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/SRR3344124_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:  13,650,672
 Normal Paired: 11,527,004 (84.44%)
 Chimeric Paired: 1,404,022 (10.29%)
 Chimeric Ambiguous: 374,344 (2.74%)
 Unmapped: 345,302 (2.53%)
 Ligation Motif Present: 645 (0.00%)
Alignable (Normal+Chimeric Paired): 12,931,026 (94.73%)
WARN [2024-01-15T08:14:53,947]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 3,834,408 (28.09%)
PCR Duplicates: 9,096,618 (66.64%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 3,990,644
Intra-fragment Reads: 1,967,571 (14.41% / 51.31%)
Below MAPQ Threshold: 772,128 (5.66% / 20.14%)
Hi-C Contacts: 1,094,709 (8.02% / 28.55%)
 Ligation Motif Present: 121  (0.00% / 0.00%)
 3' Bias (Long Range): 75% - 25%
 Pair Type intra chrom %(L-I-O-R): 10% - 60% - 22% - 9%
 Pair Type inter chrom %(L-I-O-R): 26% - 24% - 25% - 26%
 DE: 61%
 Cis/all (FF and RR orient): 94.4%
Inter-chromosomal: 23,043  (0.17% / 0.60%)
Intra-chromosomal: 1,071,666  (7.85% / 27.95%)
Short Range (<20,000bp): 926,506  (6.79% / 24.16%)
Long Range (>20,000bp): 145,160  (1.06% / 3.79%)