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/SRR3343960_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:  27,884,781
 Normal Paired: 17,629,968 (63.22%)
 Chimeric Paired: 5,337,719 (19.14%)
 Chimeric Ambiguous: 3,619,668 (12.98%)
 Unmapped: 1,297,426 (4.65%)
 Ligation Motif Present: 2,436 (0.01%)
Alignable (Normal+Chimeric Paired): 22,967,687 (82.37%)
WARN [2024-01-14T21:20:24,667]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 15,412,579 (55.27%)
PCR Duplicates: 7,555,108 (27.09%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 26,740,422
Intra-fragment Reads: 6,110,432 (21.91% / 39.65%)
Below MAPQ Threshold: 4,854,747 (17.41% / 31.50%)
Hi-C Contacts: 4,447,400 (15.95% / 28.86%)
 Ligation Motif Present: 1,189  (0.00% / 0.01%)
 3' Bias (Long Range): 63% - 37%
 Pair Type intra chrom %(L-I-O-R): 16% - 50% - 17% - 17%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 24%
 DE: 33%
 Cis/all (FF and RR orient): 94.2%
Inter-chromosomal: 174,084  (0.62% / 1.13%)
Intra-chromosomal: 4,273,316  (15.32% / 27.73%)
Short Range (<20,000bp): 3,143,962  (11.27% / 20.40%)
Long Range (>20,000bp): 1,129,354  (4.05% / 7.33%)