0 0,0,0 chr1 186672822 186672823 chr1 188617939 188617940 DUP NA - + [Svaba_SR=0,Svaba_PE=21],[Manta_PE=16,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PTGS2;DisruptR=;ClosestL=PACERR;ClosestR= 186672817 186672817 0,0,0 0,0,0 chr1 186672822 186672823 chr21 32343521 32343522 TRA NA - - [Svaba_SR=0,Svaba_PE=15] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PTGS2;DisruptR=URB1;ClosestL=PACERR;ClosestR= 186672817 32739134 0,0,0 0,0,0 chr1 186672823 186672824 chr12 67114875 67114876 TRA NA - + [Svaba_SR=65,Svaba_PE=61],[Manta_PE=49,Manta_SR=74],[Lumpy_PE=28,Lumpy_SR=49] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PTGS2;DisruptR=;ClosestL=PACERR;ClosestR=RAB11AP2 186672817 67923115 54,186672823,67114877 0,0,0 chr1 188617780 188617781 chr3 13545970 13545971 TRA NA - + [Svaba_SR=0,Svaba_PE=34],[Manta_PE=17,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=FBLN2 186672817 10083194 0,0,0 0,0,0 chr1 188617780 188617781 chr6 144660335 144660336 TRA NA - + [Svaba_SR=0,Svaba_PE=12] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=UTRN;ClosestL=;ClosestR= 186672817 130003967 0,0,0 0,0,0 chr1 188617781 188617782 chr21 32343522 32343523 TRA NA - - [Svaba_SR=92,Svaba_PE=24],[Manta_PE=12,Manta_SR=77],[Lumpy_PE=4,Lumpy_SR=61] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=URB1;ClosestL=;ClosestR= 186672817 32739134 54,188617781,32343521 0,0,0 chr1 188617939 188617940 chr12 67114681 67114682 TRA NA + - [Svaba_SR=71,Svaba_PE=32],[Manta_PE=21,Manta_SR=62],[Lumpy_PE=16,Lumpy_SR=45] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=RAB11AP2 186672817 67923115 45,188617941,67114680 0,0,0 chr1 200173681 200173682 chr1 200175120 200175121 DEL NA + - [Svaba_SR=16,Svaba_PE=15],[Manta_PE=13,Manta_SR=15],[Lumpy_PE=9,Lumpy_SR=8] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=NR5A2;DisruptR=NR5A2;ClosestL=;ClosestR= 200934768 200934768 12,200173679,200175119 0,0,0 chr1 200899901 200899902 chr21 7949041 7949042 TRA NA - + [Svaba_SR=71,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=INAVA;DisruptR=;ClosestL=MROH3P;ClosestR= 200934768 5030587 2,200899899,7949042 0,0,0 chr1 200900231 200900232 chr10 29373569 29373570 TRA NA + - [Manta_PE=50,Manta_SR=152],[Lumpy_PE=3,Lumpy_SR=93] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=INAVA;DisruptR=;ClosestL=MROH3P;ClosestR= 200934768 29240316 43,200900233,29373568 0,0,0 chr1 200900290 200900291 chr5 164930882 164930883 TRA NA + - [Manta_PE=81,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=INAVA;DisruptR=AC109466.1;Fusion=INAVA-AC109466.1;ClosestL=MROH3P;ClosestR=RNU6-209P 200934768 164930825 0,0,0 0,0,0 chr1 200908919 200908920 chr20 8765271 8765272 TRA NA - - [Svaba_SR=70,Svaba_PE=86],[Manta_PE=90,Manta_SR=49],[Lumpy_PE=66,Lumpy_SR=34] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=INAVA;DisruptR=PLCB1;ClosestL=MROH3P;ClosestR= 200934768 8764420 42,200908920,8765270 0,0,0 chr1 200934816 200934817 chr10 29240543 29240544 TRA NA + + [Svaba_SR=84,Svaba_PE=99],[Manta_PE=103,Manta_SR=75],[Lumpy_PE=70,Lumpy_SR=56] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=MROH3P;DisruptR=;ClosestL=RNU6-704P;ClosestR= 200934769 29240316 54,200934818,29240548 0,0,0 chr1 202013942 202013943 chr1 202424227 202424228 DUP NA - + [Svaba_SR=70,Svaba_PE=101],[Manta_PE=91,Manta_SR=62],[Lumpy_PE=72,Lumpy_SR=50] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=ELF3;DisruptL=ELF3,AL691482.3;DisruptR=PPP1R12B;Fusion=PPP1R12B+ELF3|PPP1R12B+AL691482.3;ClosestL=ELF3-AS1;ClosestR=RNU6-89P 202013977 202476271 47,202013942,202424229 0,0,0 chr1 202223003 202223004 chr1 202475925 202475926 DUP NA - + [Svaba_SR=78,Svaba_PE=69],[Manta_PE=73,Manta_SR=65],[Lumpy_PE=57,Lumpy_SR=45] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LGR6;DisruptR=PPP1R12B;Fusion=PPP1R12B+LGR6;ClosestL=;ClosestR=AC099336.2 202013978 202476271 37,202223006,202475927 0,0,0 chr1 203360676 203360677 chr1 223431545 223431546 DUP NA - + [Svaba_SR=262,Svaba_PE=270],[Manta_PE=339,Manta_SR=260],[Lumpy_PE=293,Lumpy_SR=193] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=SLC45A3,MDM4,ELK4;DisruptL=;DisruptR=;ClosestL=AL359837.1;ClosestR= 203360619 223431562 97,203360677,223431550 0,0,0 chr1 203425428 203425429 chr1 203429109 203429110 INV NA + + [Svaba_SR=74,Svaba_PE=89],[Manta_PE=88,Manta_SR=63],[Lumpy_PE=70,Lumpy_SR=50] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 203360619 203360619 6,203425427,203429111 0,0,0 chr1 205097876 205097877 chr1 235138998 235138999 DEL NA + - [Svaba_SR=77,Svaba_PE=100],[Manta_PE=86,Manta_SR=77],[Lumpy_PE=59,Lumpy_SR=49] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=SLC45A3,ELK4,H3F3A;DisruptL=RBBP5;DisruptR=RBM34,ARID4B;Fusion=RBM34+RBBP5|ARID4B+RBBP5;ClosestL=AL583832.1;ClosestR=TOMM20 205097986 234957837 38,205097891,235138997 0,0,0 chr1 208617537 208617538 chr1 208618087 208618088 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=LINC01735;ClosestR=LINC01735 211808611 211808611 3,208617528,208618086 0,0,0 chr1 209171311 209171312 chr13 108157081 108157082 TRA NA + + [Svaba_SR=63,Svaba_PE=71],[Manta_PE=72,Manta_SR=62],[Lumpy_PE=44,Lumpy_SR=48] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC092810.2;ClosestR= 211808611 108157041 44,209171312,108157083 0,0,0 chr1 209244791 209244792 chr1 212681433 212681434 DUP NA - + [Svaba_SR=9,Svaba_PE=56],[Manta_PE=91,Manta_SR=41],[Lumpy_PE=85,Lumpy_SR=21] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;ClosestL=AC092810.1;ClosestR=BATF3 211808611 212996331 18,209244791,212681444 0,0,0 chr1 211388560 211388561 chr2 104320969 104320970 TRA NA - - [Svaba_SR=49,Svaba_PE=68],[Manta_PE=69,Manta_SR=49],[Lumpy_PE=47,Lumpy_SR=36] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC00467;DisruptR=;ClosestL=TRAF5;ClosestR= 211808611 103111952 42,211388547,104320968 0,0,0 chr1 211808734 211808735 chr19 14950825 14950826 TRA NA + + [Svaba_SR=59,Svaba_PE=53],[Manta_PE=70,Manta_SR=51],[Lumpy_PE=57,Lumpy_SR=35] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LPGAT1;DisruptR=SLC1A6;ClosestL=RF00019;ClosestR=OR7C2 211808612 14707748 41,211808735,14950827 0,0,0 chr1 212301721 212301722 chr6 30029837 30029838 TRA NA - - [Svaba_SR=196,Svaba_PE=254],[Manta_PE=258,Manta_SR=164],[Lumpy_PE=193,Lumpy_SR=141] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AL360091.3,PPP2R5A;DisruptR=ZNRD1ASP;Fusion=ZNRD1ASP-PPP2R5A;ClosestL=AL360091.2;ClosestR=ETF1P1 212301637 32487100 87,212301724,30029836 0,0,0 chr1 213000165 213000166 chr8 121698470 121698471 TRA NA + - [Svaba_SR=70,Svaba_PE=93],[Manta_PE=82,Manta_SR=58] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ANGEL2;DisruptR=AC104233.1;ClosestL=VASH2;ClosestR=AC104233.2 212996332 121698091 41,213000167,121698467 0,0,0 chr1 213013350 213013351 chr2 86422893 86422894 TRA NA - - [Manta_PE=4,Manta_SR=5],[Lumpy_PE=3,Lumpy_SR=2] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ANGEL2;DisruptR=;ClosestL=;ClosestR=KDM3A 212996332 88772978 4,213013349,86422886 0,0,0 chr1 213395883 213395884 chr20 18807975 18807976 TRA NA + - [Svaba_SR=7,Svaba_PE=0],[Manta_PE=3,Manta_SR=6] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=C20orf78 212996332 22252838 6,213395882,18807974 0,0,0 chr1 217777448 217777449 chr11 29804982 29804983 TRA NA - + [Svaba_SR=170,Svaba_PE=169],[Manta_PE=154,Manta_SR=154] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SPATA17;DisruptR=AC107973.1;Fusion=AC107973.1-SPATA17;ClosestL=SPATA17-AS1;ClosestR= 217777418 29804998 77,217777448,29804984 0,0,0 chr1 220803994 220803995 chrX 87103995 87103996 TRA NA - - [Svaba_SR=57,Svaba_PE=79],[Manta_PE=74,Manta_SR=59],[Lumpy_PE=53,Lumpy_SR=44] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=MARC1;DisruptR=;ClosestL=MARC2;ClosestR= 220805315 87103947 46,220803997,87103994 0,0,0 chr1 221676688 221676689 chr7 140930514 140930515 TRA NA - + [Svaba_SR=79,Svaba_PE=90],[Manta_PE=73,Manta_SR=75],[Lumpy_PE=48,Lumpy_SR=60] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=AC006006.1 221668390 140911187 52,221676690,140930516 0,0,0 chr1 221973415 221973416 chr13 51174600 51174601 TRA NA + + [Svaba_SR=0,Svaba_PE=9] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC02474,LINC02257;DisruptR=C13orf42;Fusion=LINC02474-C13orf42;ClosestL=;ClosestR=AL157817.1 221668390 68670604 6,221973384,51174701 3,221973384,51174701 chr1 222787229 222787230 chr1 222795328 222795329 INV NA + + [Svaba_SR=95,Svaba_PE=101],[Manta_PE=90,Manta_SR=81],[Lumpy_PE=75,Lumpy_SR=63] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=AL392172.1 222786581 222786581 50,222787229,222795330 0,0,0 chr1 222794716 222794717 chr18 73989233 73989234 TRA NA - - [Svaba_SR=65,Svaba_PE=84],[Manta_PE=83,Manta_SR=43],[Lumpy_PE=72,Lumpy_SR=31] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=AC090125.1;ClosestL=;ClosestR= 222786581 73989169 36,222794718,73989232 0,0,0 chr1 223347597 223347598 chrX 46583708 46583709 TRA NA - - [Manta_PE=21,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SUSD4;DisruptR=CHST7;Fusion=SUSD4-CHST7;ClosestL=;ClosestR=SLC9A7 223431562 47658808 0,0,0 0,0,0 chr1 234957883 234957884 chr1 235095124 235095125 DUP NA - + [Svaba_SR=54,Svaba_PE=82],[Manta_PE=76,Manta_SR=47],[Lumpy_PE=68,Lumpy_SR=36] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL391832.1,AL391832.2;DisruptR=;ClosestL=;ClosestR=AL732292.1 234957837 234957837 36,234957886,235095126 0,0,0 chr1 234972979 234972980 chr1 235146066 235146067 DUP NA - + [Svaba_SR=71,Svaba_PE=79],[Manta_PE=73,Manta_SR=52],[Lumpy_PE=62,Lumpy_SR=34] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=RBM34,ARID4B;ClosestL=AL391832.2;ClosestR=TOMM20 234957837 234957837 5,234972981,235146067 0,0,0 chr1 234999665 234999666 chr1 235000186 235000187 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AL391832.3;ClosestR=AL391832.3 234957837 234957837 0,0,0 0,0,0 chr1 246598539 246598540 chr1 246600082 246600083 DEL NA + - [Svaba_SR=80,Svaba_PE=77],[Manta_PE=75,Manta_SR=66],[Lumpy_PE=57,Lumpy_SR=43] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CNST;DisruptR=CNST;ClosestL=AL591623.1;ClosestR=AL591623.1 248946322 248946322 50,246598539,246600081 0,0,0 chr1 247222638 247222639 chr19 34641348 34641349 TRA NA - + [Manta_PE=15,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL390728.5;DisruptR=SCGB2B2;Fusion=AL390728.5-SCGB2B2;ClosestL=AL390728.1;ClosestR=AC020910.1 248946322 24018596 0,0,0 0,0,0 chr2 2752746 2752747 chr6 52542329 52542330 TRA NA - - [Svaba_SR=53,Svaba_PE=43],[Manta_PE=48,Manta_SR=52],[Lumpy_PE=39,Lumpy_SR=40] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=TRAM2;ClosestL=;ClosestR=EFHC1 10005 52679253 42,2752747,52542328 0,0,0 chr2 2752962 2752963 chr14 102959581 102959582 TRA NA + + [Svaba_SR=61,Svaba_PE=14],[Manta_PE=9,Manta_SR=67] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=CDC42BPB;ClosestL=;ClosestR= 10005 104243063 27,2752963,102959583 0,0,0 chr2 2752962 2752963 chr17 1788504 1788505 TRA NA + - [Svaba_SR=0,Svaba_PE=8] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=SMYD4;ClosestL=;ClosestR=SERPINF1 10005 168977 0,0,0 0,0,0 chr2 2752962 2752963 chr17 35740374 35740375 TRA NA + + [Svaba_SR=0,Svaba_PE=10],[Manta_PE=13,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=RASL10B,TAF15;ClosestL=;ClosestR=GAS2L2 10005 36041470 0,0,0 0,0,0 chr2 2752962 2752963 chr2 91414359 91414360 DEL NA + - [Manta_PE=12,Manta_SR=52] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=MYCN,PCBP1,C2orf44,NCOA1,ASXL2,SIX2,EPAS1,MSH6,FBXO11,BCL11A,REL,XPO1,DCTN1,DNMT3A,STRN,EML4,MSH2,ALK,BIRC6;DisruptL=;DisruptR=;ClosestL=;ClosestR= 10005 88778964 0,0,0 0,0,0 chr2 20726878 20726879 chr2 20774844 20774845 DEL NA + - [Svaba_SR=18,Svaba_PE=21],[Manta_PE=20,Manta_SR=15],[Lumpy_PE=18,Lumpy_SR=8] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LDAH;DisruptR=LDAH;ClosestL=;ClosestR= 24576134 24576134 14,20726880,20774843 0,0,0 chr2 24579528 24579529 chr2 24695351 24695352 DUP NA - + [Svaba_SR=75,Svaba_PE=105],[Manta_PE=98,Manta_SR=69],[Lumpy_PE=88,Lumpy_SR=49] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=NCOA1;DisruptL=NCOA1;DisruptR=NCOA1;ClosestL=RNA5SP88;ClosestR=RNU6-936P 24576135 24695333 51,24579529,24695353 0,0,0 chr2 33705112 33705113 chr2 33705891 33705892 DEL NA + - [Svaba_SR=20,Svaba_PE=15],[Manta_PE=10,Manta_SR=12],[Lumpy_PE=9,Lumpy_SR=11] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=LINC01317;ClosestR=LINC01317 37783334 37783334 11,33705113,33705890 0,0,0 chr2 37825636 37825637 chr17 72487322 72487323 TRA NA - - [Svaba_SR=50,Svaba_PE=71],[Manta_PE=72,Manta_SR=66],[Lumpy_PE=55,Lumpy_SR=38] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=LINC00511;ClosestL=LINC00211;ClosestR= 37783435 67148388 44,37825628,72487319 0,0,0 chr2 38612518 38612519 chr2 38613024 38613025 DEL NA + - [Svaba_SR=6,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=HNRNPLL;ClosestR=HNRNPLL 37783435 37783435 3,38612521,38613055 3,38612489,38613023 chr2 38736484 38736485 chr2 38737001 38737002 DEL NA + - [Svaba_SR=3,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=GALM;DisruptR=GALM;ClosestL=SRSF7;ClosestR=SRSF7 37783435 37783435 2,38736456,38737000 2,38736471,38737015 chr2 43636641 43636642 chr17 72729682 72729683 TRA NA + - [Svaba_SR=0,Svaba_PE=14] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=SLC39A11;ClosestL=PLEKHH2;ClosestR= 37783435 67148388 7,43636586,72729477 0,0,0 chr2 54143492 54143493 chr2 54144014 54144015 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ACYP2;DisruptR=ACYP2;ClosestL=;ClosestR= 62620851 62620851 2,54143479,54144013 0,0,0 chr2 56036441 56036442 chr2 56036958 56036959 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC011306.1,MIR217HG;DisruptR=AC011306.1,MIR217HG;ClosestL=;ClosestR= 62620851 62620851 2,56036468,56037002 0,0,0 chr2 61429217 61429218 chr2 61429804 61429805 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=USP34;DisruptR=USP34;ClosestL=SNORA70B;ClosestR=SNORA70B 62620851 62620851 2,61429191,61429803 0,0,0 chr2 62290737 62290738 chr5 105772044 105772045 TRA NA - + [Svaba_SR=0,Svaba_PE=14] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 62620851 87057657 24,62290654,105772046 3,62290654,105772046 chr2 62620835 62620836 chr2 63261205 63261206 DUP NA - + [Manta_PE=114,Manta_SR=115] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AC092155.1;DisruptR=WDPCP;Fusion=AC092155.1+WDPCP;ClosestL=;ClosestR= 62620851 63608437 2,62620843,63261207 0,0,0 chr2 63034488 63034489 chr13 16683886 16683887 TRA NA - + [Manta_PE=8,Manta_SR=27],[Lumpy_PE=8,Lumpy_SR=1] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=EHBP1;DisruptR=;ClosestL=AC009501.1;ClosestR= 62620851 16022426 28,63034489,16683890 0,0,0 chr2 89030048 89030049 chr2 90170406 90170407 INV NA + + [Svaba_SR=0,Svaba_PE=10],[Manta_PE=10,Manta_SR=193] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;gap;DisruptL=;DisruptR=;ClosestL=IGKV3-11;ClosestR=IGKV3D-11 88778964 88778964 64,89029966,90170600 0,0,0 chr2 91414360 91414361 chr14 102959494 102959495 TRA NA - - [Svaba_SR=73,Svaba_PE=3],[Manta_PE=4,Manta_SR=73] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=CDC42BPB;ClosestL=;ClosestR= 88778964 104243063 16,91414360,102959493 0,0,0 chr2 91414462 91414463 chr17 1788504 1788505 TRA NA + - [Svaba_SR=0,Svaba_PE=12] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=SMYD4;ClosestL=;ClosestR=SERPINF1 88778964 168977 0,0,0 0,0,0 chr2 91414462 91414463 chr17 35740374 35740375 TRA NA + + [Svaba_SR=65,Svaba_PE=0],[Manta_PE=3,Manta_SR=63] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=RASL10B,TAF15;ClosestL=;ClosestR=GAS2L2 88778964 36041470 40,91414462,35740376 0,0,0 chr2 91414656 91414657 chr9 72458107 72458108 TRA NA + + [Manta_PE=19,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=AL445646.1 88778964 65515655 0,0,0 0,0,0 chr2 95932717 95932718 chr13 108955080 108955081 TRA NA + + [Svaba_SR=0,Svaba_PE=11] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ANKRD36C;DisruptR=MYO16;Fusion=MYO16-ANKRD36C;ClosestL=;ClosestR= 99488531 108951936 10,95932719,108955082 0,0,0 chr2 96182289 96182290 chr2 96182876 96182877 DEL NA + - [Svaba_SR=2,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=STARD7;ClosestR=STARD7 99488531 99488531 2,96182462,96182770 0,0,0 chr2 96997335 96997336 chr11 73060366 73060367 TRA NA + + [Svaba_SR=76,Svaba_PE=83],[Manta_PE=83,Manta_SR=66] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=FCHSD2;ClosestL=AC079395.3;ClosestR= 99488531 73060315 42,96997336,73060368 0,0,0 chr2 97814209 97814210 chr22 28275521 28275522 TRA NA + + [Manta_PE=5,Manta_SR=5] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TMEM131;DisruptR=TTC28;ClosestL=HMGN1P36;ClosestR= 99488531 29285918 5,97814211,28275523 0,0,0 chr2 99435881 99435882 chr2 103741227 103741228 INV NA - - [Svaba_SR=11,Svaba_PE=16],[Manta_PE=13,Manta_SR=12],[Lumpy_PE=9,Lumpy_SR=9] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=AFF3;DisruptL=REV1;DisruptR=;ClosestL=;ClosestR= 99488531 103111952 10,99435880,103741226 0,0,0 chr2 99500341 99500342 chr2 101098846 101098847 DEL NA + - [Svaba_SR=14,Svaba_PE=15],[Manta_PE=19,Manta_SR=14],[Lumpy_PE=15,Lumpy_SR=6] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=AFF3;DisruptL=;DisruptR=TBC1D8;ClosestL=REV1;ClosestR= 99488531 99488531 7,99500343,101098845 0,0,0 chr2 99677001 99677002 chr22 24803524 24803525 TRA NA - + [Svaba_SR=27,Svaba_PE=48],[Manta_PE=52,Manta_SR=51],[Lumpy_PE=31,Lumpy_SR=36] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=AFF3;DisruptL=AFF3;DisruptR=;ClosestL=;ClosestR=SGSM1 99488531 23762694 39,99677001,24803526 0,0,0 chr2 99696052 99696053 chr2 99745352 99745353 INV NA + + [Svaba_SR=52,Svaba_PE=35],[Manta_PE=55,Manta_SR=45],[Lumpy_PE=49,Lumpy_SR=39] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=AFF3;DisruptL=AFF3;DisruptR=AFF3;ClosestL=;ClosestR= 99488531 99488531 21,99696052,99745354 0,0,0 chr2 100094212 100094213 chr2 104093617 104093618 INV NA - - [Svaba_SR=8,Svaba_PE=15],[Manta_PE=11,Manta_SR=7],[Lumpy_PE=9,Lumpy_SR=2] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=AFF3;DisruptL=AFF3;DisruptR=;ClosestL=AC092667.1;ClosestR=LINC01965 99488531 103111952 7,100094213,104093616 0,0,0 chr2 101119638 101119639 chr10 38528505 38528506 TRA NA - - [Svaba_SR=51,Svaba_PE=65] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TBC1D8;DisruptR=;ClosestL=;ClosestR= 99488531 38483627 33,101119642,38528504 0,0,0 chr2 101119900 101119901 chr10 38527882 38527883 TRA NA + - [Lumpy_PE=55,Lumpy_SR=26] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TBC1D8;DisruptR=;ClosestL=;ClosestR= 99488531 38483627 17,101119900,38527880 0,0,0 chr2 101672709 101672710 chr10 38925618 38925619 TRA NA - + [Manta_PE=3,Manta_SR=8],[Lumpy_PE=3,Lumpy_SR=4] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 103111952 38581843 7,101672713,38925625 0,0,0 chr2 103110745 103110746 chr2 103111960 103111961 INV NA + + [Svaba_SR=65,Svaba_PE=71],[Manta_PE=73,Manta_SR=54],[Lumpy_PE=64,Lumpy_SR=44] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC073987.1;DisruptR=AC073987.1;ClosestL=;ClosestR= 103111952 103111952 43,103110745,103111962 0,0,0 chr2 103221168 103221169 chr2 103222716 103222717 DUP NA - + [Svaba_SR=12,Svaba_PE=15],[Manta_PE=10,Manta_SR=12],[Lumpy_PE=11,Lumpy_SR=11] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 103111952 103111952 10,103221169,103222718 0,0,0 chr2 103221390 103221391 chr2 103221966 103221967 INV NA + + [Manta_PE=11,Manta_SR=12],[Lumpy_PE=10,Lumpy_SR=11] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 103111952 103111952 12,103221392,103221968 0,0,0 chr2 104061834 104061835 chr22 49964192 49964193 TRA NA - + [Svaba_SR=53,Svaba_PE=64],[Manta_PE=52,Manta_SR=49],[Lumpy_PE=36,Lumpy_SR=37] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC01965;DisruptR=;ClosestL=;ClosestR=PIM3 103111952 50808368 41,104061833,49964194 0,0,0 chr2 104063183 104063184 chr22 49963830 49963831 TRA NA - - [Svaba_SR=66,Svaba_PE=60],[Manta_PE=74,Manta_SR=59],[Lumpy_PE=48,Lumpy_SR=45] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC01965;DisruptR=PIM3;ClosestL=;ClosestR=MIR6821 103111952 50808368 47,104063183,49963829 0,0,0 chr2 104240194 104240195 chr16 465006 465007 TRA NA + - [Svaba_SR=112,Svaba_PE=137],[Manta_PE=120,Manta_SR=88],[Lumpy_PE=88,Lumpy_SR=73] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=RAB11FIP3;ClosestL=;ClosestR=AL049542.1 103111952 452830 58,104240194,465005 0,0,0 chr2 104379092 104379093 chr2 104390383 104390384 DEL NA + - [Svaba_SR=4,Svaba_PE=5],[Manta_PE=6,Manta_SR=3],[Lumpy_PE=4,Lumpy_SR=3] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AHCYP3;ClosestR=AHCYP3 103111952 103111952 3,104379089,104390382 0,0,0 chr2 109290685 109290686 chr18 24684289 24684290 TRA NA - + [Svaba_SR=43,Svaba_PE=53],[Manta_PE=51,Manta_SR=38],[Lumpy_PE=39,Lumpy_SR=29] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SH3RF3;DisruptR=;ClosestL=;ClosestR=RAC1P1 109199785 24684278 30,109290684,24684292 0,0,0 chr2 114725269 114725270 chr18 63805018 63805019 TRA NA + - [Svaba_SR=41,Svaba_PE=53],[Manta_PE=49,Manta_SR=37],[Lumpy_PE=40,Lumpy_SR=24] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=DPP10;DisruptR=SERPINB7;Fusion=DPP10-SERPINB7;ClosestL=;ClosestR= 114973555 63805005 31,114725273,63805016 0,0,0 chr2 114974129 114974130 chr21 32740681 32740682 TRA NA + + [Svaba_SR=66,Svaba_PE=51],[Manta_PE=52,Manta_SR=62],[Lumpy_PE=38,Lumpy_SR=40] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=DPP10;DisruptR=PAXBP1-AS1,PAXBP1;Fusion=DPP10-PAXBP1;ClosestL=;ClosestR=SYNJ1 114973556 32739135 2,114974135,32740683 0,0,0 chr2 115753396 115753397 chr22 28670291 28670292 TRA NA - + [Manta_PE=33,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=DPP10;DisruptR=TTC28;ClosestL=;ClosestR=CHEK2 114973556 29285918 0,0,0 0,0,0 chr2 115753450 115753451 chr22 28669982 28669983 TRA NA + - [Svaba_SR=30,Svaba_PE=15],[Manta_PE=14,Manta_SR=35],[Lumpy_PE=5,Lumpy_SR=28] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=DPP10;DisruptR=TTC28;ClosestL=;ClosestR=CHEK2 114973556 29285918 2,115753453,28669984 0,0,0 chr2 131870853 131870854 chr21 13506276 13506277 TRA NA - - [Manta_PE=4,Manta_SR=97] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=GTF2IP2 114973556 13507200 71,131870853,13506274 0,0,0 chr2 135367225 135367226 chr2 135375203 135375204 DEL NA + - [Svaba_SR=116,Svaba_PE=133],[Manta_PE=142,Manta_SR=124],[Lumpy_PE=91,Lumpy_SR=101] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ZRANB3;DisruptR=ZRANB3;ClosestL=;ClosestR= 152347874 152347874 74,135367224,135375202 0,0,0 chr2 142877181 142877182 chr2 142883246 142883247 DEL NA + - [Manta_PE=92,Manta_SR=66],[Lumpy_PE=66,Lumpy_SR=40] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=KYNU;ClosestL=KYNU;ClosestR= 152347874 152347874 44,142877187,142883245 0,0,0 chr2 152347817 152347818 chr2 152457171 152457172 DEL NA + - [Svaba_SR=80,Svaba_PE=102],[Manta_PE=90,Manta_SR=64],[Lumpy_PE=64,Lumpy_SR=57] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=FMNL2;DisruptR=FMNL2;ClosestL=;ClosestR= 152347874 152457124 45,152347818,152457170 0,0,0 chr2 154086668 154086669 chr2 154188587 154188588 DEL NA + - [Lumpy_PE=3,Lumpy_SR=1] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=GALNT13;DisruptR=GALNT13;ClosestL=;ClosestR= 152457124 152457124 0,0,0 0,0,0 chr2 165399970 165399971 chr2 166129437 166129438 DUP NA - + [Svaba_SR=125,Svaba_PE=163],[Manta_PE=144,Manta_SR=113],[Lumpy_PE=121,Lumpy_SR=89] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=AC010127.1,SCN1A;ClosestL=SCN2A;ClosestR=RF00019 152457124 152457124 74,165399973,166129439 0,0,0 chr2 169589891 169589892 chr2 169590392 169590393 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PPIG;DisruptR=PPIG;ClosestL=AC093899.1;ClosestR=AC093899.1 152457124 152457124 0,0,0 0,0,0 chr2 179388075 179388076 chrX 4728101 4728102 TRA NA + - [Svaba_SR=104,Svaba_PE=131],[Manta_PE=85,Manta_SR=104] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC068042.1;ClosestR= 152457124 10446 41,179388069,4728100 0,0,0 chr2 179388334 179388335 chrX 4728528 4728529 TRA NA - + [Svaba_SR=120,Svaba_PE=115],[Manta_PE=95,Manta_SR=107],[Lumpy_PE=61,Lumpy_SR=44] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC068042.1;ClosestR= 152457124 10446 56,179388337,4728530 0,0,0 chr2 187552041 187552042 chr2 187556879 187556880 DEL NA + - [Svaba_SR=47,Svaba_PE=69],[Manta_PE=56,Manta_SR=65],[Lumpy_PE=46,Lumpy_SR=9] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC007319.1,TFPI;DisruptR=TFPI;ClosestL=;ClosestR=AC007319.1 152457124 152457124 43,187552043,187556878 0,0,0 chr2 188399228 188399229 chr10 61749857 61749858 TRA NA + + [Svaba_SR=0,Svaba_PE=9] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=GULP1;DisruptR=CABCOCO1;ClosestL=LINC01090;ClosestR= 152457124 63904555 0,0,0 0,0,0 chr2 188399228 188399229 chr5 59193764 59193765 TRA NA + - [Svaba_SR=32,Svaba_PE=0],[Manta_PE=2,Manta_SR=30],[Lumpy_PE=2,Lumpy_SR=26] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=GULP1;DisruptR=PDE4D;ClosestL=LINC01090;ClosestR= 152457124 32366973 24,188399230,59193763 0,0,0 chr2 218087110 218087111 chr2 218098245 218098246 DEL NA + - [Svaba_SR=88,Svaba_PE=111],[Manta_PE=94,Manta_SR=78],[Lumpy_PE=66,Lumpy_SR=54] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=RUFY4;DisruptR=;ClosestL=;ClosestR=RUFY4 242183395 242183395 50,218087112,218098244 0,0,0 chr2 231346157 231346158 chr6 31326327 31326328 TRA NA - - [Manta_PE=8,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ARMC9;DisruptR=HLA-B;Fusion=HLA-B-ARMC9;ClosestL=MIR4777;ClosestR=AL671883.1 242183395 32487100 2,231346247,31326315 0,0,0 chr3 9307908 9307909 chr3 9404959 9404960 DUP NA - + [Svaba_SR=141,Svaba_PE=206],[Manta_PE=185,Manta_SR=160],[Lumpy_PE=169,Lumpy_SR=74] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SRGAP3,AC026191.1;DisruptR=SETD5;ClosestL=;ClosestR=THUMPD3-AS1 9307882 9404942 0,0,0 0,0,0 chr3 9676589 9676590 chr3 10083212 10083213 DUP NA - + [Svaba_SR=101,Svaba_PE=154],[Manta_PE=238,Manta_SR=215],[Lumpy_PE=207,Lumpy_SR=143] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=FANCD2;DisruptL=MTMR14;DisruptR=FANCD2,FANCD2OS;Fusion=FANCD2+MTMR14;ClosestL=;ClosestR= 9676504 10083194 92,9676588,10083214 0,0,0 chr3 13545519 13545520 chr9 72457733 72457734 TRA NA - - [Manta_PE=56,Manta_SR=60],[Lumpy_PE=16,Lumpy_SR=43] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=FBLN2;ClosestR=AL445646.1 10083194 65515655 43,13545512,72457732 0,0,0 chr3 13545970 13545971 chr6 144660231 144660232 TRA NA + - [Svaba_SR=78,Svaba_PE=51],[Manta_PE=32,Manta_SR=75],[Lumpy_PE=17,Lumpy_SR=55] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=UTRN;ClosestL=FBLN2;ClosestR= 10083194 130003967 44,13545972,144660224 0,0,0 chr3 13546016 13546017 chr21 32343817 32343818 TRA NA + + [Manta_PE=41,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=URB1;ClosestL=FBLN2;ClosestR= 10083194 32739134 0,0,0 0,0,0 chr3 37547039 37547040 chr3 37719792 37719793 DUP NA - + [Svaba_SR=120,Svaba_PE=156],[Manta_PE=143,Manta_SR=99],[Lumpy_PE=114,Lumpy_SR=74] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ITGA9;DisruptR=ITGA9;ClosestL=;ClosestR= 37547021 37719800 67,37547042,37719794 0,0,0 chr3 39770251 39770252 chr3 41312685 41312686 DUP NA - + [Manta_PE=246,Manta_SR=194],[Lumpy_PE=229,Lumpy_SR=153] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=CTNNB1;DisruptL=;DisruptR=ULK4;ClosestL=;ClosestR= 39770243 41312676 90,39770256,41312692 0,0,0 chr3 40113427 40113428 chr3 40113941 40113942 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MYRIP;DisruptR=MYRIP;ClosestL=;ClosestR= 39770243 39770243 2,40113430,40113972 0,0,0 chr3 41157963 41157964 chrX 87668583 87668584 TRA NA + - [Svaba_SR=0,Svaba_PE=8],[Manta_PE=28,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=KLHL4;ClosestL=AC009743.1;ClosestR= 41312675 87103947 0,0,0 0,0,0 chr3 41158029 41158030 chr14 100903975 100903976 TRA NA + + [Manta_PE=20,Manta_SR=57],[Lumpy_PE=8,Lumpy_SR=44] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=AL117190.1,MEG8;ClosestL=AC009743.1;ClosestR=RF02146 41312675 104243063 27,41158031,100903977 0,0,0 chr3 41158172 41158173 chr11 80765383 80765384 TRA NA + + [Manta_PE=16,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC009743.1;ClosestR=AP002759.1 41312675 80765206 0,0,0 0,0,0 chr3 52565285 52565286 chr3 52629472 52629473 DEL NA + - [Svaba_SR=159,Svaba_PE=142],[Manta_PE=162,Manta_SR=148],[Lumpy_PE=20,Lumpy_SR=73] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=PBRM1;DisruptL=SMIM4,PBRM1;DisruptR=PBRM1;ClosestL=RNU6ATAC16P;ClosestR= 52565238 52629454 52,52565284,52629471 0,0,0 chr3 85183520 85183521 chr3 85187151 85187152 INV NA - - [Svaba_SR=160,Svaba_PE=111],[Manta_PE=120,Manta_SR=153],[Lumpy_PE=81,Lumpy_SR=117] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CADM2;DisruptR=CADM2;ClosestL=;ClosestR= 85183522 85183523 82,85183519,85187150 0,0,0 chr3 85660778 85660779 chr3 85663710 85663711 DEL NA + - [Svaba_SR=115,Svaba_PE=143],[Manta_PE=145,Manta_SR=123],[Lumpy_PE=102,Lumpy_SR=91] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CADM2;DisruptR=CADM2;ClosestL=;ClosestR= 85183523 85183523 72,85660777,85663709 0,0,0 chr3 89237131 89237132 chr3 89237724 89237725 DEL NA + - [Svaba_SR=2,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=EPHA3;DisruptL=EPHA3;DisruptR=EPHA3;ClosestL=;ClosestR= 85183523 85183523 2,89237121,89237723 0,0,0 chr3 91672220 91672221 chr3 95006137 95006138 DUP NA - + [Svaba_SR=54,Svaba_PE=9] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;DisruptL=;DisruptR=LINC00879;ClosestL=;ClosestR= 93455911 95006170 35,91672224,95006139 0,0,0 chr3 94678278 94678279 chr10 61749704 61749705 TRA NA - - [Svaba_SR=16,Svaba_PE=6],[Manta_PE=6,Manta_SR=14],[Lumpy_PE=3,Lumpy_SR=14] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=CABCOCO1;ClosestL=;ClosestR= 95006170 63904555 12,94678277,61749703 0,0,0 chr3 95900220 95900221 chr5 153304740 153304741 TRA NA + - [Svaba_SR=16,Svaba_PE=22],[Manta_PE=12,Manta_SR=14],[Lumpy_PE=8,Lumpy_SR=4] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 95006171 164930824 13,95900222,153304738 0,0,0 chr3 117319407 117319408 chr3 117323182 117323183 DEL NA + - [Svaba_SR=64,Svaba_PE=56],[Manta_PE=76,Manta_SR=64],[Lumpy_PE=49,Lumpy_SR=42] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 95006171 95006171 43,117319408,117323181 0,0,0 chr3 118777822 118777823 chr11 27802442 27802443 TRA NA + - [Manta_PE=19,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=AC103796.1;ClosestL=;ClosestR=CBX3P1 95006171 27802357 18,118777671,27802427 0,0,0 chr3 118888078 118888079 chr3 118888600 118888601 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=IGSF11;ClosestR=IGSF11 95006171 95006171 4,118888060,118888599 0,0,0 chr3 125715080 125715081 chr8 11917875 11917876 TRA NA + + [Svaba_SR=0,Svaba_PE=22] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=OR7E29P;ClosestR=OR7E158P 95006171 71162 6,125715094,11917855 3,125715094,11917855 chr3 126089031 126089032 chr3 126135677 126135678 DEL NA + - [Svaba_SR=70,Svaba_PE=92],[Manta_PE=80,Manta_SR=55],[Lumpy_PE=60,Lumpy_SR=40] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SLC41A3,AC079848.1;DisruptR=ALDH1L1;Fusion=ALDH1L1+SLC41A3;ClosestL=ALDH1L1;ClosestR= 95006171 95006171 43,126089033,126135676 0,0,0 chr3 132552072 132552073 chr21 16887338 16887339 TRA NA + - [Svaba_SR=13,Svaba_PE=10],[Manta_PE=8,Manta_SR=13],[Lumpy_PE=3,Lumpy_SR=10] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=ACAD11;ClosestR=AF212831.1 95006171 17474345 12,132552074,16887337 0,0,0 chr3 156596536 156596537 chr20 22251588 22251589 TRA NA - - [Svaba_SR=52,Svaba_PE=53],[Manta_PE=35,Manta_SR=46],[Lumpy_PE=26,Lumpy_SR=17] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=LINC01427 170316051 22252838 37,156596535,22251587 0,0,0 chr3 156596713 156596714 chr20 22253039 22253040 TRA NA + - [Svaba_SR=51,Svaba_PE=53],[Manta_PE=29,Manta_SR=42],[Lumpy_PE=17,Lumpy_SR=22] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=LINC01427 170316051 22252839 34,156596713,22253038 0,0,0 chr3 170317088 170317089 chr3 195524531 195524532 INV NA - - [Svaba_SR=76,Svaba_PE=87],[Manta_PE=85,Manta_SR=65],[Lumpy_PE=60,Lumpy_SR=51] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=SOX2,EIF4A2,TBL1XR1,PIK3CA,ETV5,BCL6,MAP3K13,IGF2BP2,MB21D2,LPP,TP63;DisruptL=;DisruptR=PPP1R2;ClosestL=PRKCI;ClosestR=RNU6ATAC24P 170316052 194247704 50,170317087,195524530 0,0,0 chr3 172508108 172508109 chr3 172508637 172508638 DEL NA + - [Svaba_SR=4,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TNFSF10;DisruptR=TNFSF10;ClosestL=AC007919.1;ClosestR=AC007919.1 173658862 173658862 0,0,0 0,0,0 chr3 173507699 173507700 chr3 195524477 195524478 INV NA + + [Svaba_SR=87,Svaba_PE=98],[Manta_PE=97,Manta_SR=81],[Lumpy_PE=84,Lumpy_SR=36] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=SOX2,EIF4A2,TBL1XR1,PIK3CA,ETV5,BCL6,MAP3K13,IGF2BP2,MB21D2,LPP,TP63;DisruptL=NLGN1;DisruptR=PPP1R2;Fusion=NLGN1+PPP1R2;ClosestL=;ClosestR=RNU6ATAC24P 173658862 194247704 2,173507702,195524476 0,0,0 chr3 173507997 173507998 chr3 194247718 194247719 INV NA - - [Svaba_SR=95,Svaba_PE=78],[Manta_PE=80,Manta_SR=72],[Lumpy_PE=71,Lumpy_SR=18] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=SOX2,EIF4A2,TBL1XR1,PIK3CA,ETV5,BCL6,MAP3K13,IGF2BP2,MB21D2,LPP,TP63;DisruptL=NLGN1;DisruptR=LINC02036,LINC02037;Fusion=LINC02036+NLGN1;ClosestL=;ClosestR= 173658862 194247704 0,0,0 0,0,0 chr3 183359784 183359785 chr5 139903988 139903989 TRA NA - - [Manta_PE=32,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=MCF2L2;DisruptR=NRG2;ClosestL=;ClosestR= 173658863 140717308 0,0,0 0,0,0 chr3 184847740 184847741 chr3 184849216 184849217 DEL NA + - [Svaba_SR=20,Svaba_PE=17],[Manta_PE=14,Manta_SR=17],[Lumpy_PE=11,Lumpy_SR=10] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=VPS8;DisruptR=VPS8;ClosestL=;ClosestR= 194247703 194247703 16,184847741,184849215 0,0,0 chr3 193906127 193906128 chr3 193912491 193912492 DEL NA + - [Svaba_SR=112,Svaba_PE=158],[Manta_PE=178,Manta_SR=149],[Lumpy_PE=112,Lumpy_SR=88] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 194247703 194247703 85,193906127,193912490 0,0,0 chr3 195633717 195633718 chr3 195955631 195955632 INV NA + + [Svaba_SR=0,Svaba_PE=8] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=MUC4;DisruptL=;DisruptR=;ClosestL=AC233280.19;ClosestR=AC124944.3 194247704 194247704 0,0,0 0,0,0 chr3 195962022 195962023 chr5 257351 257352 TRA NA + + [Lumpy_PE=4,Lumpy_SR=1] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SDHAP1;DisruptR=;ClosestL=AC124944.3;ClosestR=SDHA 194247704 11484 0,0,0 0,0,0 chr3 198139640 198139641 chr9 138203526 138203527 TRA NA - + [Svaba_SR=10,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;ClosestL=FAM157A;ClosestR=AL954642.1 198139690 138313848 46,198139650,138203528 20,198139650,138203528 chr4 11268 11269 chr20 36928702 36928703 TRA NA - - [Manta_PE=1,Manta_SR=54] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=SAMHD1;ClosestL=;ClosestR= 10011 36912931 40,11267,36928701 0,0,0 chr4 1662627 1662628 chr4 1663152 1663153 DEL NA + - [Svaba_SR=3,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAM53A;DisruptR=FAM53A;ClosestL=;ClosestR= 10011 10011 3,1662611,1663151 2,1662611,1663151 chr4 7325452 7325453 chr10 51269343 51269344 TRA NA + - [Svaba_SR=250,Svaba_PE=139],[Manta_PE=236,Manta_SR=241],[Lumpy_PE=159,Lumpy_SR=202] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SORCS2;DisruptR=PRKG1;Fusion=SORCS2-PRKG1;ClosestL=MIR4798;ClosestR= 7325438 39340909 101,7325452,51269342 0,0,0 chr4 7325537 7325538 chr10 51033186 51033187 TRA NA + - [Manta_PE=30,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SORCS2;DisruptR=PRKG1;Fusion=SORCS2-PRKG1;ClosestL=MIR4798;ClosestR= 7325438 39340909 0,0,0 0,0,0 chr4 7325566 7325567 chr10 51033707 51033708 TRA NA + - [Manta_PE=14,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SORCS2;DisruptR=PRKG1;Fusion=SORCS2-PRKG1;ClosestL=MIR4798;ClosestR= 7325438 39340909 0,0,0 0,0,0 chr4 7334742 7334743 chr10 50990887 50990888 TRA NA - + [Svaba_SR=0,Svaba_PE=148] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SORCS2;DisruptR=;ClosestL=;ClosestR=PRKG1 7334738 39340909 0,0,0 0,0,0 chr4 7334743 7334744 chr10 50991309 50991310 TRA NA - + [Svaba_SR=172,Svaba_PE=258],[Manta_PE=234,Manta_SR=160],[Lumpy_PE=185,Lumpy_SR=124] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SORCS2;DisruptR=PRKG1;Fusion=PRKG1-SORCS2;ClosestL=;ClosestR= 7334738 39340909 84,7334745,50991311 0,0,0 chr4 13541213 13541214 chr4 13542655 13542656 DEL NA + - [Svaba_SR=79,Svaba_PE=90],[Manta_PE=76,Manta_SR=64],[Lumpy_PE=49,Lumpy_SR=54] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=NKX3-2;DisruptR=NKX3-2;ClosestL=LINC01096;ClosestR=LINC01096 14827697 14827697 48,13541212,13542654 0,0,0 chr4 14827425 14827426 chr4 15665086 15665087 DUP NA - + [Svaba_SR=120,Svaba_PE=120],[Manta_PE=118,Manta_SR=107],[Lumpy_PE=97,Lumpy_SR=71] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC00504;DisruptR=FBXL5;Fusion=LINC00504+FBXL5;ClosestL=;ClosestR=FAM200B 14827697 15665044 66,14827427,15665088 0,0,0 chr4 22959992 22959993 chr4 22967233 22967234 DEL NA + - [Svaba_SR=124,Svaba_PE=155],[Manta_PE=207,Manta_SR=187],[Lumpy_PE=138,Lumpy_SR=149] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;ClosestL=;ClosestR= 22959993 22967181 93,22959992,22967232 0,0,0 chr4 37747941 37747942 chr4 37749092 37749093 DEL NA + - [Svaba_SR=58,Svaba_PE=92],[Manta_PE=57,Manta_SR=59],[Lumpy_PE=59,Lumpy_SR=39] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 22967181 22967181 43,37747943,37749087 0,0,0 chr4 41713489 41713490 chr4 41722276 41722277 DEL NA + - [Svaba_SR=66,Svaba_PE=70],[Manta_PE=64,Manta_SR=57],[Lumpy_PE=49,Lumpy_SR=30] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=OR5M14P;ClosestR=OR5M14P 52771714 52771714 44,41713489,41722275 0,0,0 chr4 49105206 49105207 chr20 31063266 31063267 TRA NA + + [Lumpy_PE=3,Lumpy_SR=1] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 52771714 31001398 3,49105454,31063399 2,49105439,31063154 chr4 49116427 49116428 chr20 31158101 31158102 TRA NA + + [Lumpy_PE=6,Lumpy_SR=1] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 52771714 31245066 12,49116671,31157871 3,49116671,31157871 chr4 53357079 53357080 chr17 26663485 26663486 TRA NA - + [Svaba_SR=0,Svaba_PE=8] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SCFD2;DisruptR=;ClosestL=;ClosestR= 52771742 22044138 0,0,0 0,0,0 chr4 53357080 53357081 chr20 31572615 31572616 TRA NA - - [Svaba_SR=10,Svaba_PE=13],[Manta_PE=9,Manta_SR=10],[Lumpy_PE=7,Lumpy_SR=4] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SCFD2;DisruptR=HM13,HM13-AS1;Fusion=SCFD2-HM13;ClosestL=;ClosestR=AL110115.2 52771742 31539639 8,53357077,31572614 0,0,0 chr4 54132841 54132842 chr4 54134550 54134551 DEL NA + - [Svaba_SR=81,Svaba_PE=90],[Manta_PE=83,Manta_SR=69],[Lumpy_PE=56,Lumpy_SR=47] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC058822.1;DisruptR=AC058822.1;ClosestL=;ClosestR= 52771742 52771742 51,54132841,54134549 0,0,0 chr4 57019050 57019051 chr7 56443992 56443993 TRA NA - - [Svaba_SR=53,Svaba_PE=59],[Manta_PE=60,Manta_SR=52],[Lumpy_PE=38,Lumpy_SR=42] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=POLR2B;DisruptR=AC092447.7;Fusion=AC092447.7-POLR2B;ClosestL=IGFBP7;ClosestR=AC092447.10 57018942 57487363 39,57019050,56443991 0,0,0 chr4 59828040 59828041 chr4 59828615 59828616 DEL NA + - [Manta_PE=199,Manta_SR=249] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=RF00019;ClosestR=RF00019 59832663 59832663 102,59828042,59828615 0,0,0 chr4 59832640 59832641 chr9 28551943 28551944 TRA NA + - [Svaba_SR=246,Svaba_PE=154],[Manta_PE=290,Manta_SR=232] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=LINGO2;ClosestL=RF00019;ClosestR= 59832663 28551865 104,59832641,28551942 0,0,0 chr4 62845468 62845469 chr8 45569174 45569175 TRA NA - - [Svaba_SR=0,Svaba_PE=40],[Manta_PE=5,Manta_SR=177] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 62845466 44968553 0,0,0 0,0,0 chr4 65266719 65266720 chr11 69365928 69365929 TRA NA + - [Manta_PE=357,Manta_SR=309] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=MYEOV;ClosestL=;ClosestR=AP005233.2 65266705 69356467 105,65266721,69365927 0,0,0 chr4 82823868 82823869 chr8 97238613 97238614 TRA NA - + [Svaba_SR=105,Svaba_PE=84],[Manta_PE=46,Manta_SR=101],[Lumpy_PE=18,Lumpy_SR=75] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=SEC31A;DisruptR=;ClosestL=;ClosestR=AP003115.1 89015232 97238582 54,82823867,97238615 0,0,0 chr4 82823983 82823984 chr8 96324292 96324293 TRA NA + - [Svaba_SR=145,Svaba_PE=0],[Manta_PE=63,Manta_SR=131],[Lumpy_PE=21,Lumpy_SR=66] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=SEC31A;DisruptR=PTDSS1;ClosestL=;ClosestR=RF00019 89015232 96324266 66,82823985,96324285 0,0,0 chr4 91384071 91384072 chr18 61626507 61626508 TRA NA + - [Svaba_SR=161,Svaba_PE=218],[Manta_PE=197,Manta_SR=138],[Lumpy_PE=152,Lumpy_SR=97] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=CCSER1;DisruptR=AC105094.2;ClosestL=;ClosestR=AC090409.1 91384038 61626460 79,91384073,61626505 0,0,0 chr4 91964436 91964437 chr4 91968879 91968880 INV NA - - [Svaba_SR=118,Svaba_PE=134],[Manta_PE=134,Manta_SR=121] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;ClosestL=;ClosestR= 91964420 91964420 69,91964435,91968878 0,0,0 chr4 92714812 92714813 chr4 92741756 92741757 INV NA + + [Svaba_SR=8,Svaba_PE=13],[Manta_PE=13,Manta_SR=7],[Lumpy_PE=22,Lumpy_SR=14] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=GRID2;DisruptR=GRID2;ClosestL=MTND1P19;ClosestR= 91964420 91964420 7,92714814,92741758 0,0,0 chr4 92714816 92714817 chr4 92741712 92741713 INV NA - - [Svaba_SR=14,Svaba_PE=14],[Manta_PE=14,Manta_SR=13],[Lumpy_PE=22,Lumpy_SR=14] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=GRID2;DisruptR=GRID2;ClosestL=MTND1P19;ClosestR= 91964420 91964420 10,92714815,92741704 0,0,0 chr4 189021274 189021275 chr4 189022112 189022113 DUP NA - + [Svaba_SR=75,Svaba_PE=87],[Manta_PE=72,Manta_SR=64],[Lumpy_PE=65,Lumpy_SR=45] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC122138.1;ClosestR= 190066290 190066290 51,189021273,189022114 0,0,0 chr4 189021849 189021850 chr4 189024736 189024737 DEL NA + - [Svaba_SR=70,Svaba_PE=64],[Manta_PE=67,Manta_SR=65],[Lumpy_PE=43,Lumpy_SR=44] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;ClosestL=AC122138.1;ClosestR= 190066290 190066290 44,189021851,189024730 0,0,0 chr5 11509436 11509437 chr10 3336263 3336264 TRA NA + - [Svaba_SR=61,Svaba_PE=46],[Manta_PE=66,Manta_SR=56],[Lumpy_PE=44,Lumpy_SR=47] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=CTNND2;DisruptL=CTNND2;DisruptR=;ClosestL=;ClosestR= 11509602 3336246 21,11509433,3336262 0,0,0 chr5 23767939 23767940 chr5 23769678 23769679 DEL NA + - [Svaba_SR=70,Svaba_PE=85],[Manta_PE=68,Manta_SR=64],[Lumpy_PE=46,Lumpy_SR=47] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 32366972 32366972 47,23767941,23769673 0,0,0 chr5 28710819 28710820 chr5 28711436 28711437 DEL NA + - [Svaba_SR=149,Svaba_PE=153],[Lumpy_PE=165,Lumpy_SR=143] lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 32366972 32366972 2,28710821,28711429 0,0,0 chr5 30463531 30463532 chr5 30475422 30475423 DEL NA + - [Svaba_SR=55,Svaba_PE=80],[Manta_PE=71,Manta_SR=50],[Lumpy_PE=51,Lumpy_SR=38] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;ClosestL=;ClosestR= 32366972 32366972 41,30463532,30475421 0,0,0 chr5 32366999 32367000 chr10 63904597 63904598 TRA NA + + [Svaba_SR=106,Svaba_PE=108],[Manta_PE=116,Manta_SR=101],[Lumpy_PE=75,Lumpy_SR=73] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ZFR;DisruptR=AC022387.1;Fusion=AC022387.1-ZFR;ClosestL=;ClosestR=RPL7AP50 32366973 63904556 58,32367001,63904599 0,0,0 chr5 43171736 43171737 chr5 43188686 43188687 DEL NA + - [Svaba_SR=46,Svaba_PE=25],[Manta_PE=20,Manta_SR=41],[Lumpy_PE=11,Lumpy_SR=19] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ZNF131;DisruptR=ZNF131;ClosestL=;ClosestR=NIM1K 32366973 32366973 34,43171736,43188685 0,0,0 chr5 59193924 59193925 chr10 61749857 61749858 TRA NA + + [Manta_PE=3,Manta_SR=17],[Lumpy_PE=4,Lumpy_SR=11] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PDE4D;DisruptR=CABCOCO1;Fusion=CABCOCO1-PDE4D;ClosestL=;ClosestR= 32366973 63904555 17,59193926,61749859 0,0,0 chr5 59747086 59747087 chr5 59755805 59755806 DUP NA - + [Svaba_SR=16,Svaba_PE=12],[Manta_PE=10,Manta_SR=15],[Lumpy_PE=7,Lumpy_SR=15] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PDE4D;DisruptR=PDE4D;ClosestL=;ClosestR= 87038731 87038731 14,59747085,59755807 0,0,0 chr5 76588049 76588050 chr10 12934286 12934287 TRA NA - + [Svaba_SR=75,Svaba_PE=34],[Manta_PE=31,Manta_SR=68],[Lumpy_PE=19,Lumpy_SR=50] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=IQGAP2;DisruptR=CCDC3;ClosestL=AC026725.1;ClosestR=RNA5SP300 87038731 3336246 50,76588048,12934288 0,0,0 chr5 76588332 76588333 chr7 43643802 43643803 TRA NA + + [Manta_PE=23,Manta_SR=43],[Lumpy_PE=13,Lumpy_SR=36] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=IQGAP2;DisruptR=COA1;Fusion=IQGAP2-COA1;ClosestL=AC026725.1;ClosestR=STK17A 87038731 43477639 31,76588334,43643804 0,0,0 chr5 78710196 78710197 chr5 78727227 78727228 DEL NA + - [Svaba_SR=74,Svaba_PE=102],[Manta_PE=88,Manta_SR=63],[Lumpy_PE=82,Lumpy_SR=2] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC008802.1,LHFPL2;DisruptR=LHFPL2;Fusion=LHFPL2+AC008802.1;ClosestL=;ClosestR=AC008802.1 87038731 87038731 46,78710197,78727226 0,0,0 chr5 84214981 84214982 chr5 84215503 84215504 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=EDIL3;DisruptR=EDIL3;ClosestL=RNU6-448P;ClosestR=RNU6-448P 87038731 87038731 2,84214972,84215502 0,0,0 chr5 101330082 101330083 chr5 101342606 101342607 DEL NA + - [Svaba_SR=69,Svaba_PE=88],[Manta_PE=86,Manta_SR=57],[Lumpy_PE=65,Lumpy_SR=42] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 87057657 87057657 44,101330082,101342605 0,0,0 chr5 102801795 102801796 chr5 102874958 102874959 DEL NA + - [Svaba_SR=40,Svaba_PE=74],[Manta_PE=67,Manta_SR=65] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PAM;DisruptR=PAM;ClosestL=;ClosestR= 87057657 87057657 0,0,0 0,0,0 chr5 114587648 114587649 chr5 114630660 114630661 DEL NA + - [Svaba_SR=53,Svaba_PE=64],[Manta_PE=58,Manta_SR=55],[Lumpy_PE=43,Lumpy_SR=30] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC010230.1;DisruptR=AC010230.1;ClosestL=LINC01957;ClosestR= 140717308 140717308 40,114587649,114630649 0,0,0 chr5 114622908 114622909 chr5 114630139 114630140 DEL NA + - [Svaba_SR=20,Svaba_PE=22],[Manta_PE=20,Manta_SR=17] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC010230.1;DisruptR=AC010230.1;ClosestL=;ClosestR= 140717308 140717308 0,0,0 0,0,0 chr5 114622909 114622910 chr5 114628999 114629000 DEL NA + - [Lumpy_PE=3,Lumpy_SR=3] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC010230.1;DisruptR=AC010230.1;ClosestL=;ClosestR= 140717308 140717308 2,114622906,114628998 0,0,0 chr5 120820992 120820993 chr5 120828971 120828972 INV NA + + [Svaba_SR=18,Svaba_PE=10],[Manta_PE=20,Manta_SR=19],[Lumpy_PE=17,Lumpy_SR=16] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 140717308 140717308 17,120820994,120828978 0,0,0 chr5 120821055 120821056 chr5 120829446 120829447 INV NA - - [Svaba_SR=7,Svaba_PE=12],[Manta_PE=14,Manta_SR=6] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 140717308 140717308 6,120821058,120829445 0,0,0 chr5 134838428 134838429 chr5 134838947 134838948 DEL NA + - [Svaba_SR=7,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=DDX46;DisruptR=DDX46;ClosestL=C5orf24;ClosestR=C5orf24 140717308 140717308 2,134838410,134838946 0,0,0 chr5 139904400 139904401 chr7 82672674 82672675 TRA NA + + [Manta_PE=58,Manta_SR=85],[Lumpy_PE=38,Lumpy_SR=56] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=NRG2;DisruptR=;ClosestL=;ClosestR=AC004006.1 140717308 84167774 54,139904402,82672676 0,0,0 chr5 139904402 139904403 chr21 41877998 41877999 TRA NA + + [Svaba_SR=0,Svaba_PE=53],[Manta_PE=36,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=NRG2;DisruptR=PRDM15;ClosestL=;ClosestR=AP001619.1 140717308 41825926 0,0,0 0,0,0 chr5 145140233 145140234 chr5 145141116 145141117 DEL NA + - [Lumpy_PE=2,Lumpy_SR=3] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 140724488 140724488 3,145140230,145141115 0,0,0 chr5 154695628 154695629 chr5 154762331 154762332 DEL NA + - [Svaba_SR=69,Svaba_PE=78],[Manta_PE=71,Manta_SR=64] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=LARP1;ClosestL=MIR1303;ClosestR= 164930824 164930824 39,154695630,154762323 0,0,0 chr5 162164809 162164810 chr5 162165327 162165328 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=GABRG2;ClosestR=GABRG2 164930824 164930824 0,0,0 0,0,0 chr5 164930879 164930880 chr10 29373648 29373649 TRA NA - + [Svaba_SR=83,Svaba_PE=32],[Manta_PE=32,Manta_SR=117],[Lumpy_PE=3,Lumpy_SR=26] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC109466.1;DisruptR=;ClosestL=RNU6-209P;ClosestR= 164930825 29240316 2,164930877,29373647 0,0,0 chr5 166229022 166229023 chr5 176905028 176905029 DUP NA - + [Svaba_SR=0,Svaba_PE=31],[Manta_PE=17,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=NPM1,TLX3;DisruptL=;DisruptR=UIMC1;ClosestL=;ClosestR=HK3 165579622 179626939 0,0,0 0,0,0 chr5 166229023 166229024 chr5 171130631 171130632 DUP NA - + [Svaba_SR=62,Svaba_PE=13],[Manta_PE=10,Manta_SR=0],[Lumpy_PE=10,Lumpy_SR=2] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=RANBP17;ClosestL=;ClosestR= 165579622 171131351 0,0,0 0,0,0 chr5 166229096 166229097 chr13 103143872 103143873 TRA NA + + [Svaba_SR=65,Svaba_PE=23],[Manta_PE=16,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=28] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 165579622 103143847 0,0,0 0,0,0 chr5 169123666 169123667 chr5 171131427 171131428 DUP NA - + [Svaba_SR=58,Svaba_PE=81],[Manta_PE=74,Manta_SR=50],[Lumpy_PE=66,Lumpy_SR=34] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SLIT3;DisruptR=RANBP17;ClosestL=;ClosestR= 169123092 171131352 37,169123666,171131429 0,0,0 chr5 170686418 170686419 chr13 104720019 104720020 TRA NA - - [Svaba_SR=74,Svaba_PE=47],[Manta_PE=52,Manta_SR=71],[Lumpy_PE=42,Lumpy_SR=1] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=KCNIP1;DisruptR=;ClosestL=AC027312.1;ClosestR= 171131351 103143847 0,0,0 0,0,0 chr5 170686434 170686435 chr13 104711356 104711357 TRA NA + + [Svaba_SR=74,Svaba_PE=31],[Manta_PE=32,Manta_SR=43] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=KCNIP1;DisruptR=;ClosestL=AC027312.1;ClosestR= 171131351 103143847 3,170686435,104711362 0,0,0 chr5 170686434 170686435 chr5 172804770 172804771 DEL NA + - [Svaba_SR=0,Svaba_PE=20],[Manta_PE=17,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=NPM1,TLX3;DisruptL=KCNIP1;DisruptR=;ClosestL=AC027312.1;ClosestR=AC110011.1 171131351 171131352 0,0,0 0,0,0 chr5 171130473 171130474 chr5 176905028 176905029 DUP NA - + [Svaba_SR=0,Svaba_PE=15],[Manta_PE=39,Manta_SR=69],[Lumpy_PE=38,Lumpy_SR=22] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=NPM1,TLX3;DisruptL=RANBP17;DisruptR=UIMC1;ClosestL=;ClosestR=HK3 171131351 179626939 0,0,0 0,0,0 chr5 171130631 171130632 chr13 103143872 103143873 TRA NA + + [Svaba_SR=94,Svaba_PE=11],[Manta_PE=25,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=RANBP17;DisruptR=;ClosestL=;ClosestR= 171131351 103143847 0,0,0 0,0,0 chr5 172804771 172804772 chr13 104711181 104711182 TRA NA - - [Svaba_SR=48,Svaba_PE=56],[Manta_PE=48,Manta_SR=50],[Lumpy_PE=33,Lumpy_SR=37] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC110011.1;ClosestR= 171131352 103143847 38,172804773,104711180 0,0,0 chr5 173535074 173535075 chr21 17229345 17229346 TRA NA + - [Svaba_SR=50,Svaba_PE=61],[Manta_PE=55,Manta_SR=50],[Lumpy_PE=38,Lumpy_SR=28] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=NEK4P1 171131352 17474345 36,173535079,17229341 0,0,0 chr5 179626987 179626988 chr5 179641488 179641489 INV NA + + [Svaba_SR=92,Svaba_PE=282],[Manta_PE=427,Manta_SR=234],[Lumpy_PE=394,Lumpy_SR=94] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HNRNPH1;DisruptR=;ClosestL=RF00017;ClosestR=C5orf60 179626940 179641489 95,179626986,179641490 0,0,0 chr6 5651671 5651672 chr7 137445279 137445280 TRA NA - - [Svaba_SR=75,Svaba_PE=38],[Manta_PE=26,Manta_SR=73],[Lumpy_PE=10,Lumpy_SR=51] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FARS2;DisruptR=DGKI;Fusion=DGKI-FARS2;ClosestL=AL022097.1;ClosestR= 882088 137445254 37,5651672,137445273 0,0,0 chr6 5651753 5651754 chr10 37195765 37195766 TRA NA + - [Svaba_SR=65,Svaba_PE=43],[Manta_PE=16,Manta_SR=63],[Lumpy_PE=6,Lumpy_SR=29] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FARS2;DisruptR=ANKRD30A;Fusion=FARS2-ANKRD30A;ClosestL=AL022097.1;ClosestR= 882088 37167258 25,5651754,37195764 0,0,0 chr6 10615716 10615717 chr6 10671378 10671379 INV NA - - [Svaba_SR=12,Svaba_PE=19],[Manta_PE=20,Manta_SR=10],[Lumpy_PE=17,Lumpy_SR=6] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=GCNT2;DisruptR=;ClosestL=GCNT2P;ClosestR=C6orf52 882088 882088 10,10615718,10671377 0,0,0 chr6 24909910 24909911 chr13 23788151 23788152 TRA NA + - [Svaba_SR=74,Svaba_PE=97],[Manta_PE=93,Manta_SR=67],[Lumpy_PE=66,Lumpy_SR=45] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=RIPOR2;DisruptR=MIPEP;Fusion=MIPEP-RIPOR2;ClosestL=;ClosestR= 24909915 23788057 48,24909912,23788146 0,0,0 chr6 27975816 27975817 chr6 27977762 27977763 DUP NA - + [Lumpy_PE=2,Lumpy_SR=2] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=OR2W4P;ClosestL=OR2W4P;ClosestR=RPLP2P1 24909916 24909916 2,27975819,27977763 0,0,0 chr6 31251005 31251006 chr6 31342048 31342049 DEL NA + - [Manta_PE=12,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=HLA-B;ClosestL=HLA-C;ClosestR=MIR6891 32487100 32487100 0,0,0 0,0,0 chr6 31282776 31282777 chr6 31676535 31676536 DUP NA - + [Svaba_SR=100,Svaba_PE=117],[Manta_PE=128,Manta_SR=143],[Lumpy_PE=110,Lumpy_SR=21] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=HLA-B;DisruptR=;ClosestL=RPL3P2;ClosestR=LY6G5C 32487100 32487100 2,31282774,31676533 0,0,0 chr6 36092690 36092691 chr11 72659713 72659714 TRA NA + - [Svaba_SR=79,Svaba_PE=85],[Manta_PE=80,Manta_SR=70],[Lumpy_PE=51,Lumpy_SR=48] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=MAPK14;DisruptR=PDE2A;ClosestL=Z95152.1;ClosestR=AP003065.1 36092705 72659717 50,36092689,72659712 0,0,0 chr6 37947053 37947054 chr6 37948416 37948417 INV NA - - [Svaba_SR=95,Svaba_PE=124],[Manta_PE=140,Manta_SR=133],[Lumpy_PE=105,Lumpy_SR=80] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq 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=133,Svaba_PE=170],[Manta_PE=167,Manta_SR=123],[Lumpy_PE=113,Lumpy_SR=99] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ZFAND3;DisruptR=AC103855.2;Fusion=AC103855.2-ZFAND3;ClosestL=;ClosestR= 38141254 45539525 74,38119596,45539584 0,0,0 chr6 38131029 38131030 chr6 38141273 38141274 INV NA + + [Svaba_SR=90,Svaba_PE=128],[Manta_PE=141,Manta_SR=140],[Lumpy_PE=121,Lumpy_SR=87] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ZFAND3;DisruptR=ZFAND3;ClosestL=;ClosestR= 38141254 38141255 75,38131029,38141275 0,0,0 chr6 38475453 38475454 chr6 38488043 38488044 DEL NA + - [Svaba_SR=62,Svaba_PE=74],[Manta_PE=70,Manta_SR=56],[Lumpy_PE=45,Lumpy_SR=43] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=BTBD9;DisruptR=BTBD9;ClosestL=BTBD9-AS1;ClosestR=BTBD9-AS1 38141255 38141255 45,38475453,38488042 0,0,0 chr6 51934058 51934059 chr6 51937863 51937864 INV NA + + [Svaba_SR=67,Svaba_PE=70],[Manta_PE=64,Manta_SR=58],[Lumpy_PE=47,Lumpy_SR=48] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PKHD1;DisruptR=PKHD1;ClosestL=;ClosestR= 52220478 52220478 44,51934060,51937865 0,0,0 chr6 52220975 52220976 chr13 110468790 110468791 TRA NA - + [Svaba_SR=84,Svaba_PE=98],[Manta_PE=88,Manta_SR=71],[Lumpy_PE=57,Lumpy_SR=53] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=COL4A2;ClosestL=IL17F;ClosestR=COL4A2-AS2 52220479 110418576 48,52220974,110468792 0,0,0 chr6 52542327 52542328 chr14 102959583 102959584 TRA NA - + [Svaba_SR=0,Svaba_PE=27],[Manta_PE=24,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TRAM2;DisruptR=CDC42BPB;Fusion=TRAM2-CDC42BPB;ClosestL=EFHC1;ClosestR= 52679253 104243063 0,0,0 0,0,0 chr6 52542328 52542329 chr17 35740374 35740375 TRA NA - + [Svaba_SR=0,Svaba_PE=9] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TRAM2;DisruptR=RASL10B,TAF15;ClosestL=EFHC1;ClosestR=GAS2L2 52679253 36041470 0,0,0 0,0,0 chr6 52679254 52679255 chr18 23971471 23971472 TRA NA + + [Svaba_SR=177,Svaba_PE=240],[Manta_PE=257,Manta_SR=177],[Lumpy_PE=170,Lumpy_SR=95] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TMEM14A;DisruptR=AC010754.1;Fusion=TMEM14A-AC010754.1;ClosestL=GSTA8P;ClosestR=LAMA3 52679254 23971375 85,52679253,23971473 0,0,0 chr6 53892612 53892613 chr6 53893328 53893329 DEL NA + - [Svaba_SR=74,Svaba_PE=101],[Manta_PE=68,Manta_SR=65],[Lumpy_PE=61,Lumpy_SR=57] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LRRC1;DisruptR=LRRC1;ClosestL=;ClosestR= 54303355 54303355 49,53892611,53893327 0,0,0 chr6 54303391 54303392 chr15 76561854 76561855 TRA NA + - [Svaba_SR=18,Svaba_PE=0],[Manta_PE=32,Manta_SR=62],[Lumpy_PE=21,Lumpy_SR=46] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=SCAPER;ClosestL=TINAG;ClosestR= 54303356 72362590 35,54303392,76561853 0,0,0 chr6 54303391 54303392 chr16 67651996 67651997 TRA NA + + [Svaba_SR=111,Svaba_PE=34],[Manta_PE=32,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=CARMIL2;ClosestL=TINAG;ClosestR=ACD 54303356 90226217 0,0,0 0,0,0 chr6 54303392 54303393 chr8 118959310 118959311 TRA NA + - [Manta_PE=15,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=TINAG;ClosestR=TNFRSF11B 54303356 121698090 0,0,0 0,0,0 chr6 58157667 58157668 chr13 110418585 110418586 TRA NA - + [Svaba_SR=163,Svaba_PE=200],[Manta_PE=70,Manta_SR=148],[Lumpy_PE=45,Lumpy_SR=27] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL445250.1;DisruptR=COL4A2;Fusion=COL4A2-AL445250.1;ClosestL=;ClosestR=AL159153.1 59823890 110418576 83,58157667,110418587 0,0,0 chr6 58190428 58190429 chr11 78640457 78640458 TRA NA + + [Svaba_SR=162,Svaba_PE=178],[Manta_PE=165,Manta_SR=146] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL445250.1;DisruptR=;ClosestL=;ClosestR=TENM4 59823890 78640469 87,58190430,78640459 0,0,0 chr6 82898488 82898489 chr6 82899849 82899850 DEL NA + - [Svaba_SR=67,Svaba_PE=58],[Manta_PE=53,Manta_SR=59] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=UBE3D;DisruptR=UBE3D;ClosestL=;ClosestR= 78326602 78326602 47,82898490,82899848 0,0,0 chr6 108428792 108428793 chr6 108701375 108701376 DEL NA + - [Svaba_SR=55,Svaba_PE=55],[Manta_PE=47,Manta_SR=44],[Lumpy_PE=32,Lumpy_SR=32] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=FOXO3;DisruptL=AFG1L;DisruptR=;ClosestL=;ClosestR=FOXO3 129707604 129707604 39,108428791,108701374 0,0,0 chr6 119711508 119711509 chr6 119739228 119739229 DUP NA - + [Lumpy_PE=4,Lumpy_SR=3] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 129707604 129707604 3,119711512,119739229 0,0,0 chr6 129707662 129707663 chr6 130004047 130004048 DUP NA - + [Svaba_SR=107,Svaba_PE=197],[Manta_PE=261,Manta_SR=163],[Lumpy_PE=217,Lumpy_SR=131] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ARHGAP18;DisruptR=;ClosestL=;ClosestR=L3MBTL3 129707605 130003967 2,129707660,130004044 0,0,0 chr6 144660335 144660336 chr12 67114680 67114681 TRA NA + - [Svaba_SR=0,Svaba_PE=13] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=UTRN;DisruptR=;ClosestL=;ClosestR=RAB11AP2 130003967 67923115 0,0,0 0,0,0 chr6 144660335 144660336 chr21 32343657 32343658 TRA NA + + [Svaba_SR=70,Svaba_PE=8],[Manta_PE=7,Manta_SR=77],[Lumpy_PE=14,Lumpy_SR=56] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=UTRN;DisruptR=URB1;Fusion=UTRN-URB1;ClosestL=;ClosestR= 130003967 32739134 48,144660336,32343659 0,0,0 chr6 149608685 149608686 chr6 149664022 149664023 DEL NA + - [Svaba_SR=7,Svaba_PE=6],[Lumpy_PE=6,Lumpy_SR=2] svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=KATNA1;DisruptR=LATS1;Fusion=LATS1+KATNA1;ClosestL=RF00410;ClosestR=KATNA1 165311198 165311198 4,149608687,149664021 0,0,0 chr6 160507491 160507492 chr6 160660979 160660980 DEL NA + - [Manta_PE=12,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=LPAL2;DisruptR=LPA;Fusion=LPA+LPAL2;ClosestL=;ClosestR=AL109933.2 165311198 165311198 0,0,0 0,0,0 chr6 166891543 166891544 chr16 13287330 13287331 TRA NA - - [Svaba_SR=77,Svaba_PE=53],[Manta_PE=80,Manta_SR=63],[Lumpy_PE=52,Lumpy_SR=52] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL159163.1,RPS6KA2;DisruptR=U91319.1;Fusion=AL159163.1-U91319.1|RPS6KA2-U91319.1;ClosestL=RPS6KA2-AS1;ClosestR= 166890853 13289377 50,166891543,13287329 0,0,0 chr6 168164289 168164290 chr6 168191518 168191519 DUP NA - + [Svaba_SR=71,Svaba_PE=35],[Manta_PE=37,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=AL611929.1 166890853 166890853 0,0,0 0,0,0 chr7 29985174 29985175 chr11 76901510 76901511 TRA NA - + [Svaba_SR=0,Svaba_PE=10] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SCRN1;DisruptR=ACER3;ClosestL=AC007285.1;ClosestR= 43477638 78640469 0,0,0 0,0,0 chr7 29985175 29985176 chr22 28499903 28499904 TRA NA - + [Svaba_SR=82,Svaba_PE=20],[Manta_PE=27,Manta_SR=101],[Lumpy_PE=6,Lumpy_SR=49] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SCRN1;DisruptR=TTC28;Fusion=SCRN1-TTC28;ClosestL=AC007285.1;ClosestR= 43477638 29285918 53,29985176,28499905 0,0,0 chr7 29985277 29985278 chr21 14331478 14331479 TRA NA + - [Svaba_SR=0,Svaba_PE=44],[Manta_PE=30,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SCRN1;DisruptR=ABCC13;ClosestL=AC007285.1;ClosestR= 43477638 14332448 0,0,0 0,0,0 chr7 35418936 35418937 chr14 104300815 104300816 TRA NA + + [Lumpy_PE=5,Lumpy_SR=1] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=AL590079.1 43477638 104326322 4,35418935,104300929 5,35418929,104300944 chr7 43477683 43477684 chr17 67148382 67148383 TRA NA - + [Svaba_SR=227,Svaba_PE=276],[Manta_PE=243,Manta_SR=210],[Lumpy_PE=174,Lumpy_SR=159] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HECW1;DisruptR=HELZ;ClosestL=;ClosestR= 43477639 67148387 95,43477682,67148384 0,0,0 chr7 44883006 44883007 chr7 44913656 44913657 DUP NA - + [Svaba_SR=0,Svaba_PE=161] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PURB;DisruptR=;ClosestL=MIR4657;ClosestR=AC004854.1 43477639 43477639 0,0,0 0,0,0 chr7 44883007 44883008 chr7 44913973 44913974 DUP NA - + [Svaba_SR=158,Svaba_PE=273],[Manta_PE=243,Manta_SR=167],[Lumpy_PE=219,Lumpy_SR=106] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PURB;DisruptR=;ClosestL=MIR4657;ClosestR=AC004854.1 43477639 43477639 80,44883003,44913976 0,0,0 chr7 47787889 47787890 chr21 13481495 13481496 TRA NA - + [Svaba_SR=62,Svaba_PE=45],[Manta_PE=32,Manta_SR=49] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HUS1,PKD1L1;DisruptR=GTF2IP2;Fusion=HUS1-GTF2IP2|PKD1L1-GTF2IP2;ClosestL=C7orf69;ClosestR=VN1R8P 50144341 13507200 43,47787891,13481497 0,0,0 chr7 47788066 47788067 chr7 57377873 57377874 DEL NA + - [Svaba_SR=52,Svaba_PE=57],[Manta_PE=39,Manta_SR=47],[Lumpy_PE=22,Lumpy_SR=24] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=ZNF479,EGFR,IKZF1;DisruptL=HUS1,PKD1L1;DisruptR=;ClosestL=C7orf69;ClosestR= 50144341 57487363 40,47788066,57377872 0,0,0 chr7 53748552 53748553 chr7 53753362 53753363 DEL NA + - [Svaba_SR=153,Svaba_PE=203],[Manta_PE=214,Manta_SR=155],[Lumpy_PE=154,Lumpy_SR=128] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC01446;DisruptR=LINC01446;ClosestL=;ClosestR= 53753365 53753365 87,53748553,53753361 0,0,0 chr7 57224566 57224567 chr7 63487943 63487944 INV NA - - [Svaba_SR=63,Svaba_PE=60] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;DisruptL=;DisruptR=;ClosestL=AC099654.1;ClosestR=AC006457.1 57487363 62742672 43,57224563,63487939 0,0,0 chr7 57377872 57377873 chr21 13481490 13481491 TRA NA - + [Svaba_SR=0,Svaba_PE=9] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=GTF2IP2;ClosestL=;ClosestR=VN1R8P 57487363 13507200 0,0,0 0,0,0 chr7 58051690 58051691 chr7 58055595 58055596 INV NA + + [Lumpy_PE=3,Lumpy_SR=1] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 57497083 57497083 0,0,0 0,0,0 chr7 60931856 60931857 chr7 62300817 62300818 INV NA + + [Lumpy_PE=3,Lumpy_SR=1] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;DisruptL=;DisruptR=;ClosestL=;ClosestR= 62116180 62454737 0,0,0 0,0,0 chr7 61041202 61041203 chr18 21481531 21481532 TRA NA - - [Svaba_SR=10,Svaba_PE=9],[Manta_PE=9,Manta_SR=8],[Lumpy_PE=8,Lumpy_SR=4] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=GREB1L;ClosestL=;ClosestR= 62116180 20553042 7,61041202,21481530 0,0,0 chr7 61261066 61261067 chr7 61442364 61442365 DEL NA + - [Svaba_SR=0,Svaba_PE=22],[Manta_PE=17,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;ClosestL=;ClosestR= 62116180 62116180 0,0,0 0,0,0 chr7 62742736 62742737 chr7 87327156 87327157 DEL NA + - [Svaba_SR=0,Svaba_PE=25],[Manta_PE=22,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=SBDS,ELN,HIP1,GRM3;DisruptL=;DisruptR=TP53TG1;ClosestL=;ClosestR=RF02195 62742672 84789193 0,0,0 0,0,0 chr7 62742736 62742737 chr8 134414517 134414518 TRA NA + + [Svaba_SR=57,Svaba_PE=29],[Manta_PE=30,Manta_SR=52],[Lumpy_PE=15,Lumpy_SR=34] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 62742672 145078494 41,62742738,134414519 0,0,0 chr7 69920183 69920184 chr7 70236713 70236714 DEL NA + - [Svaba_SR=62,Svaba_PE=89],[Manta_PE=77,Manta_SR=57],[Lumpy_PE=61,Lumpy_SR=41] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AUTS2;DisruptR=AUTS2;ClosestL=;ClosestR= 69920124 70236680 43,69920183,70236712 0,0,0 chr7 82613835 82613836 chr21 41878419 41878420 TRA NA - - [Svaba_SR=26,Svaba_PE=28],[Manta_PE=27,Manta_SR=27],[Lumpy_PE=19,Lumpy_SR=17] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=PRDM15;ClosestL=;ClosestR=AP001619.1 84167774 41825926 18,82613834,41878417 0,0,0 chr7 82616051 82616052 chr10 51349321 51349322 TRA NA + - [Svaba_SR=100,Svaba_PE=18],[Manta_PE=13,Manta_SR=97],[Lumpy_PE=7,Lumpy_SR=80] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=PRKG1;ClosestL=;ClosestR= 84167774 39340909 50,82616053,51349320 0,0,0 chr7 82616051 82616052 chr17 20111623 20111624 TRA NA + - [Svaba_SR=0,Svaba_PE=18],[Manta_PE=15,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=SPECC1;DisruptL=;DisruptR=SPECC1;ClosestL=;ClosestR=KCTD9P1 84167774 21968703 0,0,0 0,0,0 chr7 82672503 82672504 chr21 41877945 41877946 TRA NA - + [Svaba_SR=0,Svaba_PE=74],[Manta_PE=52,Manta_SR=84],[Lumpy_PE=31,Lumpy_SR=62] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=PRDM15;ClosestL=AC004006.1;ClosestR=AP001619.1 84167774 41825926 58,82672505,41878048 0,0,0 chr7 86257760 86257761 chr21 26634844 26634845 TRA NA - + [Svaba_SR=51,Svaba_PE=82],[Manta_PE=74,Manta_SR=61],[Lumpy_PE=50,Lumpy_SR=44] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 84789193 26634791 45,86257759,26634846 0,0,0 chr7 87327163 87327164 chr8 134414383 134414384 TRA NA - - [Svaba_SR=54,Svaba_PE=11],[Manta_PE=7,Manta_SR=48],[Lumpy_PE=4,Lumpy_SR=36] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TP53TG1;DisruptR=;ClosestL=RF02195;ClosestR= 84789193 145078494 36,87327163,134414382 0,0,0 chr7 89265302 89265303 chr7 89268691 89268692 DEL NA + - [Svaba_SR=56,Svaba_PE=60],[Manta_PE=62,Manta_SR=47],[Lumpy_PE=48,Lumpy_SR=1] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ZNF804B;DisruptR=ZNF804B;ClosestL=;ClosestR= 92202778 92202778 0,0,0 0,0,0 chr7 90184001 90184002 chr8 46361573 46361574 TRA NA - - [Svaba_SR=0,Svaba_PE=8] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=STEAP2-AS1,STEAP2;DisruptR=;ClosestL=STEAP1;ClosestR= 92202778 46943804 0,0,0 0,0,0 chr7 92202777 92202778 chr7 92380664 92380665 DEL NA + - [Svaba_SR=80,Svaba_PE=90],[Manta_PE=72,Manta_SR=74],[Lumpy_PE=56,Lumpy_SR=37] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC000120.1,KRIT1;DisruptR=ANKIB1;ClosestL=RF00019;ClosestR= 92202778 92380603 55,92202778,92380663 0,0,0 chr7 116918744 116918745 chrX 57506628 57506629 TRA NA - + [Svaba_SR=83,Svaba_PE=83],[Manta_PE=65,Manta_SR=60] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CAPZA2;DisruptR=;ClosestL=RF00019;ClosestR=FAAH2 116918673 57506640 48,116918745,57506630 0,0,0 chr7 137445279 137445280 chr10 37195765 37195766 TRA NA - - [Svaba_SR=116,Svaba_PE=51],[Manta_PE=46,Manta_SR=68] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq 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=98,Svaba_PE=110],[Manta_PE=109,Manta_SR=70],[Lumpy_PE=78,Lumpy_SR=50] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=BRAF;DisruptL=BRAF;DisruptR=;ClosestL=;ClosestR= 140911187 140911187 50,140911266,140955782 0,0,0 chr7 141230709 141230710 chr7 141238330 141238331 DEL NA + - [Svaba_SR=74,Svaba_PE=93],[Manta_PE=79,Manta_SR=64],[Lumpy_PE=51,Lumpy_SR=51] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TMEM178B;DisruptR=TMEM178B;ClosestL=;ClosestR= 141311252 141311252 48,141230711,141238329 0,0,0 chr7 141234566 141234567 chr7 141311291 141311292 INV NA + + [Svaba_SR=69,Svaba_PE=76],[Manta_PE=38,Manta_SR=0],[Lumpy_PE=55,Lumpy_SR=28] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TMEM178B;DisruptR=TMEM178B;ClosestL=;ClosestR= 141311252 141311253 10,141234568,141311293 0,0,0 chr8 4676739 4676740 chr16 80949853 80949854 TRA NA - - [Manta_PE=9,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CSMD1;DisruptR=;ClosestL=;ClosestR=CMC2 71162 90226217 0,0,0 0,0,0 chr8 10846875 10846876 chr20 47268863 47268864 TRA NA - - [Svaba_SR=83,Svaba_PE=61],[Manta_PE=43,Manta_SR=72],[Lumpy_PE=17,Lumpy_SR=56] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=ZMYND8;ClosestL=AC011008.1;ClosestR= 71162 39349451 54,10846878,47268862 0,0,0 chr8 10847021 10847022 chr20 47225235 47225236 TRA NA + + [Svaba_SR=73,Svaba_PE=43],[Manta_PE=38,Manta_SR=59],[Lumpy_PE=18,Lumpy_SR=43] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=ZMYND8;ClosestL=AC011008.1;ClosestR= 71162 39349451 46,10847023,47225237 0,0,0 chr8 38073703 38073704 chr8 38074256 38074257 DEL NA + - [Svaba_SR=109,Svaba_PE=97],[Manta_PE=106,Manta_SR=104] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AP006545.1;ClosestR=AP006545.1 36461421 36461421 38,38073700,38074255 0,0,0 chr8 43475992 43475993 chr11 70550642 70550643 TRA NA - + [Svaba_SR=422,Svaba_PE=223],[Manta_PE=852,Manta_SR=672],[Lumpy_PE=610,Lumpy_SR=509] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=SHANK2;ClosestL=AC134698.4;ClosestR= 43475933 70550614 114,43475994,70550644 0,0,0 chr8 43586013 43586014 chr8 43586515 43586516 DEL NA + - [Svaba_SR=10,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 43646293 43646293 9,43585997,43586514 0,0,0 chr8 43634132 43634133 chr8 43635536 43635537 INV NA + + [Svaba_SR=0,Svaba_PE=50],[Manta_PE=176,Manta_SR=217],[Lumpy_PE=131,Lumpy_SR=77] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 43646293 43646293 75,43634275,43635538 0,0,0 chr8 43646325 43646326 chr14 104763654 104763655 TRA NA + + [Svaba_SR=92,Svaba_PE=182],[Manta_PE=350,Manta_SR=326],[Lumpy_PE=223,Lumpy_SR=217] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=SIVA1;ClosestL=;ClosestR=AL583722.2 43646294 104326323 108,43646326,104763656 0,0,0 chr8 45059287 45059288 chr8 45740160 45740161 DEL NA + - [Svaba_SR=0,Svaba_PE=8] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 44968553 44968553 0,0,0 0,0,0 chr8 46943846 46943847 chr8 60480162 60480163 DEL NA + - [Svaba_SR=64,Svaba_PE=81],[Manta_PE=60,Manta_SR=50] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=TCEA1,PLAG1,CHCHD7;DisruptL=;DisruptR=LINC01301;ClosestL=AC091163.2;ClosestR= 46943805 60480054 42,46943847,60480161 0,0,0 chr8 47813737 47813738 chr11 58189360 58189361 TRA NA - - [Svaba_SR=113,Svaba_PE=128],[Manta_PE=133,Manta_SR=90],[Lumpy_PE=102,Lumpy_SR=53] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=PRKDC;DisruptR=OR9Q2;Fusion=PRKDC-OR9Q2;ClosestL=RF00019;ClosestR=OR9Q1 46943805 58828468 64,47813739,58189359 0,0,0 chr8 54214812 54214813 chr8 54215331 54215332 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 60480053 60480053 0,0,0 0,0,0 chr8 60642425 60642426 chr8 60724569 60724570 DEL NA + - [Svaba_SR=69,Svaba_PE=75],[Manta_PE=84,Manta_SR=0],[Lumpy_PE=62,Lumpy_SR=23] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=CHD7;ClosestL=AC068389.1;ClosestR= 60480054 60480054 51,60642425,60724568 0,0,0 chr8 70009727 70009728 chr8 70010288 70010289 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 69408004 69408004 2,70009680,70010261 0,0,0 chr8 80571008 80571009 chr16 22585150 22585151 TRA NA - - [Manta_PE=5,Manta_SR=47] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC009812.2;ClosestR=AC106788.1 69408004 24481285 40,80571008,22585148 0,0,0 chr8 86158932 86158933 chr8 86203983 86203984 INV NA + + [Manta_PE=46,Manta_SR=0],[Lumpy_PE=11,Lumpy_SR=61] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=AC084128.1;ClosestL=ATP6V0D2;ClosestR=SLC7A13 96324265 96324265 32,86158943,86203825 0,0,0 chr8 86159125 86159126 chr8 86205028 86205029 DUP NA - + [Manta_PE=20,Manta_SR=0],[Lumpy_PE=3,Lumpy_SR=46] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=AC084128.1;ClosestL=ATP6V0D2;ClosestR=SLC7A13 96324265 96324265 0,0,0 0,0,0 chr8 86159415 86159416 chr8 86201237 86201238 DEL NA + - [Svaba_SR=82,Svaba_PE=98],[Manta_PE=87,Manta_SR=102],[Lumpy_PE=58,Lumpy_SR=77] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=AC084128.1;ClosestL=ATP6V0D2;ClosestR=SLC7A13 96324265 96324265 59,86159417,86201234 0,0,0 chr8 86201236 86201237 chr8 86204869 86204870 DUP NA - + [Svaba_SR=0,Svaba_PE=16] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC084128.1;DisruptR=AC084128.1;ClosestL=SLC7A13;ClosestR=SLC7A13 96324265 96324265 0,0,0 0,0,0 chr8 86754211 86754212 chr8 86754744 86754745 DEL NA + - [Svaba_SR=6,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC090572.3;DisruptR=AC090572.3;ClosestL=CNGB3;ClosestR=CNGB3 96324265 96324265 0,0,0 0,0,0 chr8 88879692 88879693 chr8 102821044 102821045 INV NA + + [Svaba_SR=53,Svaba_PE=22],[Manta_PE=19,Manta_SR=57],[Lumpy_PE=2,Lumpy_SR=35] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=COX6C,NBN,CDH17,PABPC1,RUNX1T1,UBR5;DisruptL=;DisruptR=;ClosestL=;ClosestR=AZIN1 96324265 101450537 31,88879694,102821046 0,0,0 chr8 88879692 88879693 chr8 88884416 88884417 DEL NA + - [Svaba_SR=69,Svaba_PE=7],[Manta_PE=37,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 96324265 96324265 0,0,0 0,0,0 chr8 88884416 88884417 chr8 102820935 102820936 INV NA - - [Svaba_SR=31,Svaba_PE=35],[Manta_PE=28,Manta_SR=42],[Lumpy_PE=8,Lumpy_SR=16] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=COX6C,NBN,CDH17,PABPC1,RUNX1T1,UBR5;DisruptL=;DisruptR=;ClosestL=;ClosestR=AZIN1 96324265 101450537 24,88884418,102820934 0,0,0 chr8 91199097 91199098 chr8 91422898 91422899 DEL NA + - [Manta_PE=4,Manta_SR=3] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LRRC69;DisruptR=;ClosestL=MIR4661;ClosestR= 96324265 96324265 3,91199099,91422895 0,0,0 chr8 94880300 94880301 chr8 94902717 94902718 DEL NA + - [Svaba_SR=54,Svaba_PE=64],[Manta_PE=79,Manta_SR=84],[Lumpy_PE=57,Lumpy_SR=57] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=INTS8,CCNE2;DisruptR=NDUFAF6;Fusion=INTS8+NDUFAF6;ClosestL=AC087752.4;ClosestR=CCNE2 96324265 96324265 58,94880302,94902716 0,0,0 chr8 96324290 96324291 chr8 97238613 97238614 DUP NA - + [Svaba_SR=0,Svaba_PE=47],[Manta_PE=120,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq 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=89,Svaba_PE=0],[Manta_PE=165,Manta_SR=128],[Lumpy_PE=109,Lumpy_SR=103] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AP001208.2;DisruptR=;ClosestL=AP001207.3;ClosestR=AP007216.1 101450536 69779347 75,101450517,69897842 0,0,0 chr8 101451844 101451845 chr11 69897285 69897286 TRA NA - - [Svaba_SR=0,Svaba_PE=23],[Manta_PE=60,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AP001208.2;DisruptR=;ClosestL=AP001207.3;ClosestR=AP007216.1 101450537 69779347 0,0,0 0,0,0 chr8 101451845 101451846 chr8 113801324 113801325 INV NA - - [Svaba_SR=84,Svaba_PE=54],[Manta_PE=69,Manta_SR=0],[Lumpy_PE=16,Lumpy_SR=28] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=EIF3E,UBR5,RSPO2,CSMD3;DisruptL=AP001208.2;DisruptR=;ClosestL=AP001207.3;ClosestR= 101450537 113801448 12,101451839,113801144 0,0,0 chr8 102577650 102577651 chr8 102826797 102826798 DUP NA - + [Manta_PE=8,Manta_SR=10],[Lumpy_PE=6,Lumpy_SR=10] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=AZIN1;ClosestL=ODF1;ClosestR=GASAL1 101450537 101450537 10,102577656,102826805 0,0,0 chr8 112077674 112077675 chr8 112087837 112087838 DEL NA + - [Svaba_SR=48,Svaba_PE=74],[Manta_PE=65,Manta_SR=41],[Lumpy_PE=49,Lumpy_SR=22] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 111464796 111464796 31,112077673,112087836 0,0,0 chr8 113730713 113730714 chr8 113847230 113847231 INV NA + + [Svaba_SR=132,Svaba_PE=123],[Manta_PE=116,Manta_SR=117],[Lumpy_PE=98,Lumpy_SR=95] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 113801448 113801449 66,113730714,113847232 0,0,0 chr8 113801314 113801315 chr11 69780162 69780163 TRA NA + + [Manta_PE=243,Manta_SR=179],[Lumpy_PE=177,Lumpy_SR=135] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=FGF4 113801448 69779347 87,113801316,69780164 0,0,0 chr8 113801461 113801462 chr11 69897286 69897287 TRA NA + - [Svaba_SR=131,Svaba_PE=77],[Manta_PE=93,Manta_SR=119],[Lumpy_PE=64,Lumpy_SR=105] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=AP007216.1 113801449 69779347 75,113801459,69897285 0,0,0 chr8 113817587 113817588 chr8 114411853 114411854 INV NA - - [Svaba_SR=120,Svaba_PE=120],[Manta_PE=120,Manta_SR=104],[Lumpy_PE=81,Lumpy_SR=78] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;ClosestL=;ClosestR= 113801449 114412277 65,113817589,114411852 0,0,0 chr8 114825543 114825544 chr8 114826068 114826069 DEL NA + - [Svaba_SR=5,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 114412278 114412278 2,114825530,114826067 0,0,0 chr8 117297894 117297895 chr8 117323013 117323014 DEL NA + - [Svaba_SR=72,Svaba_PE=101],[Manta_PE=89,Manta_SR=61],[Lumpy_PE=62,Lumpy_SR=53] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;ClosestL=RF00322;ClosestR=RF00322 114412278 114412278 45,117297889,117323012 0,0,0 chr8 118959276 118959277 chr15 76562149 76562150 TRA NA - + [Manta_PE=23,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=SCAPER;ClosestL=TNFRSF11B;ClosestR= 121698090 72362590 0,0,0 0,0,0 chr8 118959452 118959453 chr16 67651851 67651852 TRA NA - - [Svaba_SR=57,Svaba_PE=16],[Manta_PE=9,Manta_SR=64],[Lumpy_PE=4,Lumpy_SR=40] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=CARMIL2;ClosestL=TNFRSF11B;ClosestR=ACD 121698090 90226217 45,118959451,67651850 0,0,0 chr8 118959598 118959599 chr13 24968358 24968359 TRA NA + - [Svaba_SR=0,Svaba_PE=16] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=TPTE2P1;ClosestL=TNFRSF11B;ClosestR= 121698090 24952568 0,0,0 0,0,0 chr8 118959598 118959599 chr9 131565190 131565191 TRA NA + + [Manta_PE=24,Manta_SR=74],[Lumpy_PE=13,Lumpy_SR=59] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=TNFRSF11B;ClosestR=PRRT1B 121698090 127070382 54,118959600,131565192 0,0,0 chr8 122992392 122992393 chr8 123075947 123075948 DEL NA + - [Svaba_SR=136,Svaba_PE=156],[Manta_PE=189,Manta_SR=175],[Lumpy_PE=122,Lumpy_SR=136] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=TBC1D31;ClosestL=AC104316.2;ClosestR= 121698091 121698091 31,122992391,123075946 0,0,0 chr8 124474095 124474096 chr8 124482983 124482984 DEL NA + - [Manta_PE=11,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=RNF139-AS1;DisruptR=RNF139;ClosestL=RNF139;ClosestR=TATDN1 121698091 121698091 0,0,0 0,0,0 chr8 139905821 139905822 chr8 139906389 139906390 DEL NA + - [Svaba_SR=1,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TRAPPC9;DisruptR=TRAPPC9;ClosestL=AC021744.1;ClosestR=AC021744.1 145078494 145078494 0,0,0 0,0,0 chr8 140358453 140358454 chr11 58902621 58902622 TRA NA - - [Svaba_SR=0,Svaba_PE=33] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=TRAPPC9;DisruptR=GLYATL2;ClosestL=;ClosestR=GLYATL1 145078494 58828469 9,140358458,58902608 0,0,0 chr8 140358492 140358493 chrX 56991139 56991140 TRA NA + - [Svaba_SR=0,Svaba_PE=27] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=TRAPPC9;DisruptR=SPIN3;Fusion=SPIN3-TRAPPC9;ClosestL=;ClosestR=AL139397.1 145078494 56991084 6,140358494,56991090 0,0,0 chr8 141993267 141993268 chr8 141993814 141993815 DEL NA + - [Svaba_SR=5,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 145078494 145078494 0,0,0 0,0,0 chr8 143023980 143023981 chr8 143042570 143042571 DEL NA + - [Svaba_SR=118,Svaba_PE=126],[Manta_PE=138,Manta_SR=113],[Lumpy_PE=24,Lumpy_SR=88] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=C8orf31;ClosestL=LY6E;ClosestR=AK3P2 145078494 145078494 2,143023983,143042574 0,0,0 chr8 144267751 144267752 chr8 144315558 144315559 DEL NA + - [Svaba_SR=85,Svaba_PE=110],[Manta_PE=102,Manta_SR=76],[Lumpy_PE=64,Lumpy_SR=72] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SCX,BOP1;DisruptR=DGAT1;Fusion=DGAT1+BOP1;ClosestL=MIR7112;ClosestR=AC233992.1 145078494 145078494 55,144267746,144315557 0,0,0 chr8 144780173 144780174 chr8 144780751 144780752 DEL NA + - [Svaba_SR=3,Svaba_PE=5] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ZNF34;DisruptR=ZNF34;ClosestL=RN7SL395P;ClosestR=RN7SL395P 145078494 145078494 2,144780160,144780750 0,0,0 chr9 33983409 33983410 chr20 15018947 15018948 TRA NA + - [Svaba_SR=7,Svaba_PE=0],[Manta_PE=3,Manta_SR=7],[Lumpy_PE=2,Lumpy_SR=5] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=UBAP2;DisruptR=MACROD2;ClosestL=OSTCP8;ClosestR=RNU6-1159P 30540069 8764420 7,33983409,15018946 0,0,0 chr9 42783553 42783554 chr9 64784635 64784636 INV NA - - [Svaba_SR=13,Svaba_PE=4],[Manta_PE=2,Manta_SR=11] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;DisruptL=;DisruptR=;ClosestL=ADGRF5P2;ClosestR=IGKV1OR-2 45516998 65079292 8,42783556,64784634 0,0,0 chr9 72457967 72457968 chr14 102959493 102959494 TRA NA + - [Svaba_SR=0,Svaba_PE=8] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=CDC42BPB;ClosestL=AL445646.1;ClosestR= 65515655 104243063 0,0,0 0,0,0 chr9 72457967 72457968 chr17 1788610 1788611 TRA NA + + [Svaba_SR=44,Svaba_PE=0],[Manta_PE=7,Manta_SR=58],[Lumpy_PE=7,Lumpy_SR=21] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=SMYD4;ClosestL=AL445646.1;ClosestR=SERPINF1 65515655 168977 38,72457969,1788613 0,0,0 chr9 72457967 72457968 chr17 35740201 35740202 TRA NA + - [Svaba_SR=101,Svaba_PE=47],[Manta_PE=43,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=RASL10B,TAF15;ClosestL=AL445646.1;ClosestR=GAS2L2 65515655 36041470 0,0,0 0,0,0 chr9 94312707 94312708 chr9 94313512 94313513 DEL NA + - [Manta_PE=18,Manta_SR=92] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;ClosestL=NUTM2F;ClosestR=NUTM2F 113363791 113363791 83,94312709,94313512 0,0,0 chr9 113363750 113363751 chr9 113614603 113614604 DUP NA - + [Svaba_SR=73,Svaba_PE=60],[Manta_PE=59,Manta_SR=74],[Lumpy_PE=58,Lumpy_SR=8] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=BSPRY;DisruptR=AL162727.3;ClosestL=HDHD3;ClosestR=AL162727.1 113363791 113614612 38,113363742,113614610 0,0,0 chr9 123290032 123290033 chr11 76901313 76901314 TRA NA + - [Svaba_SR=79,Svaba_PE=44],[Manta_PE=37,Manta_SR=95],[Lumpy_PE=24,Lumpy_SR=69] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=ACER3;ClosestL=;ClosestR= 126950429 78640469 69,123290034,76901312 0,0,0 chr9 123290032 123290033 chr22 28499617 28499618 TRA NA + - [Svaba_SR=0,Svaba_PE=48],[Manta_PE=45,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=TTC28;ClosestL=;ClosestR= 126950429 29285918 0,0,0 0,0,0 chr9 126949538 126949539 chr9 127070386 127070387 DEL NA + - [Svaba_SR=86,Svaba_PE=46],[Manta_PE=11,Manta_SR=43] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=RALGPS1;DisruptR=RALGPS1;ClosestL=;ClosestR=ANGPTL2 126950429 127070382 52,126949537,127070385 0,0,0 chr9 131564961 131564962 chr13 24968359 24968360 TRA NA - - [Svaba_SR=78,Svaba_PE=61],[Manta_PE=51,Manta_SR=62],[Lumpy_PE=30,Lumpy_SR=2] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=TPTE2P1;ClosestL=PRRT1B;ClosestR= 127070382 24952568 49,131564960,24968357 0,0,0 chr9 131565190 131565191 chr15 76561966 76561967 TRA NA + + [Svaba_SR=0,Svaba_PE=13] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=SCAPER;ClosestL=PRRT1B;ClosestR= 127070382 72362590 0,0,0 0,0,0 chr9 131565190 131565191 chr16 67651850 67651851 TRA NA + - [Svaba_SR=0,Svaba_PE=13],[Manta_PE=28,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=CARMIL2;ClosestL=PRRT1B;ClosestR=ACD 127070382 90226217 0,0,0 0,0,0 chr10 73042 73043 chr12 68509747 68509748 TRA NA + + [Manta_PE=68,Manta_SR=61],[Lumpy_PE=48,Lumpy_SR=26] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TUBB8;DisruptR=;ClosestL=IL9RP2;ClosestR= 10287 67923116 41,73044,68509749 0,0,0 chr10 1105048 1105049 chr18 22044892 22044893 TRA NA + + [Manta_PE=6,Manta_SR=7] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=WDR37;DisruptR=LINC01900;ClosestL=;ClosestR= 10287 23307595 7,1105050,22044894 0,0,0 chr10 5804888 5804889 chr10 5805427 5805428 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=GDI2;DisruptR=GDI2;ClosestL=AL596094.1;ClosestR=AL596094.1 3336246 3336246 2,5804880,5805426 0,0,0 chr10 6132180 6132181 chr10 6132746 6132747 DEL NA + - [Svaba_SR=3,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=PFKFB3;ClosestR=PFKFB3 3336246 3336246 2,6132167,6132745 0,0,0 chr10 14648942 14648943 chr10 15811458 15811459 DUP NA - + [Svaba_SR=23,Svaba_PE=23],[Manta_PE=24,Manta_SR=19] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAM107B;DisruptR=MINDY3;Fusion=FAM107B+MINDY3;ClosestL=AL158168.1;ClosestR= 23965103 23965103 0,0,0 0,0,0 chr10 14648943 14648944 chr10 14779496 14779497 INV NA - - [Lumpy_PE=4,Lumpy_SR=7] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAM107B;DisruptR=;ClosestL=AL158168.1;ClosestR=FAM107B 23965103 23965103 5,14648942,14779494 0,0,0 chr10 14779534 14779535 chr10 15811341 15811342 INV NA + + [Svaba_SR=0,Svaba_PE=9] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=MINDY3;ClosestL=FAM107B;ClosestR= 23965103 23965103 3,14779533,15811460 0,0,0 chr10 14933901 14933902 chr10 15104286 15104287 DEL NA + - [Svaba_SR=18,Svaba_PE=24],[Manta_PE=24,Manta_SR=16],[Lumpy_PE=18,Lumpy_SR=3] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=DCLRE1C;DisruptR=RPP38,NMT2;Fusion=NMT2+DCLRE1C;ClosestL=;ClosestR=C10orf111 23965103 23965103 15,14933903,15104284 0,0,0 chr10 23965110 23965111 chr10 27758065 27758066 DUP NA - + [Svaba_SR=93,Svaba_PE=112],[Manta_PE=93,Manta_SR=79],[Lumpy_PE=77,Lumpy_SR=64] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=ABI1;DisruptL=KIAA1217;DisruptR=MKX-AS1;Fusion=MKX-AS1+KIAA1217;ClosestL=;ClosestR=MKX 23965104 27759513 62,23965110,27758067 0,0,0 chr10 29469448 29469449 chr10 29471183 29471184 DEL NA + - [Svaba_SR=45,Svaba_PE=62],[Manta_PE=56,Manta_SR=45],[Lumpy_PE=36,Lumpy_SR=36] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SVIL-AS1,SVIL;DisruptR=SVIL-AS1,SVIL;ClosestL=;ClosestR= 29240316 29240316 32,29469450,29471176 0,0,0 chr10 31156109 31156110 chr10 31160849 31160850 INV NA + + [Svaba_SR=10,Svaba_PE=7],[Manta_PE=9,Manta_SR=11],[Lumpy_PE=7,Lumpy_SR=7] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 29240316 29240316 10,31156109,31160851 0,0,0 chr10 37810481 37810482 chr14 106873730 106873731 TRA NA - + [Lumpy_PE=3,Lumpy_SR=2] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ZNF248;DisruptR=;ClosestL=TLK2P2;ClosestR=IGHV4-80 37167258 106883618 2,37810481,106873735 0,0,0 chr10 38921737 38921738 chr10 38922383 38922384 INV NA - - [Manta_PE=14,Manta_SR=16],[Lumpy_PE=8,Lumpy_SR=2] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 38581843 38581843 15,38921740,38922380 0,0,0 chr10 38954387 38954388 chr22 25545339 25545340 TRA NA + + [Svaba_SR=0,Svaba_PE=8],[Manta_PE=8,Manta_SR=12],[Lumpy_PE=3,Lumpy_SR=5] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=AL022329.1 38581843 23762694 0,0,0 0,0,0 chr10 38955180 38955181 chr22 25537608 25537609 TRA NA + + [Svaba_SR=7,Svaba_PE=11],[Manta_PE=9,Manta_SR=6],[Lumpy_PE=4,Lumpy_SR=2] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=CRYBB2P1 38581843 23762694 6,38955181,25537610 0,0,0 chr10 50989311 50989312 chr10 51269726 51269727 DUP NA - + [Manta_PE=91,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=PRKG1;ClosestL=PRKG1;ClosestR= 39340909 39340909 0,0,0 0,0,0 chr10 50989427 50989428 chr10 51033474 51033475 DUP NA - + [Svaba_SR=164,Svaba_PE=61] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=PRKG1;ClosestL=PRKG1;ClosestR= 39340909 39340909 0,0,0 0,0,0 chr10 50989427 50989428 chr10 51034007 51034008 DUP NA - + [Svaba_SR=105,Svaba_PE=0],[Manta_PE=73,Manta_SR=212],[Lumpy_PE=141,Lumpy_SR=174] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=PRKG1;ClosestL=PRKG1;ClosestR= 39340909 39340909 46,50989429,51034009 0,0,0 chr10 51033383 51033384 chr10 51269485 51269486 DUP NA - + [Svaba_SR=0,Svaba_PE=9],[Manta_PE=47,Manta_SR=190],[Lumpy_PE=45,Lumpy_SR=72] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PRKG1;DisruptR=PRKG1;ClosestL=;ClosestR= 39340909 39340909 61,51033385,51269620 0,0,0 chr10 51033737 51033738 chr10 51269693 51269694 DUP NA - + [Manta_PE=71,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PRKG1;DisruptR=PRKG1;ClosestL=;ClosestR= 39340909 39340909 0,0,0 0,0,0 chr10 51349437 51349438 chr17 20111625 20111626 TRA NA + - [Lumpy_PE=4,Lumpy_SR=50] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=SPECC1;DisruptL=PRKG1;DisruptR=SPECC1;Fusion=PRKG1-SPECC1;ClosestL=;ClosestR=KCTD9P1 39340909 21968703 24,51349438,20111623 0,0,0 chr10 52646611 52646612 chr10 52650701 52650702 DUP NA - + [Lumpy_PE=7,Lumpy_SR=21] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC074327.1;DisruptR=AC074327.1;ClosestL=;ClosestR= 63904555 63904555 8,52646611,52650706 0,0,0 chr10 52646823 52646824 chr10 52650698 52650699 DEL NA + - [Svaba_SR=60,Svaba_PE=52],[Manta_PE=88,Manta_SR=84],[Lumpy_PE=14,Lumpy_SR=70] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC074327.1;DisruptR=AC074327.1;ClosestL=;ClosestR= 63904555 63904555 56,52646827,52650697 0,0,0 chr10 54306934 54306935 chr10 54494396 54494397 DEL NA + - [Svaba_SR=67,Svaba_PE=88],[Manta_PE=81,Manta_SR=55],[Lumpy_PE=59,Lumpy_SR=43] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=PCDH15;DisruptR=PCDH15,AL353784.1;ClosestL=;ClosestR= 63904555 63904555 44,54306933,54494395 0,0,0 chr10 87097352 87097353 chr10 87201988 87201989 DEL NA + - [Svaba_SR=87,Svaba_PE=104],[Manta_PE=80,Manta_SR=77],[Lumpy_PE=58,Lumpy_SR=24] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SHLD2;DisruptR=;ClosestL=GLUD1;ClosestR=NUTM2A-AS1 63904556 63904556 51,87097352,87201987 0,0,0 chr10 102637238 102637239 chr10 102638085 102638086 DUP NA - + [Svaba_SR=38,Svaba_PE=39],[Manta_PE=32,Manta_SR=39] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=SUFU;ClosestR=TRIM8 133787316 133787316 27,102637237,102638087 0,0,0 chr10 105020094 105020095 chr10 105041776 105041777 DEL NA + - [Svaba_SR=71,Svaba_PE=97],[Manta_PE=85,Manta_SR=57],[Lumpy_PE=64,Lumpy_SR=44] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=SORCS3;DisruptR=SORCS3;ClosestL=;ClosestR= 133787316 133787316 2,105020098,105041782 0,0,0 chr10 118059368 118059369 chr10 118078970 118078971 DEL NA + - [Svaba_SR=70,Svaba_PE=77],[Manta_PE=65,Manta_SR=59],[Lumpy_PE=45,Lumpy_SR=48] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CASC2;DisruptR=CASC2;ClosestL=RAB11FIP2;ClosestR= 133787316 133787316 43,118059365,118078969 0,0,0 chr10 119196355 119196356 chr10 119196883 119196884 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=GRK5;ClosestR=GRK5 133787316 133787316 4,119196340,119196882 0,0,0 chr10 124466817 124466818 chr10 124471714 124471715 DEL NA + - [Manta_PE=34,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LHPP;DisruptR=LHPP;ClosestL=NKX1-2;ClosestR=RPS10P18 133787316 133787316 0,0,0 0,0,0 chr10 126525712 126525713 chr10 126567394 126567395 INV NA - - [Svaba_SR=72,Svaba_PE=85],[Manta_PE=80,Manta_SR=64],[Lumpy_PE=56,Lumpy_SR=41] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=C10orf90;DisruptR=C10orf90;ClosestL=;ClosestR= 133787316 133787316 47,126525711,126567393 0,0,0 chr10 126526972 126526973 chr10 126555979 126555980 DUP NA - + [Svaba_SR=73,Svaba_PE=58],[Manta_PE=73,Manta_SR=59],[Lumpy_PE=61,Lumpy_SR=47] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=C10orf90;DisruptR=C10orf90;ClosestL=;ClosestR= 133787316 133787316 42,126526971,126555982 0,0,0 chr11 6030233 6030234 chr11 7289788 7289789 INV NA - - [Svaba_SR=159,Svaba_PE=94],[Manta_PE=144,Manta_SR=154],[Lumpy_PE=95,Lumpy_SR=99] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=OR56A1;DisruptR=SYT9;Fusion=OR56A1+SYT9;ClosestL=RNA5SP329;ClosestR= 6030162 7289778 81,6030230,7289787 0,0,0 chr11 6378402 6378403 chr11 54541309 54541310 INV NA + + [Manta_PE=143,Manta_SR=121],[Lumpy_PE=117,Lumpy_SR=67] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=MYOD1,FANCF,WT1,LMO2,CREB3L1,DDB2,LMO1,EXT2;DisruptL=;DisruptR=;ClosestL=SMPD1;ClosestR= 6378338 54537483 67,6378407,54541313 0,0,0 chr11 6378405 6378406 chr11 54540797 54540798 INV NA + + [Svaba_SR=0,Svaba_PE=119] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=MYOD1,FANCF,WT1,LMO2,CREB3L1,DDB2,LMO1,EXT2;DisruptL=;DisruptR=;ClosestL=SMPD1;ClosestR= 6378338 54537483 14,6378407,54540802 0,0,0 chr11 8415293 8415294 chr11 8417394 8417395 DEL NA + - [Svaba_SR=76,Svaba_PE=80],[Manta_PE=79,Manta_SR=73],[Lumpy_PE=52,Lumpy_SR=47] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=STK33;DisruptR=STK33;ClosestL=;ClosestR= 7779073 7779073 44,8415300,8417392 0,0,0 chr11 10522055 10522056 chr11 36593163 36593164 DEL NA + - [Svaba_SR=144,Svaba_PE=170],[Manta_PE=146,Manta_SR=129],[Lumpy_PE=99,Lumpy_SR=98] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=MYOD1,FANCF,WT1,LMO2;DisruptL=RNF141;DisruptR=RAG2;Fusion=RAG2+RNF141;ClosestL=MTRNR2L8;ClosestR=RAG1 10522051 36593150 76,10522054,36593162 0,0,0 chr11 11283180 11283181 chr11 39290286 39290287 DUP NA - + [Svaba_SR=152,Svaba_PE=115],[Manta_PE=181,Manta_SR=138],[Lumpy_PE=140,Lumpy_SR=88] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=MYOD1,FANCF,WT1,LMO2;DisruptL=GALNT18;DisruptR=;ClosestL=;ClosestR= 11283094 39290297 80,11283185,39290288 0,0,0 chr11 12343695 12343696 chr11 49740754 49740755 INV NA + + [Svaba_SR=132,Svaba_PE=75],[Manta_PE=126,Manta_SR=120],[Lumpy_PE=106,Lumpy_SR=80] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=MYOD1,FANCF,WT1,LMO2,CREB3L1,DDB2,EXT2;DisruptL=MICAL2;DisruptR=AC136759.1;ClosestL=;ClosestR= 12344015 49740713 73,12343696,49740766 0,0,0 chr11 18360996 18360997 chr11 18393125 18393126 DEL NA + - [Svaba_SR=62,Svaba_PE=78],[Manta_PE=78,Manta_SR=54],[Lumpy_PE=57,Lumpy_SR=34] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=GTF2H1;DisruptR=;ClosestL=;ClosestR=LDHA 12344016 12344016 42,18360997,18393124 0,0,0 chr11 47996838 47996839 chr11 51712987 51712988 INV NA - - [Svaba_SR=0,Svaba_PE=68],[Manta_PE=19,Manta_SR=63] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;DisruptL=PTPRJ;DisruptR=;ClosestL=PTPRJ-AS1;ClosestR= 48243068 49740713 58,47996839,51712925 0,0,0 chr11 48037649 48037650 chr11 48243138 48243139 INV NA + + [Svaba_SR=154,Svaba_PE=171],[Manta_PE=183,Manta_SR=126],[Lumpy_PE=166,Lumpy_SR=58] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=PTPRJ;DisruptR=;ClosestL=;ClosestR=OR4X2 48243068 48243069 74,48037651,48243140 0,0,0 chr11 48037650 48037651 chr11 48242815 48242816 INV NA + + [Svaba_SR=0,Svaba_PE=154] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=PTPRJ;DisruptR=;ClosestL=;ClosestR=OR4X2 48243068 48243068 0,0,0 0,0,0 chr11 48423266 48423267 chr11 48845188 48845189 INV NA - - [Svaba_SR=42,Svaba_PE=78],[Manta_PE=138,Manta_SR=111] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;ClosestL=OR4C2P;ClosestR= 48425478 48860163 64,48423265,48845187 0,0,0 chr11 49160038 49160039 chr11 49160546 49160547 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FOLH1;DisruptR=FOLH1;ClosestL=;ClosestR= 48860164 48860164 0,0,0 0,0,0 chr11 58190284 58190285 chr11 62369331 62369332 DEL NA + - [Svaba_SR=114,Svaba_PE=131],[Manta_PE=95,Manta_SR=97],[Lumpy_PE=79,Lumpy_SR=1] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=FEN1,SDHAF2;DisruptL=OR9Q2;DisruptR=ASRGL1;Fusion=OR9Q2+ASRGL1;ClosestL=OR9Q1;ClosestR=RCC2P6 58828468 62369231 63,58190284,62369330 0,0,0 chr11 58902609 58902610 chrX 56991096 56991097 TRA NA - - [Svaba_SR=91,Svaba_PE=73],[Manta_PE=76,Manta_SR=82] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=GLYATL2;DisruptR=SPIN3;ClosestL=GLYATL1;ClosestR=AL139397.1 58828469 56991084 0,0,0 0,0,0 chr11 59869578 59869579 chr11 68509921 68509922 DUP NA - + [Manta_PE=23,Manta_SR=55],[Lumpy_PE=11,Lumpy_SR=11] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=FEN1,MEN1,MALAT1,SDHAF2;DisruptL=;DisruptR=PPP6R3;ClosestL=TCN1;ClosestR= 59869483 69098161 0,0,0 0,0,0 chr11 59869579 59869580 chr11 65511687 65511688 DUP NA - + [Svaba_SR=63,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=FEN1,MEN1,MALAT1,SDHAF2;DisruptL=;DisruptR=;ClosestL=TCN1;ClosestR=SNRPGP19 59869483 65505250 0,0,0 0,0,0 chr11 59869585 59869586 chr11 59872428 59872429 INV NA - - [Svaba_SR=0,Svaba_PE=11] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=TCN1;ClosestR=TCN1 59869483 59869483 0,0,0 0,0,0 chr11 59871621 59871622 chr11 68509655 68509656 DUP NA - + [Svaba_SR=0,Svaba_PE=25] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=FEN1,MEN1,MALAT1,SDHAF2;DisruptL=;DisruptR=PPP6R3;ClosestL=TCN1;ClosestR= 59869483 69098161 0,0,0 0,0,0 chr11 59871621 59871622 chr12 33653292 33653293 TRA NA - + [Svaba_SR=0,Svaba_PE=13] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=TCN1;ClosestR= 59869483 12389538 0,0,0 0,0,0 chr11 59872471 59872472 chr11 65511688 65511689 INV NA + + [Lumpy_PE=3,Lumpy_SR=12] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=FEN1,MEN1,MALAT1,SDHAF2;DisruptL=;DisruptR=;ClosestL=TCN1;ClosestR=SNRPGP19 59869483 65505250 6,59872467,65511689 0,0,0 chr11 60085406 60085407 chr13 110454732 110454733 TRA NA - - [Svaba_SR=65,Svaba_PE=82],[Manta_PE=80,Manta_SR=59],[Lumpy_PE=55,Lumpy_SR=21] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=COL4A2;ClosestL=MS4A2;ClosestR=COL4A2-AS2 60293095 110418576 37,60085405,110454725 0,0,0 chr11 60279269 60279270 chr11 62579531 62579532 INV NA + + [Svaba_SR=141,Svaba_PE=160],[Manta_PE=156,Manta_SR=121],[Lumpy_PE=135,Lumpy_SR=96] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=FEN1,SDHAF2;DisruptL=;DisruptR=AP002990.1,TUT1;ClosestL=MS4A4A;ClosestR=EEF1G 60293095 62579533 2,60279272,62579531 0,0,0 chr11 60292660 60292661 chr11 60293218 60293219 INV NA + + [Svaba_SR=60,Svaba_PE=83],[Manta_PE=71,Manta_SR=51],[Lumpy_PE=70,Lumpy_SR=40] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MS4A4A;DisruptR=MS4A4A;ClosestL=;ClosestR= 60293095 60293096 38,60292660,60293220 0,0,0 chr11 63780629 63780630 chr11 63781131 63781132 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=C11orf95;ClosestR=C11orf95 62579534 62579534 2,63780648,63781174 0,0,0 chr11 63930760 63930761 chr11 63934315 63934316 INV NA + + [Svaba_SR=69,Svaba_PE=40],[Manta_PE=51,Manta_SR=4] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=NAA40;ClosestR=NAA40 62579534 62579534 61,63930729,63934317 0,0,0 chr11 63930765 63930766 chr11 63935810 63935811 INV NA - - [Svaba_SR=118,Svaba_PE=134],[Manta_PE=274,Manta_SR=233],[Lumpy_PE=46,Lumpy_SR=154] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;ClosestL=NAA40;ClosestR=NAA40 62579534 62579534 94,63930766,63935809 0,0,0 chr11 63930769 63930770 chr11 63931437 63931438 INV NA + + [Svaba_SR=0,Svaba_PE=104] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=NAA40;ClosestR=NAA40 62579534 62579534 0,0,0 0,0,0 chr11 65505166 65505167 chr11 67780973 67780974 DUP NA - + [Manta_PE=33,Manta_SR=94] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MALAT1;DisruptR=;ClosestL=RF01684;ClosestR=ALG1L8P 65505249 67782059 0,0,0 0,0,0 chr11 65505166 65505167 chr11 68509658 68509659 DUP NA - + [Svaba_SR=0,Svaba_PE=29],[Manta_PE=29,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MALAT1;DisruptR=PPP6R3;Fusion=PPP6R3+MALAT1;ClosestL=RF01684;ClosestR= 65505249 69098161 9,65505171,68509512 0,0,0 chr11 65505166 65505167 chr12 33653344 33653345 TRA NA - + [Svaba_SR=0,Svaba_PE=37],[Manta_PE=19,Manta_SR=0],[Lumpy_PE=8,Lumpy_SR=2] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MALAT1;DisruptR=;ClosestL=RF01684;ClosestR= 65505249 12389538 0,0,0 0,0,0 chr11 65511293 65511294 chr12 33652636 33652637 TRA NA - - [Svaba_SR=69,Svaba_PE=72],[Manta_PE=80,Manta_SR=65],[Lumpy_PE=56,Lumpy_SR=55] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=SNRPGP19;ClosestR= 65505250 12389538 49,65511296,33652635 0,0,0 chr11 65511687 65511688 chr11 68509833 68509834 DEL NA + - [Manta_PE=13,Manta_SR=46] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=PPP6R3;ClosestL=SNRPGP19;ClosestR= 65505250 69098161 0,0,0 0,0,0 chr11 65676120 65676121 chr11 65676629 65676630 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=RELA;ClosestR=RELA 65505250 65505250 2,65676105,65676628 0,0,0 chr11 67011531 67011532 chr11 67012031 67012032 DEL NA + - [Svaba_SR=5,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SYT12;DisruptR=SYT12;ClosestL=;ClosestR= 67782059 67782059 2,67011495,67012013 0,0,0 chr11 67780632 67780633 chr12 125881063 125881064 TRA NA + - [Svaba_SR=106,Svaba_PE=88],[Manta_PE=66,Manta_SR=0],[Lumpy_PE=70,Lumpy_SR=22] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=ALG1L8P;ClosestR=AC005252.1 67782059 125881076 0,0,0 0,0,0 chr11 67780709 67780710 chr11 68509799 68509800 DUP NA - + [Manta_PE=14,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=PPP6R3;ClosestL=ALG1L8P;ClosestR= 67782059 69098161 0,0,0 0,0,0 chr11 67780880 67780881 chr12 33653292 33653293 TRA NA - + [Svaba_SR=0,Svaba_PE=25],[Manta_PE=17,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=ALG1L8P;ClosestR= 67782059 12389538 0,0,0 0,0,0 chr11 68509503 68509504 chr12 33653292 33653293 TRA NA - + [Svaba_SR=77,Svaba_PE=52],[Manta_PE=55,Manta_SR=84],[Lumpy_PE=34,Lumpy_SR=67] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PPP6R3;DisruptR=;ClosestL=;ClosestR= 69098161 12389538 58,68509504,33653294 0,0,0 chr11 68509847 68509848 chr12 33653085 33653086 TRA NA + - [Manta_PE=13,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PPP6R3;DisruptR=;ClosestL=;ClosestR= 69098161 12389538 0,0,0 0,0,0 chr11 69098215 69098216 chr11 69099668 69099669 INV NA - - [Svaba_SR=123,Svaba_PE=127],[Manta_PE=826,Manta_SR=687] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TPCN2;DisruptR=TPCN2;ClosestL=AP003071.1;ClosestR=AP003071.1 69098162 69098162 4,69098218,69099667 0,0,0 chr11 69440462 69440463 chr20 29214877 29214878 TRA NA - - [Manta_PE=16,Manta_SR=99] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AP000439.1;DisruptR=;ClosestL=AP000439.3;ClosestR= 69356467 28791094 73,69440462,29214875 0,0,0 chr11 69444063 69444064 chr11 69444589 69444590 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AP000439.1;DisruptR=AP000439.1;ClosestL=AP000439.3;ClosestR=AP000439.3 69356467 69356467 3,69444053,69444588 0,0,0 chr11 69757101 69757102 chr14 21263990 21263991 TRA NA + + [Svaba_SR=77,Svaba_PE=62],[Manta_PE=241,Manta_SR=443],[Lumpy_PE=76,Lumpy_SR=323] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=HNRNPC;ClosestL=FGF4;ClosestR= 69779346 21264197 110,69757103,21263992 0,0,0 chr11 69757139 69757140 chr11 69769207 69769208 INV NA + + [Manta_PE=284,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=FGF4;ClosestR=FGF4 69779346 69779346 0,0,0 0,0,0 chr11 69769200 69769201 chr14 21263862 21263863 TRA NA + - [Svaba_SR=78,Svaba_PE=57],[Manta_PE=169,Manta_SR=363],[Lumpy_PE=53,Lumpy_SR=292] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=HNRNPC;ClosestL=FGF4;ClosestR= 69779346 21264197 105,69769197,21263861 0,0,0 chr11 70388704 70388705 chr11 70389216 70389217 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AP000487.1;DisruptR=AP000487.1;ClosestL=PPFIA1;ClosestR=PPFIA1 70550613 70550613 3,70388688,70389215 0,0,0 chr11 73534605 73534606 chr11 73698866 73698867 DUP NA - + [Svaba_SR=41,Svaba_PE=56],[Manta_PE=56,Manta_SR=42],[Lumpy_PE=52,Lumpy_SR=16] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAM168A;DisruptR=RAB6A;Fusion=FAM168A+RAB6A;ClosestL=;ClosestR= 73060315 73060315 12,73534606,73698868 0,0,0 chr11 76901510 76901511 chr22 28499618 28499619 TRA NA + - [Svaba_SR=104,Svaba_PE=22],[Manta_PE=70,Manta_SR=99],[Lumpy_PE=43,Lumpy_SR=51] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=ACER3;DisruptR=TTC28;ClosestL=;ClosestR= 78640469 29285918 0,0,0 0,0,0 chr11 80765279 80765280 chr14 100903883 100903884 TRA NA + - [Svaba_SR=0,Svaba_PE=25],[Manta_PE=26,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=AL117190.1,MEG8;ClosestL=AP002759.1;ClosestR=RF02146 80765206 104243063 0,0,0 0,0,0 chr11 80765279 80765280 chrX 87668752 87668753 TRA NA + + [Svaba_SR=54,Svaba_PE=31],[Manta_PE=31,Manta_SR=43],[Lumpy_PE=13,Lumpy_SR=39] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=KLHL4;ClosestL=AP002759.1;ClosestR= 80765206 87103947 37,80765278,87668754 0,0,0 chr11 121197469 121197470 chr11 121472976 121472977 DUP NA - + [Svaba_SR=72,Svaba_PE=57],[Manta_PE=49,Manta_SR=59],[Lumpy_PE=37,Lumpy_SR=8] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=SORL1;ClosestL=TECTA;ClosestR=AP000977.1 121197407 121472903 43,121197470,121472978 0,0,0 chr12 25346053 25346054 chr12 25347333 25347334 DUP NA - + [Svaba_SR=73,Svaba_PE=86],[Manta_PE=80,Manta_SR=59] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 12389538 12389538 44,25346052,25347335 0,0,0 chr12 37654140 37654141 chr12 37658684 37658685 DUP NA - + [Lumpy_PE=95,Lumpy_SR=27] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 56255706 56255706 0,0,0 0,0,0 chr12 37654199 37654200 chr12 37658674 37658675 DEL NA + - [Svaba_SR=35,Svaba_PE=0],[Lumpy_PE=17,Lumpy_SR=21] lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 56255706 56255706 28,37654199,37658663 0,0,0 chr12 37654605 37654606 chr12 37658765 37658766 INV NA - - [Svaba_SR=38,Svaba_PE=45],[Lumpy_PE=27,Lumpy_SR=44] lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 56255706 56255706 47,37654609,37658764 0,0,0 chr12 37654605 37654606 chr12 37658777 37658778 DUP NA - + [Svaba_SR=84,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 56255706 56255706 0,0,0 0,0,0 chr12 37654615 37654616 chr12 37658938 37658939 DEL NA + - [Lumpy_PE=22,Lumpy_SR=31] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 56255706 56255706 38,37654612,37658937 0,0,0 chr12 37656929 37656930 chr12 38268739 38268740 INV NA + + [Svaba_SR=82,Svaba_PE=49],[Manta_PE=45,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=RF00019 56255706 56255706 0,0,0 0,0,0 chr12 37656930 37656931 chr12 37658031 37658032 DEL NA + - [Lumpy_PE=6,Lumpy_SR=20] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 56255706 56255706 20,37656927,37658030 0,0,0 chr12 37657372 37657373 chr12 38301158 38301159 INV NA - - [Svaba_SR=63,Svaba_PE=82],[Manta_PE=84,Manta_SR=73],[Lumpy_PE=50,Lumpy_SR=48] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=ALG10B 56255706 56255706 54,37657369,38301157 0,0,0 chr12 37658101 37658102 chr12 38268739 38268740 INV NA + + [Svaba_SR=49,Svaba_PE=17],[Lumpy_PE=8,Lumpy_SR=24] lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=RF00019 56255706 56255706 19,37658097,38268741 0,0,0 chr12 49263676 49263677 chr12 49265087 49265088 DEL NA + - [Svaba_SR=69,Svaba_PE=90],[Manta_PE=88,Manta_SR=48],[Lumpy_PE=66,Lumpy_SR=37] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TUBA1C,AC010173.1;DisruptR=TUBA1C;ClosestL=AC125611.3;ClosestR=AC125611.3 56255706 56255706 35,49263672,49265086 0,0,0 chr12 53511135 53511136 chr12 53512474 53512475 DEL NA + - [Lumpy_PE=3,Lumpy_SR=1] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC023509.3,ATF7;DisruptR=AC023509.3,ATF7;Fusion=ATF7+AC023509.3|AC023509.3+ATF7;ClosestL=AC023509.2;ClosestR=AC023509.2 56255706 56255706 0,0,0 0,0,0 chr12 56255681 56255682 chr12 61144864 61144865 DUP NA - + [Svaba_SR=215,Svaba_PE=282],[Manta_PE=254,Manta_SR=211],[Lumpy_PE=214,Lumpy_SR=141] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;Cancer_census=NAB2,GLI1,DDIT3,CDK4,NACA,STAT6,LRIG3;DisruptL=ANKRD52;DisruptR=;ClosestL=COQ10A;ClosestR= 56255706 61144794 91,56255678,61144869 0,0,0 chr12 65713912 65713913 chr12 112325573 112325574 INV NA - - [Manta_PE=1220,Manta_SR=1046] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=BTG1,PTPRB,USP44,SH2B3,HMGA2,MDM2,CHST11,ALDH2;DisruptL=;DisruptR=HECTD4;ClosestL=;ClosestR=AC004217.2 65713850 112325531 115,65713916,112325569 0,0,0 chr12 65856872 65856873 chr12 67766189 67766190 DEL NA + - [Svaba_SR=83,Svaba_PE=91],[Manta_PE=87,Manta_SR=67],[Lumpy_PE=55,Lumpy_SR=58] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=HMGA2;DisruptL=AC090673.1,HMGA2;DisruptR=;ClosestL=;ClosestR=AC022513.1 65713850 67923115 49,65856873,67766188 0,0,0 chr12 66145833 66145834 chr12 66682452 66682453 DUP NA - + [Svaba_SR=56,Svaba_PE=83],[Manta_PE=76,Manta_SR=55],[Lumpy_PE=69,Lumpy_SR=37] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC078927.1,TMBIM4;DisruptR=GRIP1;Fusion=AC078927.1+GRIP1|TMBIM4+GRIP1;ClosestL=LLPH-DT;ClosestR= 65713850 65713850 40,66145834,66682454 0,0,0 chr12 66362648 66362649 chr12 68497810 68497811 DUP NA - + [Svaba_SR=147,Svaba_PE=126],[Manta_PE=175,Manta_SR=140],[Lumpy_PE=154,Lumpy_SR=108] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=GRIP1;DisruptR=;ClosestL=HELB;ClosestR=AC008033.2 65713850 67923116 77,66362649,68497812 0,0,0 chr12 66410668 66410669 chr12 69873475 69873476 DEL NA + - [Svaba_SR=46,Svaba_PE=64],[Manta_PE=53,Manta_SR=64],[Lumpy_PE=41,Lumpy_SR=37] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=MDM2;DisruptL=GRIP1;DisruptR=MYRFL;ClosestL=;ClosestR=AC025263.2 65713850 69869147 46,66410665,69873474 0,0,0 chr12 66453482 66453483 chr12 68613971 68613972 DEL NA + - [Svaba_SR=90,Svaba_PE=139],[Manta_PE=165,Manta_SR=144],[Lumpy_PE=110,Lumpy_SR=115] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=GRIP1;DisruptR=RAP1B;ClosestL=;ClosestR=RPL10P12 65713850 67923116 79,66453484,68613970 0,0,0 chr12 67114680 67114681 chr21 32343521 32343522 TRA NA - - [Svaba_SR=0,Svaba_PE=42],[Manta_PE=38,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=URB1;ClosestL=RAB11AP2;ClosestR= 67923115 32739134 0,0,0 0,0,0 chr12 67919941 67919942 chr12 67923109 67923110 INV NA + + [Svaba_SR=100,Svaba_PE=160],[Manta_PE=300,Manta_SR=258],[Lumpy_PE=259,Lumpy_SR=219] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;ClosestL=LINC01479;ClosestR=LINC01479 67923115 67923115 49,67919943,67923111 0,0,0 chr12 69782621 69782622 chr12 69869191 69869192 DEL NA + - [Svaba_SR=405,Svaba_PE=185],[Manta_PE=609,Manta_SR=551],[Lumpy_PE=92,Lumpy_SR=406] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=RAB3IP;DisruptR=MYRFL;Fusion=RAB3IP+MYRFL;ClosestL=AC025263.2;ClosestR=AC025263.2 69782593 69869147 114,69782622,69869190 0,0,0 chr12 69967248 69967249 chr12 70003771 70003772 INV NA + + [Svaba_SR=55,Svaba_PE=47],[Manta_PE=67,Manta_SR=58],[Lumpy_PE=60,Lumpy_SR=45] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC025159.1;DisruptR=AC025159.1;ClosestL=MYRFL;ClosestR= 69869147 69869147 43,69967248,70003773 0,0,0 chr12 71740511 71740512 chr12 71741016 71741017 DEL NA + - [Svaba_SR=9,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=RAB21;ClosestR=RAB21 71964313 71964313 4,71740514,71741032 0,0,0 chr12 71972105 71972106 chr12 71993496 71993497 DUP NA - + [Svaba_SR=77,Svaba_PE=79],[Manta_PE=73,Manta_SR=90],[Lumpy_PE=63,Lumpy_SR=44] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq 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=179,Svaba_PE=198],[Manta_PE=195,Manta_SR=159],[Lumpy_PE=146,Lumpy_SR=118] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=TPH2;DisruptR=TPH2;ClosestL=;ClosestR= 71964314 71964314 79,71975433,72007829 0,0,0 chr12 72510655 72510656 chr12 72511895 72511896 INV NA + + [Svaba_SR=115,Svaba_PE=166],[Manta_PE=441,Manta_SR=338],[Lumpy_PE=380,Lumpy_SR=240] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=TRHDE;DisruptR=TRHDE;ClosestL=;ClosestR= 72511836 72511837 109,72510657,72511897 0,0,0 chr12 72534503 72534504 chr12 72535081 72535082 DUP NA - + [Svaba_SR=45,Svaba_PE=50],[Manta_PE=39,Manta_SR=41],[Lumpy_PE=33,Lumpy_SR=28] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TRHDE;DisruptR=TRHDE;ClosestL=;ClosestR= 72511837 72511837 31,72534504,72535083 0,0,0 chr12 96149120 96149121 chr12 96166173 96166174 DEL NA + - [Svaba_SR=88,Svaba_PE=88],[Manta_PE=71,Manta_SR=70],[Lumpy_PE=48,Lumpy_SR=52] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=LINC02452;ClosestL=LINC02452;ClosestR= 101739241 101739241 48,96149120,96166172 0,0,0 chr12 101739294 101739295 chr12 101984547 101984548 DUP NA - + [Svaba_SR=0,Svaba_PE=80] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SYCP3,CHPT1;DisruptR=DRAM1;Fusion=DRAM1+CHPT1;ClosestL=GNPTAB;ClosestR= 101739242 101984829 0,0,0 0,0,0 chr12 101739295 101739296 chr12 101984856 101984857 DUP NA - + [Svaba_SR=74,Svaba_PE=80],[Manta_PE=70,Manta_SR=65],[Lumpy_PE=63,Lumpy_SR=49] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SYCP3,CHPT1;DisruptR=DRAM1;Fusion=DRAM1+CHPT1;ClosestL=GNPTAB;ClosestR= 101739242 101984830 44,101739295,101984858 0,0,0 chr12 102778450 102778451 chr12 102781372 102781373 DEL NA + - [Manta_PE=8,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 101984830 101984830 0,0,0 0,0,0 chr12 112316935 112316936 chr12 112384855 112384856 DUP NA - + [Svaba_SR=413,Svaba_PE=224],[Manta_PE=656,Manta_SR=524] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=HECTD4;DisruptR=;ClosestL=AC004217.2;ClosestR=HECTD4 112325530 112386380 114,112316936,112384857 0,0,0 chr12 112317524 112317525 chr12 112386389 112386390 INV NA + + [Manta_PE=642,Manta_SR=502],[Lumpy_PE=569,Lumpy_SR=405] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HECTD4;DisruptR=;ClosestL=AC004217.2;ClosestR=HECTD4 112325530 112386381 112,112317526,112386391 0,0,0 chr12 112317527 112317528 chr12 112385960 112385961 INV NA + + [Svaba_SR=0,Svaba_PE=151] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HECTD4;DisruptR=;ClosestL=AC004217.2;ClosestR=HECTD4 112325530 112386380 0,0,0 0,0,0 chr12 112367062 112367063 chr12 112367567 112367568 DEL NA + - [Svaba_SR=8,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HECTD4;DisruptR=HECTD4;ClosestL=;ClosestR= 112386380 112386380 2,112367050,112367566 0,0,0 chr12 114637665 114637666 chr12 114638182 114638183 DEL NA + - [Svaba_SR=1,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC010177.1;ClosestR=AC010177.1 112386381 112386381 0,0,0 0,0,0 chr12 123419143 123419144 chr12 123419720 123419721 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=RILPL2;DisruptR=RILPL2;ClosestL=KMT5A;ClosestR=KMT5A 125881076 125881076 2,123419126,123419719 0,0,0 chr13 16325052 16325053 chr13 16964070 16964071 DUP NA - + [Manta_PE=7,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 16022426 16022426 0,0,0 2,16325175,16963889 chr13 18248992 18248993 chr18 21464558 21464559 TRA NA - - [Svaba_SR=3,Svaba_PE=6],[Lumpy_PE=5,Lumpy_SR=3] lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL356585.10;DisruptR=GREB1L;Fusion=AL356585.10-GREB1L;ClosestL=GGT4P;ClosestR=AC015878.1 18408580 20553042 3,18248991,21464557 0,0,0 chr13 18251626 18251627 chr18 21472012 21472013 TRA NA - - [Svaba_SR=2,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=GREB1L;ClosestL=GGT4P;ClosestR= 18408580 20553042 2,18251627,21472011 0,0,0 chr13 25024466 25024467 chr13 25030471 25030472 DEL NA + - [Svaba_SR=84,Svaba_PE=92],[Manta_PE=79,Manta_SR=74],[Lumpy_PE=54,Lumpy_SR=45] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;ClosestL=AL590099.1;ClosestR=AL590099.1 24952568 24952568 52,25024465,25030470 0,0,0 chr13 28880457 28880458 chr13 98509424 98509425 DEL NA + - [Svaba_SR=170,Svaba_PE=206],[Manta_PE=194,Manta_SR=148],[Lumpy_PE=134,Lumpy_SR=115] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;gap;Cancer_census=CYSLTR2,SOX21,BRCA2,LHFP,FOXO1,RB1,NBEA,LCP1,GPC5;DisruptL=MTUS2;DisruptR=STK24;ClosestL=;ClosestR= 28880402 98509395 85,28880457,98509423 0,0,0 chr13 97331894 97331895 chr13 97689069 97689070 DEL NA + - [Svaba_SR=82,Svaba_PE=84],[Manta_PE=68,Manta_SR=72],[Lumpy_PE=47,Lumpy_SR=49] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=MBNL2;DisruptR=;ClosestL=;ClosestR=AL359502.1 97331911 97689109 53,97331894,97689068 0,0,0 chr13 101085680 101085681 chr13 101107648 101107649 DEL NA + - [Svaba_SR=65,Svaba_PE=94],[Manta_PE=82,Manta_SR=53],[Lumpy_PE=66,Lumpy_SR=26] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=NALCN;DisruptR=NALCN;ClosestL=;ClosestR= 102234406 102234406 40,101085680,101107647 0,0,0 chr13 102238357 102238358 chr21 18481781 18481782 TRA NA - + [Svaba_SR=78,Svaba_PE=86],[Manta_PE=81,Manta_SR=69],[Lumpy_PE=61,Lumpy_SR=45] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FGF14;DisruptR=TMPRSS15,AL109763.1;Fusion=FGF14-TMPRSS15|FGF14-AL109763.1;ClosestL=;ClosestR= 102234407 18481760 51,102238356,18481783 0,0,0 chr13 104720083 104720084 chr21 17226144 17226145 TRA NA - + [Svaba_SR=0,Svaba_PE=24],[Lumpy_PE=6,Lumpy_SR=5] svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=NEK4P1 103143847 17474345 7,104720018,17226146 0,0,0 chr13 107326514 107326515 chr13 107327081 107327082 INV NA - - [Svaba_SR=75,Svaba_PE=34],[Lumpy_PE=2,Lumpy_SR=31] lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAM155A;DisruptR=FAM155A;ClosestL=SNORD31B;ClosestR=SNORD31B 107326195 107326195 14,107326511,107327077 0,0,0 chr13 107326584 107326585 chr18 3047570 3047571 TRA NA + - [Svaba_SR=85,Svaba_PE=55],[Manta_PE=25,Manta_SR=0],[Lumpy_PE=23,Lumpy_SR=42] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAM155A;DisruptR=;ClosestL=SNORD31B;ClosestR=MYOM1 107326195 3047304 17,107326584,3047569 0,0,0 chr13 107327081 107327082 chr18 3047570 3047571 TRA NA - - [Svaba_SR=112,Svaba_PE=62],[Manta_PE=45,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAM155A;DisruptR=;ClosestL=SNORD31B;ClosestR=MYOM1 107326195 3047304 0,0,0 0,0,0 chr13 107559858 107559859 chr13 108952134 108952135 DUP NA - + [Svaba_SR=0,Svaba_PE=20] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAM155A;DisruptR=MYO16;ClosestL=;ClosestR= 107326195 108951936 0,0,0 0,0,0 chr13 107559859 107559860 chr13 108859484 108859485 DUP NA - + [Lumpy_PE=25,Lumpy_SR=27] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAM155A;DisruptR=MYO16;ClosestL=;ClosestR= 107326195 108951935 11,107559859,108859485 0,0,0 chr13 107560030 107560031 chr13 108859489 108859490 INV NA - - [Svaba_SR=71,Svaba_PE=50],[Manta_PE=60,Manta_SR=70],[Lumpy_PE=13,Lumpy_SR=59] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAM155A;DisruptR=MYO16;Fusion=FAM155A+MYO16;ClosestL=;ClosestR= 107326195 108951935 51,107560032,108859488 0,0,0 chr13 107560301 107560302 chr13 108954298 108954299 DEL NA + - [Svaba_SR=80,Svaba_PE=71],[Manta_PE=56,Manta_SR=67],[Lumpy_PE=30,Lumpy_SR=52] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FAM155A;DisruptR=MYO16;ClosestL=;ClosestR= 107326195 108951936 49,107560301,108954297 0,0,0 chr13 108858990 108858991 chr13 108859645 108859646 DUP NA - + [Manta_PE=22,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR= 108951935 108951935 0,0,0 0,0,0 chr13 108859285 108859286 chr13 108952396 108952397 DEL NA + - [Svaba_SR=101,Svaba_PE=0],[Manta_PE=49,Manta_SR=85] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR= 108951935 108951936 11,108859287,108952274 0,0,0 chr13 108859328 108859329 chr13 108952203 108952204 DUP NA - + [Svaba_SR=23,Svaba_PE=0],[Manta_PE=22,Manta_SR=57],[Lumpy_PE=17,Lumpy_SR=45] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR= 108951935 108951936 28,108859329,108952205 0,0,0 chr13 108859488 108859489 chr13 108954297 108954298 INV NA - - [Svaba_SR=0,Svaba_PE=22],[Manta_PE=13,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR= 108951935 108951936 0,0,0 0,0,0 chr13 108860016 108860017 chr13 108951977 108951978 DEL NA + - [Svaba_SR=0,Svaba_PE=29] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR= 108951935 108951936 0,0,0 0,0,0 chr13 108860095 108860096 chr13 108920673 108920674 INV NA + + [Manta_PE=19,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR= 108951935 108951935 0,0,0 0,0,0 chr13 108920232 108920233 chr13 108951853 108951854 INV NA - - [Manta_PE=21,Manta_SR=0],[Lumpy_PE=12,Lumpy_SR=1] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR= 108951935 108951935 0,0,0 0,0,0 chr13 108920603 108920604 chr13 108951862 108951863 DEL NA + - [Manta_PE=10,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MYO16;DisruptR=MYO16;ClosestL=;ClosestR= 108951935 108951935 0,0,0 0,0,0 chr14 20575192 20575193 chr14 21264283 21264284 DUP NA - + [Svaba_SR=131,Svaba_PE=154],[Manta_PE=134,Manta_SR=116],[Lumpy_PE=104,Lumpy_SR=91] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=;DisruptR=HNRNPC;ClosestL=AL163195.3;ClosestR= 20575159 21264198 70,20575195,21264285 0,0,0 chr14 21142428 21142429 chr14 21142946 21142947 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=OR5AU1;ClosestR=OR5AU1 21264197 21264197 2,21142403,21142939 0,0,0 chr14 28611571 28611572 chr22 28669722 28669723 TRA NA + - [Svaba_SR=0,Svaba_PE=83] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC02300,TTC28;DisruptR=TTC28;Fusion=TTC28-LINC02300;ClosestL=EIF4A1P12;ClosestR=CHEK2 32961967 29285918 0,0,0 0,0,0 chr14 28611571 28611572 chr22 28669871 28669872 TRA NA - - [Manta_PE=19,Manta_SR=0],[Lumpy_PE=17,Lumpy_SR=11] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC02300,TTC28;DisruptR=TTC28;ClosestL=EIF4A1P12;ClosestR=CHEK2 32961967 29285918 0,0,0 0,0,0 chr14 28611590 28611591 chr22 28670295 28670296 TRA NA + + [Manta_PE=4,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC02300,TTC28;DisruptR=TTC28;ClosestL=EIF4A1P12;ClosestR=CHEK2 32961967 29285918 0,0,0 0,0,0 chr14 32961999 32962000 chr14 32970923 32970924 DEL NA + - [Svaba_SR=120,Svaba_PE=202],[Manta_PE=249,Manta_SR=185],[Lumpy_PE=183,Lumpy_SR=146] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=NPAS3;DisruptR=NPAS3;ClosestL=;ClosestR= 32961968 32970858 2,32962002,32970925 0,0,0 chr14 41463251 41463252 chr14 41474102 41474103 DEL NA + - [Svaba_SR=47,Svaba_PE=63],[Manta_PE=59,Manta_SR=46],[Lumpy_PE=50,Lumpy_SR=17] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 41200381 41200381 2,41463247,41474110 0,0,0 chr14 49629250 49629251 chr14 49629763 49629764 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=DNAAF2;DisruptR=AL139099.2,DNAAF2;Fusion=AL139099.2+DNAAF2;ClosestL=AL139099.2;ClosestR=MGAT2 41200381 41200381 3,49629221,49629762 0,0,0 chr14 50217721 50217722 chr14 50218260 50218261 DEL NA + - [Svaba_SR=1,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SOS2;DisruptR=SOS2;ClosestL=L2HGDH;ClosestR=L2HGDH 41200381 41200381 2,50217687,50218251 0,0,0 chr14 65597392 65597393 chr14 65597906 65597907 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FUT8;DisruptR=FUT8;ClosestL=;ClosestR= 41200381 41200381 2,65597367,65597905 4,65597367,65597905 chr14 73826696 73826697 chr14 73827217 73827218 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC02274;DisruptR=LINC02274;ClosestL=AC005520.4;ClosestR=AC005520.4 91109906 91109906 0,0,0 2,73826667,73827216 chr14 81201605 81201606 chr14 81202852 81202853 DUP NA - + [Svaba_SR=34,Svaba_PE=44],[Manta_PE=38,Manta_SR=27],[Lumpy_PE=30,Lumpy_SR=20] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=GTF2A1;DisruptR=GTF2A1;ClosestL=SNORA79;ClosestR=SNORA79 91109906 91109906 21,81201605,81202854 0,0,0 chr14 91109951 91109952 chr14 91493414 91493415 DUP NA - + [Svaba_SR=120,Svaba_PE=169],[Manta_PE=136,Manta_SR=123],[Lumpy_PE=113,Lumpy_SR=101] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=DGLUCY;DisruptR=PPP4R3A;ClosestL=SNORA11B;ClosestR= 91109907 91493335 55,91109952,91493416 0,0,0 chr14 100903884 100903885 chrX 87668584 87668585 TRA NA - - [Svaba_SR=55,Svaba_PE=6],[Manta_PE=3,Manta_SR=49],[Lumpy_PE=5,Lumpy_SR=39] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL117190.1,MEG8;DisruptR=KLHL4;ClosestL=RF02146;ClosestR= 104243063 87103947 21,100903895,87668583 0,0,0 chr14 102959493 102959494 chr17 35740374 35740375 TRA NA - + [Svaba_SR=0,Svaba_PE=20],[Manta_PE=18,Manta_SR=78] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CDC42BPB;DisruptR=RASL10B,TAF15;ClosestL=;ClosestR=GAS2L2 104243063 36041470 0,0,0 0,0,0 chr14 104243055 104243056 chr14 104326293 104326294 INV NA - - [Svaba_SR=76,Svaba_PE=145],[Manta_PE=387,Manta_SR=320],[Lumpy_PE=261,Lumpy_SR=257] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL590079.1;DisruptR=;ClosestL=;ClosestR= 104243063 104326322 104,104243056,104326292 0,0,0 chr14 104704163 104704164 chr14 105433354 105433355 DUP NA - + [Svaba_SR=262,Svaba_PE=207],[Manta_PE=284,Manta_SR=245],[Lumpy_PE=238,Lumpy_SR=180] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=AKT1;DisruptL=INF2;DisruptR=TEX22,MTA1;Fusion=TEX22+INF2|MTA1+INF2;ClosestL=AL583722.4;ClosestR=AL928654.1 104326323 105433357 100,104704159,105433356 0,0,0 chr14 104850273 104850274 chr14 104850810 104850811 DEL NA + - [Svaba_SR=5,Svaba_PE=6] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AL583810.2;ClosestR=AL583810.2 104326323 104326323 2,104850314,104850717 0,0,0 chr14 105074574 105074575 chr14 105075322 105075323 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=GPR132;ClosestR=GPR132 105433357 105433357 2,105074563,105075321 0,0,0 chr14 105117762 105117763 chr14 105352505 105352506 DUP NA - + [Svaba_SR=23,Svaba_PE=74],[Manta_PE=164,Manta_SR=121],[Lumpy_PE=140,Lumpy_SR=90] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=PACS2;ClosestL=AL512356.2;ClosestR=AL928654.4 105433357 105433357 75,105117762,105352507 0,0,0 chr14 105893685 105893686 chr14 105902785 105902786 DUP NA - + [Svaba_SR=0,Svaba_PE=29],[Manta_PE=19,Manta_SR=158] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC246787.2;DisruptR=;ClosestL=IGHD5-18;ClosestR=IGHD5-12 105433358 105433358 21,105893572,105902684 0,0,0 chr15 21545403 21545404 chr18 67194548 67194549 TRA NA + + [Svaba_SR=59,Svaba_PE=37],[Manta_PE=1,Manta_SR=60] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC183088.1;ClosestR= 17083473 67194596 45,21545405,67194550 0,0,0 chr15 56746798 56746799 chr15 56751379 56751380 INV NA - - [Svaba_SR=127,Svaba_PE=152],[Manta_PE=187,Manta_SR=129],[Lumpy_PE=130,Lumpy_SR=98] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AC090517.4;DisruptR=AC090517.4;ClosestL=ZNF280D;ClosestR=ZNF280D 56746779 56746779 79,56746800,56751378 0,0,0 chr15 62473857 62473858 chr15 62474396 62474397 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TLN2;DisruptR=TLN2;ClosestL=;ClosestR= 65078251 65078251 4,62473848,62474395 0,0,0 chr15 65803608 65803609 chr18 11294088 11294089 TRA NA - + [Svaba_SR=123,Svaba_PE=138],[Manta_PE=116,Manta_SR=103],[Lumpy_PE=84,Lumpy_SR=74] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=RAB11A;DisruptR=;ClosestL=DENND4A;ClosestR= 65078252 11294018 62,65803604,11294090 0,0,0 chr15 72000221 72000222 chr15 72362565 72362566 DUP NA - + [Svaba_SR=168,Svaba_PE=197],[Manta_PE=192,Manta_SR=148],[Lumpy_PE=164,Lumpy_SR=122] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC022872.1,MYO9A;DisruptR=AC009690.1,HEXA;Fusion=MYO9A+AC009690.1|MYO9A+HEXA;ClosestL=;ClosestR=AC009690.2 72000243 72362589 77,72000222,72362567 0,0,0 chr15 76561966 76561967 chr16 67651996 67651997 TRA NA + + [Svaba_SR=62,Svaba_PE=9],[Manta_PE=9,Manta_SR=72],[Lumpy_PE=11,Lumpy_SR=50] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SCAPER;DisruptR=CARMIL2;Fusion=CARMIL2-SCAPER;ClosestL=;ClosestR=ACD 72362590 90226217 42,76561967,67651998 0,0,0 chr15 83442800 83442801 chr15 83443340 83443341 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC103876.1;ClosestR=SH3GL3 72362590 72362590 0,0,0 0,0,0 chr15 84047235 84047236 chr15 84047817 84047818 DEL NA + - [Manta_PE=99,Manta_SR=126] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC027807.1;ClosestR=AC027807.1 72362590 72362590 69,84047237,84047816 0,0,0 chr15 90417947 90417948 chr22 30281382 30281383 TRA NA - + [Svaba_SR=13,Svaba_PE=15],[Manta_PE=10,Manta_SR=12],[Lumpy_PE=3,Lumpy_SR=5] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=IQGAP1;DisruptR=;ClosestL=;ClosestR=CASTOR1 101981087 29285919 11,90417949,30281384 0,0,0 chr15 90418089 90418090 chr22 30170524 30170525 TRA NA + - [Svaba_SR=25,Svaba_PE=21],[Manta_PE=14,Manta_SR=18],[Lumpy_PE=4,Lumpy_SR=17] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=IQGAP1;DisruptR=HORMAD2;Fusion=IQGAP1-HORMAD2;ClosestL=;ClosestR=AC002378.1 101981087 29285919 16,90418088,30170523 0,0,0 chr16 20892 20893 chrX 156019949 156019950 TRA NA - + [Manta_PE=23,Manta_SR=67] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=Z84723.1;DisruptR=AJ271736.1;ClosestL=WASIR2;ClosestR=WASH6P 10005 156030795 25,20893,156019953 0,0,0 chr16 515531 515532 chr17 22058252 22058253 TRA NA + + [Svaba_SR=46,Svaba_PE=51],[Manta_PE=41,Manta_SR=37] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=RAB11FIP3;DisruptR=;ClosestL=LINC00235;ClosestR=ABBA01006766.1 452830 22044138 21,515530,22058254 0,0,0 chr16 3191703 3191704 chr16 3228907 3228908 DEL NA + - [Svaba_SR=80,Svaba_PE=77],[Manta_PE=73,Manta_SR=68],[Lumpy_PE=53,Lumpy_SR=35] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AJ003147.2;DisruptR=ZNF200;ClosestL=AJ003147.1;ClosestR=AJ003147.2 452830 452830 0,0,0 0,0,0 chr16 5057651 5057652 chr16 5058229 5058230 DEL NA + - [Svaba_SR=2,Svaba_PE=5] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ALG1,C16orf89;DisruptR=ALG1,C16orf89;ClosestL=NAGPA-AS1;ClosestR=NAGPA-AS1 452830 452830 0,0,0 0,0,0 chr16 24481252 24481253 chr16 24513939 24513940 DEL NA + - [Svaba_SR=145,Svaba_PE=223],[Manta_PE=212,Manta_SR=143],[Lumpy_PE=137,Lumpy_SR=103] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AC008938.1;DisruptR=;ClosestL=;ClosestR=AC008938.1 24481285 24513922 72,24481254,24513933 0,0,0 chr16 28273135 28273136 chr16 28273654 28273655 DEL NA + - [Svaba_SR=7,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC138904.3;DisruptR=AC138904.3;ClosestL=AC138904.1;ClosestR=AC138904.1 24513922 24513922 0,0,0 0,0,0 chr16 37750074 37750075 chr21 18585121 18585122 TRA NA - + [Lumpy_PE=5,Lumpy_SR=2] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=MIR548XHG;ClosestL=;ClosestR= 34596149 18481760 0,0,0 0,0,0 chr16 70232878 70232879 chr16 70281139 70281140 DEL NA + - [Svaba_SR=86,Svaba_PE=86],[Manta_PE=29,Manta_SR=75],[Lumpy_PE=10,Lumpy_SR=45] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SMG1P7;DisruptR=AARS;Fusion=AARS+SMG1P7;ClosestL=EXOSC6;ClosestR=RN7SL279P 90226217 90226217 49,70232878,70281138 0,0,0 chr16 74657090 74657091 chr16 74659686 74659687 DEL NA + - [Svaba_SR=28,Svaba_PE=37],[Manta_PE=31,Manta_SR=26],[Lumpy_PE=19,Lumpy_SR=22] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=RFWD3;DisruptL=RFWD3;DisruptR=RFWD3;ClosestL=TMPOP2;ClosestR=TMPOP2 90226217 90226217 21,74657091,74659685 0,0,0 chr16 76745602 76745603 chr16 76759438 76759439 DEL NA + - [Svaba_SR=72,Svaba_PE=86],[Manta_PE=71,Manta_SR=65],[Lumpy_PE=50,Lumpy_SR=52] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC104151.1,AC106729.1;DisruptR=AC104151.1,AC106729.1;Fusion=AC104151.1+AC106729.1|AC106729.1+AC104151.1;ClosestL=;ClosestR= 90226217 90226217 53,76745604,76759437 0,0,0 chr16 89517377 89517378 chr16 89597850 89597851 DUP NA - + [Svaba_SR=19,Svaba_PE=0],[Manta_PE=64,Manta_SR=23],[Lumpy_PE=64,Lumpy_SR=11] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SPG7;DisruptR=;ClosestL=AC092123.1;ClosestR=CPNE7 90226217 90226217 13,89517378,89597852 0,0,0 chr17 1788505 1788506 chr17 35740201 35740202 INV NA - - [Svaba_SR=49,Svaba_PE=9],[Manta_PE=5,Manta_SR=43],[Lumpy_PE=4,Lumpy_SR=14] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=TP53,USP6,PER1,FLCN,RABEP1,GAS7,MAP2K4,NCOR1,SPECC1,NF1,SUZ12;DisruptL=SMYD4;DisruptR=RASL10B,TAF15;Fusion=SMYD4+RASL10B|SMYD4+TAF15;ClosestL=SERPINF1;ClosestR=GAS2L2 168977 36041470 2,1788503,35740202 0,0,0 chr17 21970043 21970044 chr17 21987066 21987067 DEL NA + - [Lumpy_PE=2,Lumpy_SR=2] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;ClosestL=;ClosestR= 21968703 21968703 0,0,0 0,0,0 chr17 26663485 26663486 chr20 31572794 31572795 TRA NA + + [Svaba_SR=10,Svaba_PE=8],[Manta_PE=10,Manta_SR=12],[Lumpy_PE=6,Lumpy_SR=7] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=HM13,HM13-AS1;ClosestL=;ClosestR=AL110115.2 22044138 31539639 9,26663485,31572796 0,0,0 chr17 29366934 29366935 chr17 29367456 29367457 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC068025.2;DisruptR=AC068025.2;ClosestL=AC068025.1;ClosestR=AC068025.1 34345357 34345357 3,29366916,29367455 0,0,0 chr17 34007794 34007795 chr17 34345231 34345232 INV NA - - [Svaba_SR=97,Svaba_PE=110],[Manta_PE=123,Manta_SR=131],[Lumpy_PE=79,Lumpy_SR=107] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC024610.2,AC004147.4,ASIC2;DisruptR=;ClosestL=AC123769.1;ClosestR=CCL13 34345357 34345357 74,34007794,34345230 0,0,0 chr17 34019945 34019946 chr17 43351893 43351894 DEL NA + - [Svaba_SR=131,Svaba_PE=165],[Manta_PE=146,Manta_SR=110] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=CCR7,TAF15,MLLT6,LASP1,CDK12,RARA,ERBB2,SMARCE1,STAT5B,STAT3,BRCA1;DisruptL=AC024610.2,AC004147.4,ASIC2;DisruptR=;ClosestL=AC123769.1;ClosestR=AC109326.1 34345357 43351849 69,34019945,43351892 0,0,0 chr17 35981786 35981787 chr17 35985681 35985682 INV NA - - [Svaba_SR=54,Svaba_PE=59],[Manta_PE=75,Manta_SR=54],[Lumpy_PE=46,Lumpy_SR=41] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=CCL14,AC244100.2,CCL15-CCL14;ClosestL=CCL16;ClosestR=CCL16 36041470 36041470 39,35981786,35985675 0,0,0 chr17 36183293 36183294 chr17 36184037 36184038 INV NA + + [Svaba_SR=103,Svaba_PE=152],[Manta_PE=166,Manta_SR=118],[Lumpy_PE=136,Lumpy_SR=96] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC243829.1;DisruptR=AC243829.1;ClosestL=AC243829.2;ClosestR=AC243829.2 36041471 36041471 49,36183291,36184039 0,0,0 chr17 39577411 39577412 chr17 39805140 39805141 DUP NA - + [Svaba_SR=72,Svaba_PE=141],[Manta_PE=156,Manta_SR=97],[Lumpy_PE=150,Lumpy_SR=12] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=ERBB2;DisruptL=;DisruptR=IKZF3;ClosestL=AC009283.1;ClosestR= 39577425 39805110 67,39577413,39805142 0,0,0 chr17 43375383 43375384 chr17 43382359 43382360 DEL NA + - [Lumpy_PE=2,Lumpy_SR=2] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC00910;DisruptR=LINC00910;ClosestL=RNU2-4P;ClosestR=RNU2-4P 43351849 43351849 2,43375382,43382358 0,0,0 chr17 44549222 44549223 chr17 44628027 44628028 DEL NA + - [Svaba_SR=123,Svaba_PE=128],[Manta_PE=140,Manta_SR=104],[Lumpy_PE=101,Lumpy_SR=61] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;ClosestL=FZD2;ClosestR=SMCO4P1 44549196 44627963 65,44549223,44628026 0,0,0 chr17 44682949 44682950 chr22 28755129 28755130 TRA NA - + [Lumpy_PE=3,Lumpy_SR=2] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MEIOC,CCDC43;DisruptR=HSCB;Fusion=HSCB-MEIOC;ClosestL=AC091152.2;ClosestR=CHEK2 44627963 29285918 2,44682947,28755131 0,0,0 chr17 47874903 47874904 chr17 48071891 48071892 DUP NA - + [Svaba_SR=0,Svaba_PE=189] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=CBX1;ClosestL=AC018521.7;ClosestR=AC004477.3 47874912 48072289 0,0,0 0,0,0 chr17 47874904 47874905 chr17 48072313 48072314 DUP NA - + [Svaba_SR=248,Svaba_PE=104],[Manta_PE=350,Manta_SR=274] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=CBX1;ClosestL=AC018521.7;ClosestR=AC004477.3 47874912 48072290 2,47874899,48072314 0,0,0 chr17 55526546 55526547 chr17 55537682 55537683 INV NA - - [Svaba_SR=84,Svaba_PE=54],[Manta_PE=44,Manta_SR=78],[Lumpy_PE=29,Lumpy_SR=59] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=AC105021.1;ClosestL=AC105021.1;ClosestR=GARSP1 55607901 55607901 58,55526545,55537681 0,0,0 chr17 55526721 55526722 chr21 41571013 41571014 TRA NA + - [Svaba_SR=68,Svaba_PE=70],[Manta_PE=47,Manta_SR=58],[Lumpy_PE=41,Lumpy_SR=49] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC105021.1;ClosestR=AP006748.1 55607901 41571036 46,55526722,41571012 0,0,0 chr17 55527606 55527607 chr17 55538276 55538277 INV NA + + [Svaba_SR=61,Svaba_PE=68],[Manta_PE=66,Manta_SR=55],[Lumpy_PE=58,Lumpy_SR=43] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC105021.1;DisruptR=AC105021.1;ClosestL=SMIM36;ClosestR=GARSP1 55607901 55607901 39,55527605,55538278 0,0,0 chr17 55537681 55537682 chr21 41571012 41571013 TRA NA - - [Svaba_SR=0,Svaba_PE=37],[Manta_PE=28,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC105021.1;DisruptR=;ClosestL=GARSP1;ClosestR=AP006748.1 55607901 41571036 0,0,0 0,0,0 chr17 55607904 55607905 chr17 59518907 59518908 DUP NA - + [Svaba_SR=187,Svaba_PE=274],[Manta_PE=235,Manta_SR=168],[Lumpy_PE=217,Lumpy_SR=47] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=RNF43,MSI2;DisruptL=;DisruptR=LINC01476;ClosestL=;ClosestR=RNU4-13P 55607902 59518847 87,55607906,59518909 0,0,0 chr17 67102576 67102577 chr17 67113691 67113692 INV NA - - [Svaba_SR=218,Svaba_PE=259],[Manta_PE=267,Manta_SR=203],[Lumpy_PE=197,Lumpy_SR=142] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=HELZ;DisruptR=HELZ;ClosestL=;ClosestR= 67102560 67102560 95,67102576,67113690 0,0,0 chr17 68465230 68465231 chr17 68465734 68465735 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC007780.1;DisruptR=AC007780.1;ClosestL=WIPI1;ClosestR=WIPI1 67148388 67148388 2,68465213,68465748 0,0,0 chr17 71544176 71544177 chr17 71545941 71545942 DEL NA + - [Svaba_SR=79,Svaba_PE=90],[Manta_PE=83,Manta_SR=73] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 67148388 67148388 0,0,0 0,0,0 chr17 72463523 72463524 chr17 72475017 72475018 DEL NA + - [Svaba_SR=87,Svaba_PE=60],[Manta_PE=68,Manta_SR=74],[Lumpy_PE=51,Lumpy_SR=54] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR= 67148388 67148388 57,72463525,72475015 0,0,0 chr17 72463523 72463524 chr17 72534011 72534012 DEL NA + - [Svaba_SR=0,Svaba_PE=27],[Manta_PE=27,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR= 67148388 67148388 0,0,0 0,0,0 chr17 72466028 72466029 chr17 72472943 72472944 DEL NA + - [Svaba_SR=77,Svaba_PE=84],[Manta_PE=15,Manta_SR=39],[Lumpy_PE=46,Lumpy_SR=56] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR= 67148388 67148388 52,72466023,72472942 0,0,0 chr17 72474704 72474705 chr17 72485602 72485603 DEL NA + - [Svaba_SR=67,Svaba_PE=89],[Manta_PE=82,Manta_SR=65],[Lumpy_PE=63,Lumpy_SR=43] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR= 67148388 67148388 41,72474708,72485597 0,0,0 chr17 72475233 72475234 chr17 72534012 72534013 DEL NA + - [Svaba_SR=67,Svaba_PE=48],[Manta_PE=57,Manta_SR=66],[Lumpy_PE=33,Lumpy_SR=58] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC00511;DisruptR=LINC00511;ClosestL=;ClosestR= 67148388 67148388 49,72475229,72534011 0,0,0 chr17 72487296 72487297 chrX 116501145 116501146 TRA NA + + [Svaba_SR=119,Svaba_PE=49],[Manta_PE=40,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC00511;DisruptR=;ClosestL=;ClosestR= 67148388 116456787 0,0,0 0,0,0 chr17 72487296 72487297 chrX 76243013 76243014 TRA NA + + [Svaba_SR=77,Svaba_PE=42],[Manta_PE=45,Manta_SR=73],[Lumpy_PE=32,Lumpy_SR=52] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=LINC00511;DisruptR=;ClosestL=;ClosestR=RNU6-867P 67148388 76244723 55,72487298,76243019 0,0,0 chr17 73888139 73888140 chr17 73888671 73888672 DEL NA + - [Svaba_SR=3,Svaba_PE=5] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC137735.1;ClosestR=AC137735.1 67148388 67148388 7,73888123,73888670 0,0,0 chr17 74438082 74438083 chr17 74438599 74438600 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=GPRC5C;DisruptR=GPRC5C;ClosestL=;ClosestR= 67148388 67148388 3,74438070,74438598 0,0,0 chr17 75989687 75989688 chr17 75990306 75990307 DEL NA + - [Svaba_SR=6,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TEN1,TEN1-CDK3;DisruptR=TEN1,TEN1-CDK3;Fusion=TEN1+TEN1-CDK3|TEN1-CDK3+TEN1;ClosestL=ACOX1;ClosestR=CDK3 83247341 83247341 0,0,0 0,0,0 chr17 76069654 76069655 chr17 76070155 76070156 DEL NA + - [Svaba_SR=2,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SRP68;DisruptR=SRP68;ClosestL=ZACN;ClosestR=ZACN 83247341 83247341 0,0,0 0,0,0 chr17 79302582 79302583 chr17 79303089 79303090 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=RBFOX3;DisruptR=RBFOX3;ClosestL=;ClosestR= 83247341 83247341 0,0,0 0,0,0 chr17 81921915 81921916 chr21 14696100 14696101 TRA NA - - [Svaba_SR=102,Svaba_PE=9],[Manta_PE=82,Manta_SR=107] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MAFG;DisruptR=;ClosestL=SIRT7;ClosestR= 83247341 14697922 64,81921917,14696099 0,0,0 chr17 81922131 81922132 chr21 14696028 14696029 TRA NA + - [Svaba_SR=122,Svaba_PE=80],[Manta_PE=19,Manta_SR=114],[Lumpy_PE=77,Lumpy_SR=64] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MAFG;DisruptR=;ClosestL=AC145207.8;ClosestR= 83247341 14697922 37,81922133,14696027 0,0,0 chr17 81922131 81922132 chr21 14696627 14696628 TRA NA + - [Svaba_SR=175,Svaba_PE=0],[Manta_PE=61,Manta_SR=102] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MAFG;DisruptR=;ClosestL=AC145207.8;ClosestR= 83247341 14697922 0,0,0 0,0,0 chr17 81996894 81996895 chr17 81997852 81997853 DEL NA + - [Svaba_SR=16,Svaba_PE=18],[Lumpy_PE=6,Lumpy_SR=7] svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=ASPSCR1;DisruptL=ASPSCR1;DisruptR=ASPSCR1;ClosestL=;ClosestR= 83247341 83247341 11,81996896,81997851 0,0,0 chr17 82545633 82545634 chr17 82546156 82546157 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FOXK2;DisruptR=FOXK2;ClosestL=;ClosestR= 83247341 83247341 0,0,0 0,0,0 chr18 1091199 1091200 chr18 1158740 1158741 DEL NA + - [Svaba_SR=213,Svaba_PE=173],[Manta_PE=296,Manta_SR=211],[Lumpy_PE=229,Lumpy_SR=83] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AP005328.1;DisruptR=AP005328.1;ClosestL=;ClosestR=AP005265.1 1091193 1158564 96,1091196,1158739 0,0,0 chr18 1442130 1442131 chr18 1517728 1517729 DEL NA + - [Manta_PE=22,Manta_SR=22] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=AC008109.1;ClosestL=;ClosestR= 1158564 1158564 27,1442132,1517728 0,0,0 chr18 1792586 1792587 chr18 30132066 30132067 DUP NA - + [Svaba_SR=9,Svaba_PE=11],[Lumpy_PE=9,Lumpy_SR=6] lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=SS18,ZNF521;DisruptL=;DisruptR=;ClosestL=AP005057.1;ClosestR= 1158564 30126251 9,1792587,30132068 0,0,0 chr18 2056157 2056158 chr18 2057225 2057226 INV NA + + [Svaba_SR=17,Svaba_PE=22],[Manta_PE=16,Manta_SR=14],[Lumpy_PE=11,Lumpy_SR=11] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AP005230.1;DisruptR=AP005230.1;ClosestL=;ClosestR= 1158564 1158564 13,2056154,2057227 0,0,0 chr18 5693420 5693421 chr18 10125703 10125704 DUP NA - + [Svaba_SR=62,Svaba_PE=49],[Manta_PE=66,Manta_SR=51],[Lumpy_PE=60,Lumpy_SR=17] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=AP005271.1;ClosestL=;ClosestR= 7909753 10125704 39,5693420,10125705 0,0,0 chr18 8331815 8331816 chr18 8670390 8670391 INV NA - - [Svaba_SR=70,Svaba_PE=67],[Manta_PE=59,Manta_SR=65],[Lumpy_PE=46,Lumpy_SR=51] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PTPRM;DisruptR=;ClosestL=;ClosestR=TOMM20P3 8331768 8331768 48,8331814,8670389 0,0,0 chr18 9792146 9792147 chr18 9856621 9856622 DEL NA + - [Svaba_SR=77,Svaba_PE=98],[Manta_PE=91,Manta_SR=67],[Lumpy_PE=69,Lumpy_SR=47] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=RAB31;DisruptR=RAB31;ClosestL=ZNF415P1;ClosestR=RNA5SP449 10125704 10125704 53,9792147,9856620 0,0,0 chr18 11707492 11707493 chr21 9022992 9022993 TRA NA + - [Manta_PE=129,Manta_SR=159],[Lumpy_PE=96,Lumpy_SR=1] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=GNAL;DisruptR=;ClosestL=;ClosestR=CR392039.2 11707458 5030587 68,11707494,9022991 0,0,0 chr18 12047564 12047565 chr18 12048071 12048072 DEL NA + - [Svaba_SR=8,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AP001542.2;ClosestR=AP001542.2 11707458 11707458 0,0,0 0,0,0 chr18 14810726 14810727 chr18 14817612 14817613 DEL NA + - [Svaba_SR=58,Svaba_PE=64],[Manta_PE=50,Manta_SR=48],[Lumpy_PE=44,Lumpy_SR=2] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ANKRD30B;DisruptR=AP006565.1,ANKRD30B;ClosestL=AP006565.1;ClosestR=MIR3156-2 11707458 11707458 36,14810731,14817611 0,0,0 chr18 23307636 23307637 chr20 31539702 31539703 TRA NA - - [Svaba_SR=325,Svaba_PE=123],[Manta_PE=413,Manta_SR=377],[Lumpy_PE=268,Lumpy_SR=202] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TMEM241;DisruptR=HM13;Fusion=TMEM241-HM13;ClosestL=;ClosestR=AL110115.1 23307596 31539639 104,23307637,31539701 0,0,0 chr18 24278556 24278557 chr18 24279392 24279393 INV NA + + [Svaba_SR=65,Svaba_PE=104],[Manta_PE=91,Manta_SR=51],[Lumpy_PE=81,Lumpy_SR=37] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=OSBPL1A;DisruptR=OSBPL1A;ClosestL=;ClosestR= 24279287 24279288 37,24278557,24279394 0,0,0 chr18 49180837 49180838 chr18 49181965 49181966 INV NA + + [Svaba_SR=65,Svaba_PE=28],[Manta_PE=18,Manta_SR=0],[Lumpy_PE=18,Lumpy_SR=26] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=DYM;DisruptR=DYM;ClosestL=;ClosestR= 49181919 49181920 19,49180843,49181967 0,0,0 chr18 59214242 59214243 chr18 59217204 59217205 DUP NA - + [Svaba_SR=45,Svaba_PE=63],[Manta_PE=59,Manta_SR=36],[Lumpy_PE=48,Lumpy_SR=30] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=GRP;ClosestR=GRP 59280627 59280627 31,59214241,59217206 0,0,0 chr18 59281023 59281024 chr18 60359158 60359159 DEL NA + - [Svaba_SR=41,Svaba_PE=45],[Manta_PE=38,Manta_SR=36],[Lumpy_PE=22,Lumpy_SR=31] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CPLX4;DisruptR=;ClosestL=RAX;ClosestR=MC4R 59280628 60358651 30,59281019,60359157 0,0,0 chr19 5467847 5467848 chr21 21007477 21007478 TRA NA - + [Manta_PE=3,Manta_SR=3] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=NCAM2;ClosestL=ZNRF4;ClosestR= 9163752 21140907 3,5467846,21007479 0,0,0 chr19 8257771 8257772 chr22 24989957 24989958 TRA NA - - [Svaba_SR=18,Svaba_PE=20],[Manta_PE=22,Manta_SR=22],[Lumpy_PE=16,Lumpy_SR=17] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CERS4;DisruptR=KIAA1671;ClosestL=AC022146.2;ClosestR=AL022323.3 9163752 23762694 20,8257772,24989956 0,0,0 chr19 8258007 8258008 chr22 24987321 24987322 TRA NA + - [Svaba_SR=25,Svaba_PE=24],[Manta_PE=15,Manta_SR=22],[Lumpy_PE=12,Lumpy_SR=6] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CERS4;DisruptR=KIAA1671;Fusion=CERS4-KIAA1671;ClosestL=AC022146.2;ClosestR= 9163752 23762694 20,8258009,24987320 0,0,0 chr19 9534368 9534369 chr19 9534878 9534879 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ZNF426;DisruptR=ZNF426;ClosestL=ZNF426-DT;ClosestR=ZNF426-DT 9173674 9173674 0,0,0 0,0,0 chr19 10355196 10355197 chr19 10355702 10355703 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TYK2;DisruptR=TYK2;ClosestL=ICAM3;ClosestR=ICAM3 9173674 9173674 6,10355166,10355701 0,0,0 chr19 10440886 10440887 chr19 10441388 10441389 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PDE4A;DisruptR=PDE4A;ClosestL=;ClosestR= 9173674 9173674 2,10440890,10441417 0,0,0 chr19 12858913 12858914 chr19 12880038 12880039 DEL NA + - [Svaba_SR=204,Svaba_PE=179],[Manta_PE=207,Manta_SR=198],[Lumpy_PE=158,Lumpy_SR=152] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HOOK2,MAST1;DisruptR=DNASE2;Fusion=DNASE2+HOOK2;ClosestL=MIR6794;ClosestR=AC020934.2 12858861 12880013 59,12858913,12880037 0,0,0 chr19 14082739 14082740 chr19 14088555 14088556 INV NA + + [Lumpy_PE=2,Lumpy_SR=3] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=C19orf67;DisruptR=SAMD1;ClosestL=SAMD1;ClosestR=C19orf67 14687523 14687523 4,14082738,14088556 0,0,0 chr19 14687538 14687539 chr19 14928275 14928276 INV NA - - [Svaba_SR=63,Svaba_PE=36],[Manta_PE=50,Manta_SR=230] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ADGRE3;DisruptR=;ClosestL=ZNF333;ClosestR=OR7A15P 14687524 14707748 17,14687533,14928268 0,0,0 chr19 14707786 14707787 chr19 14913582 14913583 DUP NA - + [Svaba_SR=57,Svaba_PE=163],[Manta_PE=357,Manta_SR=261],[Lumpy_PE=356,Lumpy_SR=31] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ZNF333;DisruptR=;ClosestL=ADGRE3;ClosestR=OR7A11P 14707748 14707748 0,0,0 0,0,0 chr19 14738542 14738543 chr19 14739117 14739118 DEL NA + - [Svaba_SR=3,Svaba_PE=5] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ADGRE2;DisruptR=ADGRE2;ClosestL=ZNF333;ClosestR=ZNF333 14707748 14707748 0,0,0 0,0,0 chr19 14832174 14832175 chr19 14832676 14832677 DEL NA + - [Svaba_SR=9,Svaba_PE=5] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=OR7A5,OR7C1;DisruptR=OR7A5,OR7C1;Fusion=OR7C1+OR7A5|OR7A5+OR7C1;ClosestL=OR7A10;ClosestR=OR7A10 14707748 14707748 7,14832162,14832675 0,0,0 chr19 14928300 14928301 chr19 15379943 15379944 INV NA - - [Svaba_SR=28,Svaba_PE=76],[Manta_PE=153,Manta_SR=113],[Lumpy_PE=115,Lumpy_SR=41] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=BRD4;DisruptL=;DisruptR=AC005785.1;ClosestL=OR7A15P;ClosestR=AKAP8L 14707748 15684658 57,14928302,15379942 0,0,0 chr19 15195291 15195292 chr19 15634433 15634434 DUP NA - + [Svaba_SR=5,Svaba_PE=13],[Manta_PE=46,Manta_SR=31],[Lumpy_PE=39,Lumpy_SR=27] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=BRD4;DisruptL=NOTCH3;DisruptR=;ClosestL=MIR6795;ClosestR=CYP4F8 14707748 15684658 26,15195292,15634435 0,0,0 chr19 15287515 15287516 chr19 15288022 15288023 DEL NA + - [Svaba_SR=6,Svaba_PE=5] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=BRD4;DisruptR=BRD4;ClosestL=;ClosestR= 15684658 15684658 3,15287500,15288021 0,0,0 chr19 15329197 15329198 chr19 20490430 20490431 INV NA + + [Manta_PE=142,Manta_SR=112],[Lumpy_PE=123,Lumpy_SR=42] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=TPM4,JAK3,ELL,CRTC1;DisruptL=BRD4;DisruptR=AC008554.1;Fusion=AC008554.1+BRD4;ClosestL=AC005776.1;ClosestR= 15684658 20501955 63,15329201,20490432 0,0,0 chr19 15347396 15347397 chr19 15347965 15347966 DEL NA + - [Svaba_SR=6,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC005776.2;DisruptR=AC005776.2;ClosestL=AKAP8;ClosestR=AKAP8 15684658 15684658 2,15347422,15348003 0,0,0 chr19 15384118 15384119 chr19 15506505 15506506 DEL NA + - [Manta_PE=99,Manta_SR=80],[Lumpy_PE=74,Lumpy_SR=42] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AKAP8L;DisruptR=;ClosestL=AC005785.2;ClosestR=CYP4F22 15684658 15684658 59,15384120,15506505 0,0,0 chr19 15523080 15523081 chr19 15546350 15546351 INV NA - - [Manta_PE=126,Manta_SR=153],[Lumpy_PE=120,Lumpy_SR=2] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CYP4F22;DisruptR=CYP4F22;ClosestL=AC011492.1;ClosestR=CYP4F23P 15684658 15684658 87,15523081,15546349 0,0,0 chr19 15533868 15533869 chr19 15684645 15684646 INV NA + + [Manta_PE=692,Manta_SR=604],[Lumpy_PE=550,Lumpy_SR=507] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CYP4F22;DisruptR=CYP4F12;ClosestL=AC011492.1;ClosestR=CYP4F10P 15684658 15684658 112,15533870,15684647 0,0,0 chr19 15588870 15588871 chr19 15589779 15589780 DEL NA + - [Manta_PE=459,Manta_SR=491] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=CYP4F23P;ClosestR=CYP4F23P 15684658 15684658 113,15588872,15589779 0,0,0 chr19 15632140 15632141 chr19 20137691 20137692 DEL NA + - [Svaba_SR=23,Svaba_PE=54],[Manta_PE=136,Manta_SR=118],[Lumpy_PE=103,Lumpy_SR=8] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=TPM4,JAK3,ELL,CRTC1;DisruptL=;DisruptR=AC011447.2,AC011447.3;ClosestL=CYP4F8;ClosestR=BNIP3P15 15684658 20137238 87,15632139,20137686 0,0,0 chr19 17316666 17316667 chr19 17362636 17362637 DEL NA + - [Svaba_SR=23,Svaba_PE=23],[Manta_PE=23,Manta_SR=19],[Lumpy_PE=19,Lumpy_SR=7] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=DDA1;DisruptR=AC010463.2,PLVAP;Fusion=DDA1+AC010463.2;ClosestL=ABHD8;ClosestR=GTPBP3 17134374 17134374 16,17316668,17362634 0,0,0 chr19 20300586 20300587 chr19 20303756 20303757 DEL NA + - [Svaba_SR=91,Svaba_PE=77],[Manta_PE=87,Manta_SR=72],[Lumpy_PE=60,Lumpy_SR=36] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC078899.4,AC011447.3;DisruptR=AC078899.4,AC011447.3;ClosestL=;ClosestR= 20137238 20137238 2,20300589,20303759 0,0,0 chr19 20441327 20441328 chr19 20443259 20443260 DEL NA + - [Svaba_SR=136,Svaba_PE=165],[Manta_PE=246,Manta_SR=218],[Lumpy_PE=180,Lumpy_SR=45] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC008554.1;DisruptR=BNIP3P23,AC008554.1;ClosestL=BNIP3P23;ClosestR=ZNF826P 20501955 20501955 96,20441329,20443254 0,0,0 chr19 20497266 20497267 chr19 20498447 20498448 INV NA + + [Svaba_SR=120,Svaba_PE=133],[Manta_PE=145,Manta_SR=107] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=AC008554.1;DisruptR=AC008554.1;ClosestL=;ClosestR= 20501955 20501955 66,20497268,20498449 0,0,0 chr19 20497437 20497438 chr19 20501960 20501961 DUP NA - + [Svaba_SR=120,Svaba_PE=148],[Manta_PE=142,Manta_SR=110],[Lumpy_PE=127,Lumpy_SR=37] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC008554.1;DisruptR=AC008554.1;ClosestL=;ClosestR= 20501955 20501956 71,20497438,20501962 0,0,0 chr19 20498993 20498994 chr19 20507532 20507533 DUP NA - + [Svaba_SR=125,Svaba_PE=129],[Manta_PE=120,Manta_SR=94],[Lumpy_PE=105,Lumpy_SR=66] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AC008554.1;DisruptR=AC008554.1;ClosestL=;ClosestR= 20501955 20501956 63,20498993,20507534 0,0,0 chr19 20506933 20506934 chr19 24352249 24352250 DUP NA - + [Svaba_SR=59,Svaba_PE=100],[Manta_PE=114,Manta_SR=96],[Lumpy_PE=88,Lumpy_SR=16] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=ZNF429;DisruptL=AC008554.1;DisruptR=;ClosestL=;ClosestR= 20501956 24018596 43,20506933,24352272 0,0,0 chr19 23544106 23544107 chr19 23692968 23692969 INV NA - - [Svaba_SR=0,Svaba_PE=39],[Manta_PE=28,Manta_SR=35] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ZNF675;DisruptR=;ClosestL=;ClosestR=ZNF675 23544292 23544293 0,0,0 0,0,0 chr19 23973526 23973527 chr19 24181110 24181111 DEL NA + - [Manta_PE=4,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;ClosestL=AC011503.1;ClosestR=AC073534.1 24018595 24018596 0,0,0 0,0,0 chr19 24348141 24348142 chr19 24353031 24353032 INV NA - - [Svaba_SR=111,Svaba_PE=86],[Manta_PE=122,Manta_SR=97],[Lumpy_PE=78,Lumpy_SR=70] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 24018596 24018596 63,24348141,24353030 0,0,0 chr19 24373673 24373674 chr19 24375338 24375339 DEL NA + - [Svaba_SR=89,Svaba_PE=122],[Manta_PE=124,Manta_SR=87] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 24018596 24018596 57,24373656,24375337 0,0,0 chr19 45005891 45005892 chr19 45006472 45006473 DEL NA + - [Svaba_SR=1,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;COSMIC;DisruptL=RELB;DisruptR=RELB;ClosestL=CLPTM1;ClosestR=CLPTM1 58607515 58607515 2,45005873,45006471 0,0,0 chr19 53770333 53770334 chr19 53770968 53770969 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=HMGN1P32;ClosestR=SEPT7P8 58607515 58607515 2,53770401,53770769 4,53770401,53770769 chr20 3792004 3792005 chr20 3792536 3792537 DEL NA + - [Svaba_SR=6,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CDC25B;DisruptR=CDC25B;ClosestL=CENPB;ClosestR=CENPB 67260 67260 2,3792034,3792586 0,0,0 chr20 5742529 5742530 chr20 5743048 5743049 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=SHLD1;ClosestR=SHLD1 8764419 8764419 2,5742532,5743077 0,0,0 chr20 5742912 5742913 chr20 5743469 5743470 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=SHLD1;ClosestR=SHLD1 8764419 8764419 2,5742902,5743468 0,0,0 chr20 14979687 14979688 chr20 15067580 15067581 DEL NA + - [Svaba_SR=28,Svaba_PE=0],[Manta_PE=26,Manta_SR=14] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MACROD2;DisruptR=MACROD2;ClosestL=;ClosestR= 8764420 8764420 0,0,0 0,0,0 chr20 14979687 14979688 chr20 15078264 15078265 DEL NA + - [Svaba_SR=20,Svaba_PE=2],[Manta_PE=2,Manta_SR=19] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MACROD2;DisruptR=MACROD2;ClosestL=;ClosestR= 8764420 8764420 13,14979687,15078263 0,0,0 chr20 15067580 15067581 chr20 15078347 15078348 DUP NA - + [Svaba_SR=15,Svaba_PE=6],[Manta_PE=6,Manta_SR=13] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MACROD2;DisruptR=MACROD2;ClosestL=;ClosestR= 8764420 8764420 9,15067585,15078349 0,0,0 chr20 17713043 17713044 chr20 17713605 17713606 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=BANF2;DisruptR=BANF2;ClosestL=;ClosestR= 22252838 22252838 4,17713020,17713604 0,0,0 chr20 18728214 18728215 chr20 18728770 18728771 DEL NA + - [Svaba_SR=3,Svaba_PE=5] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL121900.2,DTD1;DisruptR=AL121900.2,DTD1;Fusion=AL121900.2+DTD1|DTD1+AL121900.2;ClosestL=;ClosestR= 22252838 22252838 2,18728205,18728769 0,0,0 chr20 18763090 18763091 chr20 18763944 18763945 INV NA - - [Svaba_SR=18,Svaba_PE=13],[Manta_PE=12,Manta_SR=17],[Lumpy_PE=9,Lumpy_SR=11] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=DTD1;DisruptR=DTD1;ClosestL=AL121900.2;ClosestR=EEF1A1P34 22252838 22252838 14,18763090,18763943 0,0,0 chr20 21466706 21466707 chr20 21486367 21486368 INV NA + + [Lumpy_PE=2,Lumpy_SR=2] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR=AL133325.1 22252838 22252838 2,21466707,21486368 0,0,0 chr20 22251587 22251588 chr20 22253038 22253039 INV NA - - [Svaba_SR=0,Svaba_PE=25],[Manta_PE=25,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=LINC01427;ClosestR=LINC01427 22252838 22252839 0,0,0 0,0,0 chr20 26330213 26330214 chr20 26331691 26331692 DEL NA + - [Svaba_SR=34,Svaba_PE=78],[Manta_PE=81,Manta_SR=51] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 28506070 28506070 24,26330156,26331690 0,0,0 chr20 31360012 31360013 chr20 31377616 31377617 DUP NA - + [Lumpy_PE=3,Lumpy_SR=2] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=DEFB119;ClosestL=DEFB117;ClosestR=RF00561 31245066 31245066 2,31360011,31377617 0,0,0 chr20 31814309 31814310 chr20 31814947 31814948 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=MYLK2;ClosestR=MYLK2 31539639 31539639 2,31814276,31814923 0,0,0 chr20 31896097 31896098 chr20 31896638 31896639 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TTLL9;DisruptR=TTLL9;ClosestL=RNU1-94P;ClosestR=RNU1-94P 31539639 31539639 2,31896084,31896637 0,0,0 chr20 32560367 32560368 chr20 32560897 32560898 DUP NA - + [Svaba_SR=0,Svaba_PE=10] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=NOL4L;DisruptR=NOL4L;ClosestL=AL133343.2;ClosestR=AL133343.2 31539639 31539639 0,0,0 0,0,0 chr20 32674161 32674162 chr20 32674734 32674735 DEL NA + - [Svaba_SR=3,Svaba_PE=5] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=FO393400.1;DisruptR=FO393400.1;ClosestL=C20orf203;ClosestR=C20orf203 31539639 31539639 2,32674144,32674733 0,0,0 chr20 33961411 33961412 chr20 33961921 33961922 DEL NA + - [Svaba_SR=8,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=PIGPP3;ClosestR=PIGPP3 34228084 34228084 0,0,0 2,33961371,33961898 chr20 36914523 36914524 chr20 36933537 36933538 INV NA + + [Svaba_SR=90,Svaba_PE=96],[Manta_PE=98,Manta_SR=81],[Lumpy_PE=66,Lumpy_SR=70] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SAMHD1;DisruptR=SAMHD1;ClosestL=;ClosestR= 36912931 36912931 54,36914523,36933539 0,0,0 chr20 47103302 47103303 chr20 47104389 47104390 DEL NA + - [Svaba_SR=83,Svaba_PE=75],[Manta_PE=46,Manta_SR=63],[Lumpy_PE=49,Lumpy_SR=1] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=EYA2;DisruptR=EYA2;ClosestL=;ClosestR= 39349451 39349451 0,0,0 0,0,0 chr20 47104388 47104389 chr20 47225242 47225243 DUP NA - + [Svaba_SR=0,Svaba_PE=16],[Lumpy_PE=9,Lumpy_SR=12] svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=EYA2;DisruptR=ZMYND8;ClosestL=;ClosestR= 39349451 39349451 7,47104393,47225244 0,0,0 chr20 47225236 47225237 chr20 47268862 47268863 DEL NA + - [Svaba_SR=0,Svaba_PE=42],[Manta_PE=31,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ZMYND8;DisruptR=ZMYND8;ClosestL=;ClosestR= 39349451 39349451 0,0,0 0,0,0 chr20 47895647 47895648 chr20 48125360 48125361 INV NA + + [Lumpy_PE=3,Lumpy_SR=1] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;ClosestL=RNU7-92P;ClosestR= 39349451 39349451 2,47895686,48125256 0,0,0 chr20 48179658 48179659 chr20 48180191 48180192 DEL NA + - [Manta_PE=50,Manta_SR=72],[Lumpy_PE=36,Lumpy_SR=61] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 39349451 39349451 60,48179660,48180191 0,0,0 chr21 10561880 10561881 chr21 10570015 10570016 DUP NA - + [Svaba_SR=24,Svaba_PE=14] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TPTE,AF254983.1;DisruptR=TPTE,AF254983.1;Fusion=AF254983.1+TPTE|TPTE+AF254983.1;ClosestL=CYCSP41;ClosestR=CYCSP41 13507200 13507200 0,0,0 0,0,0 chr21 10561920 10561921 chr21 20715590 20715591 INV NA + + [Svaba_SR=25,Svaba_PE=8] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;DisruptL=TPTE,AF254983.1;DisruptR=;ClosestL=CYCSP41;ClosestR= 13507200 21140907 5,10561922,20715592 0,0,0 chr21 10570015 10570016 chr21 20715590 20715591 INV NA + + [Svaba_SR=28,Svaba_PE=21],[Manta_PE=20,Manta_SR=0] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;DisruptL=TPTE,AF254983.1;DisruptR=;ClosestL=CYCSP41;ClosestR= 13507200 21140907 0,0,0 0,0,0 chr21 13283045 13283046 chr21 13506275 13506276 DEL NA + - [Svaba_SR=178,Svaba_PE=213],[Manta_PE=164,Manta_SR=188] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;ClosestL=;ClosestR=GTF2IP2 13507200 13507200 90,13283046,13506274 0,0,0 chr21 14331478 14331479 chr22 28499903 28499904 TRA NA - + [Svaba_SR=0,Svaba_PE=37] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=ABCC13;DisruptR=TTC28;ClosestL=;ClosestR= 14332448 29285918 0,0,0 0,0,0 chr21 14696103 14696104 chr21 14696626 14696627 DEL NA + - [Manta_PE=16,Manta_SR=106] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=;ClosestR= 14697922 14697922 29,14696105,14696625 0,0,0 chr21 15873590 15873591 chr21 16679496 16679497 INV NA + + [Svaba_SR=127,Svaba_PE=164],[Manta_PE=402,Manta_SR=315] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=USP25;DisruptR=;ClosestL=;ClosestR= 15873585 17474345 4,15873593,16679497 0,0,0 chr21 16672953 16672954 chr21 17986177 17986178 DUP NA - + [Svaba_SR=150,Svaba_PE=172],[Manta_PE=336,Manta_SR=299],[Lumpy_PE=277,Lumpy_SR=251] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=CHODL;ClosestL=;ClosestR= 15873585 17986205 2,16672951,17986172 0,0,0 chr21 17474427 17474428 chr21 41078325 41078326 DUP NA - + [Svaba_SR=362,Svaba_PE=237],[Manta_PE=470,Manta_SR=371] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=OLIG2,RUNX1,ERG;DisruptL=;DisruptR=;ClosestL=;ClosestR= 17474346 41078299 110,17474426,41078327 0,0,0 chr21 17579548 17579549 chr21 17580074 17580075 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CXADR;DisruptR=CXADR;ClosestL=RF00019;ClosestR=RF00019 17474346 17474346 0,0,0 0,0,0 chr21 17592650 17592651 chr21 17621842 17621843 DUP NA - + [Svaba_SR=81,Svaba_PE=86],[Manta_PE=73,Manta_SR=70],[Lumpy_PE=65,Lumpy_SR=47] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CXADR;DisruptR=BTG3-AS1;Fusion=BTG3-AS1+CXADR;ClosestL=BTG3;ClosestR=BTG3 17474346 17474346 53,17592651,17621844 0,0,0 chr21 18583950 18583951 chr21 18584488 18584489 INV NA - - [Svaba_SR=20,Svaba_PE=18],[Manta_PE=14,Manta_SR=19],[Lumpy_PE=12,Lumpy_SR=11] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MIR548XHG;DisruptR=MIR548XHG;ClosestL=;ClosestR= 18481760 18481760 10,18583949,18584479 0,0,0 chr21 31947263 31947264 chr21 45927241 45927242 INV NA - - [Manta_PE=161,Manta_SR=0],[Lumpy_PE=155,Lumpy_SR=1] manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=OLIG2,TMPRSS2,U2AF1,RUNX1,ERG;DisruptL=HUNK;DisruptR=PCBP3;ClosestL=;ClosestR=AJ239328.1 31947284 46107841 5,31947365,45927257 0,0,0 chr21 34819613 34819614 chr21 34850895 34850896 DEL NA + - [Svaba_SR=111,Svaba_PE=122],[Manta_PE=113,Manta_SR=96],[Lumpy_PE=79,Lumpy_SR=77] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=RUNX1;DisruptL=RUNX1;DisruptR=RUNX1;ClosestL=;ClosestR= 34819639 34847755 66,34819611,34850894 0,0,0 chr21 34819613 34819614 chr21 34851199 34851200 DEL NA + - [Svaba_SR=0,Svaba_PE=10] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=RUNX1;DisruptL=RUNX1;DisruptR=RUNX1;ClosestL=;ClosestR= 34819639 34847755 0,0,0 0,0,0 chr21 34819749 34819750 chr21 34851598 34851599 DEL NA + - [Manta_PE=9,Manta_SR=0] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=RUNX1;DisruptL=RUNX1;DisruptR=RUNX1;ClosestL=;ClosestR= 34819640 34847755 0,0,0 0,0,0 chr21 40764330 40764331 chr21 44064618 44064619 INV NA - - [Svaba_SR=286,Svaba_PE=191],[Manta_PE=436,Manta_SR=302],[Lumpy_PE=330,Lumpy_SR=153] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=TMPRSS2,U2AF1;DisruptL=DSCAM;DisruptR=TRAPPC10;Fusion=DSCAM+TRAPPC10;ClosestL=;ClosestR=H2AFZP1 40764260 44064550 2,40764313,44064621 0,0,0 chr21 41822940 41822941 chr21 42103805 42103806 DUP NA - + [Svaba_SR=302,Svaba_PE=134],[Manta_PE=364,Manta_SR=320] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PRDM15;DisruptR=UMODL1-AS1,UMODL1;Fusion=PRDM15+UMODL1-AS1;ClosestL=;ClosestR= 41825925 42103808 104,41822941,42103807 0,0,0 chr21 41823975 41823976 chr21 46107855 46107856 INV NA + + [Svaba_SR=160,Svaba_PE=169],[Manta_PE=398,Manta_SR=311],[Lumpy_PE=321,Lumpy_SR=174] svaba,lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=U2AF1;DisruptL=PRDM15;DisruptR=COL6A2;Fusion=COL6A2+PRDM15;ClosestL=;ClosestR=AP001471.1 41825925 46107842 111,41823975,46107857 0,0,0 chr21 41825929 41825930 chr21 45927312 45927313 DUP NA - + [Svaba_SR=56,Svaba_PE=0],[Manta_PE=451,Manta_SR=171],[Lumpy_PE=449,Lumpy_SR=102] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=U2AF1;DisruptL=PRDM15;DisruptR=PCBP3;ClosestL=;ClosestR=AJ239328.1 41825926 46107841 73,41825930,45927314 0,0,0 chr21 41831216 41831217 chr21 41833962 41833963 DEL NA + - [Svaba_SR=106,Svaba_PE=168],[Manta_PE=379,Manta_SR=332] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PRDM15;DisruptR=PRDM15;ClosestL=;ClosestR= 41825926 41825926 105,41831218,41833961 0,0,0 chr21 42948646 42948647 chr21 42950135 42950136 DEL NA + - [Svaba_SR=118,Svaba_PE=113],[Manta_PE=192,Manta_SR=156],[Lumpy_PE=131,Lumpy_SR=74] lumpy,manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=MIR5692B;ClosestR=MIR5692B 42103809 42103809 88,42948644,42950134 0,0,0 chr22 15531539 15531540 chr22 15533440 15533441 INV NA - - [Svaba_SR=11,Svaba_PE=13] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=OR11H1;ClosestR=OR11H1 12694064 12694064 9,15531543,15533439 0,0,0 chr22 16812441 16812442 chr22 27132894 27132895 INV NA - - [Svaba_SR=21,Svaba_PE=22],[Manta_PE=20,Manta_SR=19],[Lumpy_PE=13,Lumpy_SR=14] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;gap;Cancer_census=SEPT5,DGCR8,LZTR1,MAPK1,SMARCB1,CLTCL1,BCR;DisruptL=XKR3;DisruptR=;ClosestL=HSFY1P1;ClosestR=AL008638.1 12694064 29285918 15,16812445,27132893 0,0,0 chr22 17065521 17065522 chr22 17066042 17066043 DEL NA + - [Svaba_SR=6,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AC006946.2;ClosestR=AC006946.2 12694064 12694064 0,0,0 2,17065505,17066041 chr22 17097645 17097646 chr22 17098740 17098741 INV NA + + [Svaba_SR=22,Svaba_PE=28],[Manta_PE=28,Manta_SR=16] manta,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=IL17RA;DisruptR=IL17RA;ClosestL=AC006946.1;ClosestR=AC006946.1 12694064 12694064 0,0,0 0,0,0 chr22 17097645 17097646 chr22 17134394 17134395 INV NA + + [Svaba_SR=13,Svaba_PE=3] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=IL17RA;DisruptR=;ClosestL=AC006946.1;ClosestR=LINC01664 12694064 12694064 5,17097644,17134396 0,0,0 chr22 17098738 17098739 chr22 17134337 17134338 DEL NA + - [Manta_PE=0,Manta_SR=10] manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=IL17RA;DisruptR=;ClosestL=AC006946.1;ClosestR=LINC01664 12694064 12694064 7,17098740,17134337 0,0,0 chr22 18986702 18986703 chr22 18987275 18987276 DEL NA + - [Svaba_SR=2,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=DGCR5;DisruptR=DGCR5;ClosestL=AC007326.3;ClosestR=AC007326.3 23762693 23762693 3,18986691,18987274 0,0,0 chr22 19206724 19206725 chr22 19207270 19207271 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=CLTCL1;DisruptL=CLTCL1;DisruptR=CLTCL1;ClosestL=;ClosestR= 23762693 23762693 6,19206691,19207269 2,19206691,19207269 chr22 19956264 19956265 chr22 19956817 19956818 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=COMT;DisruptR=COMT;ClosestL=MIR4761;ClosestR=MIR4761 23762693 23762693 2,19956235,19956802 0,0,0 chr22 20476966 20476967 chr22 20591962 20591963 DEL NA + - [Svaba_SR=71,Svaba_PE=78],[Manta_PE=70,Manta_SR=65],[Lumpy_PE=50,Lumpy_SR=50] manta,svaba,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=KLHL22;DisruptR=CCDC74BP1;Fusion=CCDC74BP1+KLHL22;ClosestL=RNY1P9;ClosestR=MED15 23762693 23762693 54,20476962,20591961 0,0,0 chr22 23936453 23936454 chr22 23946301 23946302 INV NA - - [Svaba_SR=46,Svaba_PE=51] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=;ClosestL=AP000350.1;ClosestR=AP000350.1 23762694 23762694 36,23936454,23946300 0,0,0 chr22 24890234 24890235 chr22 24890796 24890797 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SGSM1;DisruptR=SGSM1;ClosestL=RF00275;ClosestR=RF00275 23762694 23762694 2,24890211,24890795 0,0,0 chr22 24987318 24987319 chr22 24989955 24989956 INV NA - - [Svaba_SR=0,Svaba_PE=13] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=KIAA1671;DisruptR=KIAA1671;ClosestL=;ClosestR=AL022323.3 23762694 23762694 0,0,0 0,0,0 chr22 25536845 25536846 chr22 25555999 25556000 DEL NA + - [Svaba_SR=15,Svaba_PE=14],[Manta_PE=11,Manta_SR=16],[Lumpy_PE=2,Lumpy_SR=14] manta,lumpy,svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=CRYBB2P1;ClosestR=AL022329.1 23762694 23762694 11,25536846,25555998 0,0,0 chr22 25537440 25537441 chr22 25554129 25554130 DUP NA - + [Lumpy_PE=15,Lumpy_SR=5] lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=CRYBB2P1;ClosestR=AL022329.1 23762694 23762694 0,0,0 0,0,0 chr22 25537886 25537887 chr22 25554448 25554449 DUP NA - + [Svaba_SR=11,Svaba_PE=17],[Manta_PE=15,Manta_SR=0] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=CRYBB2P1;ClosestR=AL022329.1 23762694 23762694 10,25537888,25554450 0,0,0 chr22 25541193 25541194 chr22 25553829 25553830 INV NA - - [Manta_PE=9,Manta_SR=11],[Lumpy_PE=3,Lumpy_SR=7] lumpy,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AL022329.1;ClosestR=AL022329.1 23762694 23762694 6,25541194,25553828 0,0,0 chr22 25545140 25545141 chr22 25578592 25578593 DUP NA - + [Svaba_SR=10,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=GRK3;ClosestL=AL022329.1;ClosestR=AL022329.2 23762694 23762694 0,0,0 0,0,0 chr22 25553829 25553830 chr22 25554642 25554643 INV NA - - [Svaba_SR=16,Svaba_PE=3] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AL022329.1;ClosestR=AL022329.1 23762694 23762694 0,0,0 0,0,0 chr22 25555040 25555041 chr22 25556152 25556153 INV NA + + [Svaba_SR=10,Svaba_PE=4],[Manta_PE=6,Manta_SR=9] svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=AL022329.1;ClosestR=AL022329.1 23762694 23762694 9,25555041,25556154 0,0,0 chr22 25555780 25555781 chr22 25578243 25578244 DEL NA + - [Svaba_SR=25,Svaba_PE=4] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=;DisruptR=GRK3;ClosestL=AL022329.1;ClosestR=AL022329.2 23762694 23762694 0,0,0 0,0,0 chr22 29187776 29187777 chr22 29344401 29344402 DUP NA - + [Svaba_SR=0,Svaba_PE=132],[Manta_PE=130,Manta_SR=111],[Lumpy_PE=116,Lumpy_SR=40] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=EWSR1;DisruptL=;DisruptR=AP1B1;ClosestL=RNU6-1219P;ClosestR=MIR3653 29285918 29285919 0,0,0 0,0,0 chr22 29285161 29285162 chr22 29286804 29286805 INV NA + + [Svaba_SR=27,Svaba_PE=60],[Manta_PE=86,Manta_SR=76],[Lumpy_PE=67,Lumpy_SR=37] svaba,manta,lumpy HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=EWSR1;DisruptL=EWSR1;DisruptR=EWSR1;ClosestL=RHBDD3;ClosestR=RHBDD3 29285918 29285919 36,29285160,29286806 0,0,0 chr22 29599111 29599112 chrX 126291762 126291763 TRA NA - + [Svaba_SR=0,Svaba_PE=15] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;ClosestL=NF2;ClosestR= 29285919 118882104 0,0,0 0,0,0 chr22 30034418 30034419 chr22 30034931 30034932 DEL NA + - [Svaba_SR=5,Svaba_PE=5] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=HORMAD2-AS1;DisruptR=HORMAD2-AS1;ClosestL=MTMR3;ClosestR=MTMR3 29285919 29285919 3,30034392,30034941 0,0,0 chr22 36450382 36450383 chr22 36450896 36450897 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=AL022313.2;DisruptR=AL022313.2;ClosestL=RF00019;ClosestR=RF00019 29285919 29285919 3,36450361,36450895 0,0,0 chr22 40078433 40078434 chr22 40078957 40078958 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TNRC6B;DisruptR=TNRC6B;ClosestL=;ClosestR= 46073918 46073918 5,40078408,40078956 0,0,0 chr22 40812764 40812765 chr22 40813265 40813266 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=SLC25A17;DisruptR=SLC25A17;ClosestL=MIR4766;ClosestR=MIR4766 46073918 46073918 2,40812736,40813264 0,0,0 chr22 41110691 41110692 chr22 41111241 41111242 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=EP300;DisruptL=EP300;DisruptR=EP300;ClosestL=MIR1281;ClosestR=MIR1281 46073918 46073918 0,0,0 0,0,0 chr22 41124008 41124009 chr22 41124545 41124546 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;Cancer_census=EP300;DisruptL=EP300;DisruptR=EP300;ClosestL=;ClosestR= 46073918 46073918 3,41123997,41124544 0,0,0 chr22 42011526 42011527 chr22 42012029 42012030 DEL NA + - [Svaba_SR=5,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=WBP2NL;DisruptR=WBP2NL;ClosestL=SLC25A5P1;ClosestR=SLC25A5P1 46073918 46073918 3,42011506,42012028 0,0,0 chr22 43065921 43065922 chr22 43066469 43066470 DEL NA + - [Svaba_SR=4,Svaba_PE=0] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=TTLL1;DisruptR=TTLL1;ClosestL=AL022476.1;ClosestR=AL022476.1 46073918 46073918 2,43065907,43066468 0,0,0 chr22 46073953 46073954 chr22 46234169 46234170 DUP NA - + [Svaba_SR=86,Svaba_PE=174],[Manta_PE=255,Manta_SR=207],[Lumpy_PE=215,Lumpy_SR=160] lumpy,svaba,manta HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=MIRLET7BHG;DisruptR=PPARA;Fusion=PPARA+MIRLET7BHG;ClosestL=AL121672.2;ClosestR=CDPF1 46073919 46234134 100,46073952,46234171 0,0,0 chr22 46699842 46699843 chr22 46700468 46700469 DEL NA + - [Svaba_SR=1,Svaba_PE=5] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=CERK;DisruptR=CERK;ClosestL=;ClosestR= 46234134 46234134 3,46700059,46700361 8,46699991,46700293 chr22 50377427 50377428 chr22 50377969 50377970 DEL NA + - [Svaba_SR=2,Svaba_PE=5] svaba HCC-1143-NovaSeq--HCC-1143BL-NovaSeq known=;DisruptL=PPP6R2;DisruptR=PPP6R2;ClosestL=;ClosestR= 50808368 50808368 0,0,0 0,0,0