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/SRR3344118_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:  9,782,475
 Normal Paired: 4,079,445 (41.70%)
 Chimeric Paired: 638,514 (6.53%)
 Chimeric Ambiguous: 349,658 (3.57%)
 Unmapped: 4,714,858 (48.20%)
 Ligation Motif Present: 15,899 (0.16%)
Alignable (Normal+Chimeric Paired): 4,717,959 (48.23%)
WARN [2024-01-15T07:42:08,502]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 1,915,863 (19.58%)
PCR Duplicates: 2,802,096 (28.64%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 2,158,441
Intra-fragment Reads: 749,691 (7.66% / 39.13%)
Below MAPQ Threshold: 383,543 (3.92% / 20.02%)
Hi-C Contacts: 782,629 (8.00% / 40.85%)
 Ligation Motif Present: 461  (0.00% / 0.02%)
 3' Bias (Long Range): 65% - 35%
 Pair Type intra chrom %(L-I-O-R): 12% - 56% - 21% - 11%
 Pair Type inter chrom %(L-I-O-R): 28% - 21% - 24% - 27%
 DE: 51%
 Cis/all (FF and RR orient): 92.0%
Inter-chromosomal: 27,879  (0.28% / 1.46%)
Intra-chromosomal: 754,750  (7.72% / 39.39%)
Short Range (<20,000bp): 662,419  (6.77% / 34.58%)
Long Range (>20,000bp): 92,331  (0.94% / 4.82%)