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1 ##fileformat=VCFv4.1
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2 ##fileDate=2014-05-15 12:08:09
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3 ##source=SoftSearch.pl
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4 ##reference=chr1.small.fa
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5 ##Usage= SoftSearch.pl -l 5 -q 20 -r 5 -d 300 -m 5 -u 0 -s 6 -b Small_test.bam -f chr1.small.fa -o s_Test.vcf
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6 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
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7 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
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8 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
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9 ##INFO=<ID=ISIZE,Number=.,Type=String,Description="Size of the SV">
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10 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
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11 ##FORMAT=<ID=lSC,Number=1,Type=Integer,Description="Length of the longest soft clips supporting the BND">
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12 ##FORMAT=<ID=nSC,Number=1,Type=Integer,Description="Number of supporting soft-clips">
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13 ##FORMAT=<ID=uRP,Number=1,Type=Integer,Description="Number of unmated read pairs nearby Soft-Clips">
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14 ##FORMAT=<ID=levD_local,Number=1,Type=Float,Description="Levenstein distance between soft-clipped bases and the area around the original soft-clipped site">
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15 ##FORMAT=<ID=levD_distl,Number=1,Type=Float,Description="Levenstein distance between the soft-clipped bases and mate location">
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16 ##FORMAT=<ID=CTX,Number=1,Type=Integer,Description="Number of chromosomal translocations">
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17 ##FORMAT=<ID=DEL,Number=1,Type=Integer,Description="Number of reads supporting Large Deletions">
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18 ##FORMAT=<ID=INS,Number=1,Type=Integer,Description="Number of reads supporting Large insertions">
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19 ##FORMAT=<ID=NOV_INS,Number=1,Type=Integer,Description="Number of reads supporting novel sequence insertion">
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20 ##FORMAT=<ID=TDUP,Number=1,Type=Integer,Description="Number of reads supporting a tandem duplication">
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21 ##FORMAT=<ID=INV,Number=1,Type=Integer,Description="Number of reads supporting inversions">
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22 ##FORMAT=<ID=sDEL,Number=1,Type=Integer,Description="Number of reads supporting novel sequence insertion">
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23 ##INFO=<ID=NO_MATE_SC,Number=1,Type=Flag,Description="When there is no softclipping of the mate read location, an appromiate position is used">
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24 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Dummy value for maintaining VCF-Spec">
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25 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_Test
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26 chr1 524004 BND_yyivkoxn T T[chr1:525966[ 2.56 PASS SVTYPE=BND;EVENT=DEL;END=525966;ISIZE=1962;MATEID=BND_xxqonpqo GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:2:16:0:0:0:0:0:0:0:0
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27 chr1 525966 BND_xxqonpqo G ]chr1:524004]G 2.56 PASS SVTYPE=BND;EVENT=DEL;END=524004;ISIZE=1962;MATEID=BND_yyivkoxn GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:2:16:0:0:0:0:31:7:0:0.39
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28 chr1 773527 BND_fhfdoayv T A[chr1:773527[ 1000.00 PASS SVTYPE=BND;EVENT=INV;END=781565;ISIZE=8038;MATEID=BND_wgzrxsyj GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:1:0:0:67:6:0:0:0:0:0
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29 chr1 773527 BND_ogxdwnot T T[chr1:773527[ 1000.00 PASS SVTYPE=BND;EVENT=INV;END=781624;ISIZE=8097;MATEID=BND_hrknrygd GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:1:0:0:60:4:0:0:0:0:0
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30 chr1 773904 BND_qtchcfsd G ]chr1:773904]G 2.43 PASS SVTYPE=BND;EVENT=INV;END=781564;ISIZE=7660;MATEID=BND_ilxfwbvc GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:19:0:0:76:6:0:32:11:6:0.41
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31 chr1 773907 BND_pudmiiuj C ]chr1:773907]T 4.74 PASS SVTYPE=BND;EVENT=INV;END=781107;ISIZE=7200;MATEID=BND_wvjtpogz GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:19:0:0:100:12:0:33:7:12:0.21
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32 chr1 773928 BND_tonkbaqx C A[chr1:773928[ 16.39 PASS SVTYPE=BND;EVENT=INV;END=781562;ISIZE=7634;MATEID=BND_nyshzixi GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:3:0:0:46:5:0:0:0:0:0
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33 chr1 773963 BND_znjagoaw T ]chr1:773963]G 2.77 PASS SVTYPE=BND;EVENT=INV;END=781564;ISIZE=7601;MATEID=BND_bpepyyyk GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:19:0:0:76:6:0:36:10:6:0.36
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34 chr1 773967 BND_npgkjvzf C ]chr1:773967]T 1000.00 PASS SVTYPE=BND;EVENT=INV;END=781107;ISIZE=7140;MATEID=BND_vxbakedf GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:18:0:0:95:8:0:18:5:8:0.00
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35 chr1 781107 BND_vxbakedf T C[chr1:781107[ 1000.00 PASS SVTYPE=BND;EVENT=INV;END=773967;ISIZE=7140;MATEID=BND_npgkjvzf GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:18:0:0:95:8:0:0:0:0:0
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36 chr1 781107 BND_wvjtpogz T C[chr1:781107[ 4.74 PASS SVTYPE=BND;EVENT=INV;END=773907;ISIZE=7200;MATEID=BND_pudmiiuj GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:19:0:0:100:12:0:0:0:0:0
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37 chr1 781562 BND_nyshzixi A ]chr1:781562]C 16.39 PASS SVTYPE=BND;EVENT=INV;END=773928;ISIZE=7634;MATEID=BND_tonkbaqx GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:3:0:0:46:5:0:17:5:5:0.06
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38 chr1 781564 BND_bpepyyyk G T[chr1:781564[ 2.77 PASS SVTYPE=BND;EVENT=INV;END=773963;ISIZE=7601;MATEID=BND_znjagoaw GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:19:0:0:76:6:0:0:0:0:0
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39 chr1 781564 BND_ilxfwbvc G G[chr1:781564[ 2.43 PASS SVTYPE=BND;EVENT=INV;END=773904;ISIZE=7660;MATEID=BND_qtchcfsd GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:19:0:0:76:6:0:0:0:0:0
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40 chr1 781565 BND_wgzrxsyj A ]chr1:781565]T 1000.00 PASS SVTYPE=BND;EVENT=INV;END=773527;ISIZE=8038;MATEID=BND_fhfdoayv GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:1:0:0:67:6:0:34:12:6:0.00
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41 chr1 781624 BND_hrknrygd T ]chr1:781624]T 1000.00 PASS SVTYPE=BND;EVENT=INV;END=773527;ISIZE=8097;MATEID=BND_ogxdwnot GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:1:0:0:60:4:0:24:12:4:0.00
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42 chr1 813168 BND_qsyqdonc G G[chr1:813168[ 1000.00 PASS SVTYPE=BND;EVENT=INV;END=816792;ISIZE=3624;MATEID=BND_gicbelss GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:1:0:0:49:5:0:0:0:0:0
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43 chr1 813648 BND_jqgpjekt G G[chr1:813648[ 2.49 PASS SVTYPE=BND;EVENT=INV;END=816790;ISIZE=3142;MATEID=BND_mkjhthlc GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:56:7:0:0:0:0:0
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44 chr1 813648 BND_mqakrsii G ]chr1:813648]T 1000.00 PASS SVTYPE=BND;EVENT=INV;END=816343;ISIZE=2695;MATEID=BND_flkhmdiv GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:44:3:0:18:10:3:0.00
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45 chr1 816343 BND_flkhmdiv T G[chr1:816343[ 1000.00 PASS SVTYPE=BND;EVENT=INV;END=813648;ISIZE=2695;MATEID=BND_mqakrsii GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:44:3:0:0:0:0:0
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46 chr1 816790 BND_mkjhthlc G ]chr1:816790]G 2.49 PASS SVTYPE=BND;EVENT=INV;END=813648;ISIZE=3142;MATEID=BND_jqgpjekt GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:56:7:0:40:10:7:0.40
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47 chr1 816792 BND_gicbelss G ]chr1:816792]G 1000.00 PASS SVTYPE=BND;EVENT=INV;END=813168;ISIZE=3624;MATEID=BND_qsyqdonc GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:1:0:0:49:5:0:33:16:5:0.00
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48 chr1 854784 BND_pkqgmhxz G G[chr1:863640[ 2.93 PASS SVTYPE=BND;EVENT=DEL;END=863640;ISIZE=8856;MATEID=BND_eyaojldp GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:98:0:0:9:0:0:0:0:0
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49 chr1 854784 BND_vlxitdno G G[chr1:863642[ 4.52 PASS SVTYPE=BND;EVENT=DEL;END=863642;ISIZE=8858;MATEID=BND_bmvwcown GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:99:0:0:9:0:0:0:0:0
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50 chr1 855228 BND_qjfgagwf C ]chr1:863644]C 2.49 PASS SVTYPE=BND;EVENT=DEL;END=863644;ISIZE=8416;MATEID=BND_zjggijxo GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:104:0:0:8:0:30:18:8:0.40
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51 chr1 863640 BND_eyaojldp C ]chr1:854784]C 2.93 PASS SVTYPE=BND;EVENT=DEL;END=854784;ISIZE=8856;MATEID=BND_pkqgmhxz GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:98:0:0:9:0:35:10:9:0.34
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52 chr1 863642 BND_bmvwcown G ]chr1:854784]G 4.52 PASS SVTYPE=BND;EVENT=DEL;END=854784;ISIZE=8858;MATEID=BND_vlxitdno GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:99:0:0:9:0:18:6:9:0.22
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53 chr1 863644 BND_zjggijxo T T[chr1:855228[ 2.49 PASS SVTYPE=BND;EVENT=DEL;END=855228;ISIZE=8416;MATEID=BND_qjfgagwf GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:104:0:0:8:0:0:0:0:0
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54 chr1 903148 BND_jqxbndcc G C[chr1:903148[ 1000.00 PASS SVTYPE=BND;EVENT=INV;END=915991;ISIZE=12843;MATEID=BND_aveewewc GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:64:3:0:0:0:0:0
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55 chr1 903615 BND_fsafnyyz T ]chr1:903615]C 3.12 PASS SVTYPE=BND;EVENT=INV;END=915991;ISIZE=12376;MATEID=BND_uuhsrkwh GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:60:11:0:19:7:11:0.32
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56 chr1 903617 BND_peaqkjha C ]chr1:903617]C 1000.00 PASS SVTYPE=BND;EVENT=INV;END=915564;ISIZE=11947;MATEID=BND_dxtofeax GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:64:4:0:29:14:4:0.00
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57 chr1 903617 BND_veysrihm C G[chr1:903617[ 3.83 PASS SVTYPE=BND;EVENT=INV;END=915989;ISIZE=12372;MATEID=BND_yvvvrmzs GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:61:7:0:0:0:0:0
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58 chr1 915564 BND_dxtofeax C C[chr1:915564[ 1000.00 PASS SVTYPE=BND;EVENT=INV;END=903617;ISIZE=11947;MATEID=BND_peaqkjha GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:64:4:0:0:0:0:0
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59 chr1 915989 BND_yvvvrmzs G ]chr1:915989]C 3.83 PASS SVTYPE=BND;EVENT=INV;END=903617;ISIZE=12372;MATEID=BND_veysrihm GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:61:7:0:23:7:7:0.26
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60 chr1 915991 BND_aveewewc C ]chr1:915991]G 1000.00 PASS SVTYPE=BND;EVENT=INV;END=903148;ISIZE=12843;MATEID=BND_jqxbndcc GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:64:3:0:42:14:3:0.00
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61 chr1 915991 BND_uuhsrkwh C T[chr1:915991[ 3.12 PASS SVTYPE=BND;EVENT=INV;END=903615;ISIZE=12376;MATEID=BND_fsafnyyz GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:60:11:0:0:0:0:0
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62 chr1 937624 BND_ihjevxqn A T[chr1:937624[ 1000.00 PASS SVTYPE=BND;EVENT=INV;END=958311;ISIZE=20687;MATEID=BND_mkxueciv GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:52:3:0:0:0:0:0
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63 chr1 938004 BND_jritmtfi T ]chr1:938004]A 4.98 PASS SVTYPE=BND;EVENT=INV;END=958308;ISIZE=20304;MATEID=BND_ytttwmfe GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:59:7:0:10:5:7:0.20
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64 chr1 938006 BND_ipkrlpfe A G[chr1:938006[ 3.98 PASS SVTYPE=BND;EVENT=INV;END=958306;ISIZE=20300;MATEID=BND_khfaewsn GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:59:4:0:0:0:0:0
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65 chr1 958306 BND_khfaewsn G ]chr1:958306]A 3.98 PASS SVTYPE=BND;EVENT=INV;END=938006;ISIZE=20300;MATEID=BND_ipkrlpfe GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:59:4:0:40:10:4:0.25
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66 chr1 958308 BND_ytttwmfe A T[chr1:958308[ 4.98 PASS SVTYPE=BND;EVENT=INV;END=938004;ISIZE=20304;MATEID=BND_jritmtfi GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:59:7:0:0:0:0:0
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67 chr1 958311 BND_mkxueciv T ]chr1:958311]A 1000.00 PASS SVTYPE=BND;EVENT=INV;END=937624;ISIZE=20687;MATEID=BND_ihjevxqn GT:CTX:DEL:INS:INV:NOV_INS:TDUP:lSC:nSC:uRP:distl_levD 0/1:0:0:0:52:3:0:35:11:3:0.00
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