Experiment description: Juicer version 1.6; BWA 0.7.18-r1243-dirty; 14 threads; openjdk version "17.0.11-internal" 2024-04-16; /data/amivanov/Tools/juicer1.6_compact-main/scripts/juicer.sh -g T2T -d /data/amivanov/Projects/Embryos/MGNC_2025-04-26/Ask_K -s DpnII -y /data/amivanov/Databases/T2T-CHM13v2.0/juicer.rs/T2T-CHM13v2.0_DpnII.txt -p /data/amivanov/Databases/T2T-CHM13v2.0/hgT2T.chromsizes -z /data/amivanov/Databases/T2T-CHM13v2.0/hgT2T.fa -D /data/amivanov/Tools/juicer1.6_compact-main -t 14                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
Sequenced Read Pairs:  3,368,772
 Normal Paired: 2,136,822 (63.43%)
 Chimeric Paired: 807,150 (23.96%)
 Chimeric Ambiguous: 208,587 (6.19%)
 Unmapped: 216,213 (6.42%)
 Ligation Motif Present: 1,219,317 (36.19%)
Alignable (Normal+Chimeric Paired): 2,943,972 (87.39%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-05-17T14:35:06,051]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 1,491,279 (44.27%)
PCR Duplicates: 122,794 (3.65%)
Optical Duplicates: 1,329,899 (39.48%)
Library Complexity Estimate: 10,063,001
Intra-fragment Reads: 241,695 (7.17% / 16.21%)
Below MAPQ Threshold: 275,887 (8.19% / 18.50%)
Hi-C Contacts: 1,215,392 (36.08% / 81.50%)
 Ligation Motif Present: 440,362  (13.07% / 29.53%)
 3' Bias (Long Range): 60% - 40%
 Pair Type intra chrom %(L-I-O-R): 7% - 78% - 7% - 7%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 66%
 Cis/all (FF and RR orient): 77.6%
Inter-chromosomal: 93,043  (2.76% / 6.24%)
Intra-chromosomal: 1,122,349  (33.32% / 75.26%)
Short Range (<20,000bp): 866,591  (25.72% / 58.11%)
Long Range (>20,000bp): 255,758  (7.59% / 17.15%)