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/SRR3343998_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:  18,647,661
 Normal Paired: 11,071,483 (59.37%)
 Chimeric Paired: 3,362,210 (18.03%)
 Chimeric Ambiguous: 2,943,331 (15.78%)
 Unmapped: 1,270,637 (6.81%)
 Ligation Motif Present: 589 (0.00%)
Alignable (Normal+Chimeric Paired): 14,433,693 (77.40%)
WARN [2024-01-15T02:30:43,657]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 9,957,824 (53.40%)
PCR Duplicates: 4,475,869 (24.00%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 18,160,650
Intra-fragment Reads: 3,958,346 (21.23% / 39.75%)
Below MAPQ Threshold: 3,441,180 (18.45% / 34.56%)
Hi-C Contacts: 2,558,298 (13.72% / 25.69%)
 Ligation Motif Present: 302  (0.00% / 0.00%)
 3' Bias (Long Range): 58% - 42%
 Pair Type intra chrom %(L-I-O-R): 18% - 44% - 20% - 18%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 21%
 Cis/all (FF and RR orient): 68.8%
Inter-chromosomal: 631,580  (3.39% / 6.34%)
Intra-chromosomal: 1,926,718  (10.33% / 19.35%)
Short Range (<20,000bp): 1,253,700  (6.72% / 12.59%)
Long Range (>20,000bp): 673,018  (3.61% / 6.76%)