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/SRR3343959_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:  42,661,107
 Normal Paired: 34,937,923 (81.90%)
 Chimeric Paired: 4,653,053 (10.91%)
 Chimeric Ambiguous: 2,249,518 (5.27%)
 Unmapped: 820,613 (1.92%)
 Ligation Motif Present: 7,436 (0.02%)
Alignable (Normal+Chimeric Paired): 39,590,976 (92.80%)
WARN [2024-01-14T20:28:23,132]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 16,000,965 (37.51%)
PCR Duplicates: 23,590,011 (55.30%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 17,994,456
Intra-fragment Reads: 5,833,006 (13.67% / 36.45%)
Below MAPQ Threshold: 2,946,660 (6.91% / 18.42%)
Hi-C Contacts: 7,221,299 (16.93% / 45.13%)
 Ligation Motif Present: 2,134  (0.01% / 0.01%)
 3' Bias (Long Range): 67% - 33%
 Pair Type intra chrom %(L-I-O-R): 14% - 55% - 16% - 14%
 Pair Type inter chrom %(L-I-O-R): 26% - 25% - 25% - 24%
 DE: 41%
 Cis/all (FF and RR orient): 93.4%
Inter-chromosomal: 282,464  (0.66% / 1.77%)
Intra-chromosomal: 6,938,835  (16.27% / 43.37%)
Short Range (<20,000bp): 4,801,524  (11.26% / 30.01%)
Long Range (>20,000bp): 2,137,311  (5.01% / 13.36%)