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 GRCm39 -d /data/aapopov/Projects/ChickenOocyt/NSN_mouse_oocytes/SRR3344095_pass -s DpnII -y /data/aapopov/Projects/ChickenOocyt/Mouse_genome/GRCm39_DpnII.txt -p /data/aapopov/Projects/ChickenOocyt/Mouse_genome/GRCm39.fasta.chrom.sizes -D /home/aapopov/tool/juicer1.6_compact-main -z /data/aapopov/Projects/ChickenOocyt/Mouse_genome/GRCm39.fasta -t 20 Sequenced Read Pairs: 14,013,786 Normal Paired: 11,724,875 (83.67%) Chimeric Paired: 1,605,033 (11.45%) Chimeric Ambiguous: 436,858 (3.12%) Unmapped: 247,020 (1.76%) Ligation Motif Present: 2,342 (0.02%) Alignable (Normal+Chimeric Paired): 13,329,908 (95.12%) WARN [2024-01-15T06:34:01,226] [Globals.java:138] [main] Development mode is enabled Unique Reads: 5,126,475 (36.58%) PCR Duplicates: 8,203,433 (58.54%) Optical Duplicates: 0 (0.00%) Library Complexity Estimate: 5,665,157 Intra-fragment Reads: 2,733,730 (19.51% / 53.33%) Below MAPQ Threshold: 584,441 (4.17% / 11.40%) Hi-C Contacts: 1,808,304 (12.90% / 35.27%) Ligation Motif Present: 941 (0.01% / 0.02%) 3' Bias (Long Range): 73% - 27% Pair Type intra chrom %(L-I-O-R): 12% - 56% - 20% - 12% Pair Type inter chrom %(L-I-O-R): 25% - 25% - 26% - 24% DE: 51% Cis/all (FF and RR orient): 92.0% Inter-chromosomal: 72,123 (0.51% / 1.41%) Intra-chromosomal: 1,736,181 (12.39% / 33.87%) Short Range (<20,000bp): 1,413,372 (10.09% / 27.57%) Long Range (>20,000bp): 322,809 (2.30% / 6.30%)