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/SRR3344121_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:  13,073,552
 Normal Paired: 10,218,235 (78.16%)
 Chimeric Paired: 1,467,458 (11.22%)
 Chimeric Ambiguous: 314,654 (2.41%)
 Unmapped: 1,073,205 (8.21%)
 Ligation Motif Present: 2,978 (0.02%)
Alignable (Normal+Chimeric Paired): 11,685,693 (89.38%)
WARN [2024-01-15T07:57:01,224]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 3,416,758 (26.13%)
PCR Duplicates: 8,268,935 (63.25%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 3,548,546
Intra-fragment Reads: 1,778,230 (13.60% / 52.04%)
Below MAPQ Threshold: 570,576 (4.36% / 16.70%)
Hi-C Contacts: 1,067,952 (8.17% / 31.26%)
 Ligation Motif Present: 400  (0.00% / 0.01%)
 3' Bias (Long Range): 73% - 27%
 Pair Type intra chrom %(L-I-O-R): 10% - 59% - 22% - 10%
 Pair Type inter chrom %(L-I-O-R): 27% - 24% - 24% - 25%
 DE: 60%
 Cis/all (FF and RR orient): 92.7%
Inter-chromosomal: 30,307  (0.23% / 0.89%)
Intra-chromosomal: 1,037,645  (7.94% / 30.37%)
Short Range (<20,000bp): 895,749  (6.85% / 26.22%)
Long Range (>20,000bp): 141,896  (1.09% / 4.15%)