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/SRR3344124_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: 13,650,672 Normal Paired: 11,527,004 (84.44%) Chimeric Paired: 1,404,022 (10.29%) Chimeric Ambiguous: 374,344 (2.74%) Unmapped: 345,302 (2.53%) Ligation Motif Present: 645 (0.00%) Alignable (Normal+Chimeric Paired): 12,931,026 (94.73%) WARN [2024-01-15T08:14:53,947] [Globals.java:138] [main] Development mode is enabled Unique Reads: 3,834,408 (28.09%) PCR Duplicates: 9,096,618 (66.64%) Optical Duplicates: 0 (0.00%) Library Complexity Estimate: 3,990,644 Intra-fragment Reads: 1,967,571 (14.41% / 51.31%) Below MAPQ Threshold: 704,843 (5.16% / 18.38%) Hi-C Contacts: 1,161,994 (8.51% / 30.30%) Ligation Motif Present: 146 (0.00% / 0.00%) 3' Bias (Long Range): 75% - 25% Pair Type intra chrom %(L-I-O-R): 10% - 59% - 21% - 10% Pair Type inter chrom %(L-I-O-R): 26% - 24% - 24% - 26% DE: 59% Cis/all (FF and RR orient): 93.3% Inter-chromosomal: 30,032 (0.22% / 0.78%) Intra-chromosomal: 1,131,962 (8.29% / 29.52%) Short Range (<20,000bp): 975,634 (7.15% / 25.44%) Long Range (>20,000bp): 156,328 (1.15% / 4.08%)