some of the loci obtained in all samples have 0/0 genotypes

[ccyy11]

ctg_1 48504 5480 N 0 . SVTYPE=INV;SVLEN=6001299;END=6049803;STRANDS=++:2,--:2;IMPRECISE;CIPOS=-10,9;CIEND=-10,9;CIPOS95=-2,3;CIEND95=-3,3;SU=4;PE=2;SR=2;SNAME=U-A7:208;ALG=PROD;GCF=0.72342 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB:DHFC:DHFFC:DHBFC 0/0:200:0:-0,-83,-275:276:276:0:275:0:191:0:0:84:0:0:1.01905:1.11458:0.972727 0/0:200:0:-0,-49,-164:165:165:0:164:0:113:0:0:51:0:0:1:1.0177:0.950413 0/0:200:0:-0,-66,-219:220:220:0:219:0:158:0:0:61:0:0:0.991667:1.56579:0.944444