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/SRR3344097_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:  5,789,764
 Normal Paired: 5,002,338 (86.40%)
 Chimeric Paired: 556,349 (9.61%)
 Chimeric Ambiguous: 109,492 (1.89%)
 Unmapped: 121,585 (2.10%)
 Ligation Motif Present: 1,555 (0.03%)
Alignable (Normal+Chimeric Paired): 5,558,687 (96.01%)
WARN [2024-01-15T06:54:13,799]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 3,914,488 (67.61%)
PCR Duplicates: 1,644,199 (28.40%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 7,434,068
Intra-fragment Reads: 2,034,782 (35.14% / 51.98%)
Below MAPQ Threshold: 384,205 (6.64% / 9.81%)
Hi-C Contacts: 1,495,501 (25.83% / 38.20%)
 Ligation Motif Present: 919  (0.02% / 0.02%)
 3' Bias (Long Range): 73% - 27%
 Pair Type intra chrom %(L-I-O-R): 8% - 63% - 21% - 8%
 Pair Type inter chrom %(L-I-O-R): 24% - 23% - 25% - 28%
 DE: 66%
 Cis/all (FF and RR orient): 89.9%
Inter-chromosomal: 49,156  (0.85% / 1.26%)
Intra-chromosomal: 1,446,345  (24.98% / 36.95%)
Short Range (<20,000bp): 1,264,213  (21.84% / 32.30%)
Long Range (>20,000bp): 182,132  (3.15% / 4.65%)