Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 20 threads; openjdk version "1.8.0_152-release"; /home/aapopov/tool/juicer1.6_compact-main/scripts/juicer.sh -g b.japonicum -y /data/aapopov/Projects/HumanDros/Branchiostoma_Hi_C/B.japonicum/B.japonicum.fna_MboI.txt -d /data/aapopov/Projects/HumanDros/Branchiostoma_Hi_C/B.japonicum_HIC -s MboI -p /data/aapopov/Projects/HumanDros/Branchiostoma_Hi_C/B.japonicum/B.japonicum.fna.chrom.sizes -z /data/aapopov/Projects/HumanDros/Branchiostoma_Hi_C/B.japonicum/B.japonicum.fna -D /home/aapopov/tool/juicer1.6_compact-main -t 20 Sequenced Read Pairs: 106,681,598 Normal Paired: 52,081,168 (48.82%) Chimeric Paired: 32,500,800 (30.47%) Chimeric Ambiguous: 14,239,867 (13.35%) Unmapped: 7,859,763 (7.37%) Ligation Motif Present: 72,772,316 (68.21%) Alignable (Normal+Chimeric Paired): 84,581,968 (79.28%) WARN [2024-06-25T15:46:48,375] [Globals.java:138] [main] Development mode is enabled Unique Reads: 73,383,631 (68.79%) PCR Duplicates: 11,198,337 (10.50%) Optical Duplicates: 0 (0.00%) Library Complexity Estimate: 290,562,960 Intra-fragment Reads: 7,214,502 (6.76% / 9.83%) Below MAPQ Threshold: 23,240,952 (21.79% / 31.67%) Hi-C Contacts: 42,928,177 (40.24% / 58.50%) Ligation Motif Present: 32,038,086 (30.03% / 43.66%) 3' Bias (Long Range): 69% - 31% Pair Type intra chrom %(L-I-O-R): 16% - 52% - 16% - 16% Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25% DE: 23% Cis/all (FF and RR orient): 51.4% Inter-chromosomal: 16,169,516 (15.16% / 22.03%) Intra-chromosomal: 26,758,661 (25.08% / 36.46%) Short Range (<20,000bp): 14,584,910 (13.67% / 19.87%) Long Range (>20,000bp): 12,173,751 (11.41% / 16.59%)