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/SRR3343982_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:  14,591,320
 Normal Paired: 9,206,764 (63.10%)
 Chimeric Paired: 2,456,834 (16.84%)
 Chimeric Ambiguous: 2,141,821 (14.68%)
 Unmapped: 785,901 (5.39%)
 Ligation Motif Present: 1,121 (0.01%)
Alignable (Normal+Chimeric Paired): 11,663,598 (79.94%)
WARN [2024-01-15T01:25:45,683]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 8,936,423 (61.24%)
PCR Duplicates: 2,727,175 (18.69%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 20,879,634
Intra-fragment Reads: 3,434,608 (23.54% / 38.43%)
Below MAPQ Threshold: 2,726,664 (18.69% / 30.51%)
Hi-C Contacts: 2,775,151 (19.02% / 31.05%)
 Ligation Motif Present: 626  (0.00% / 0.01%)
 3' Bias (Long Range): 60% - 40%
 Pair Type intra chrom %(L-I-O-R): 17% - 47% - 19% - 17%
 Pair Type inter chrom %(L-I-O-R): 25% - 26% - 25% - 25%
 DE: 27%
 Cis/all (FF and RR orient): 73.8%
Inter-chromosomal: 538,845  (3.69% / 6.03%)
Intra-chromosomal: 2,236,306  (15.33% / 25.02%)
Short Range (<20,000bp): 1,576,298  (10.80% / 17.64%)
Long Range (>20,000bp): 660,008  (4.52% / 7.39%)