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/2025-04-25_Orlov/Ore1_e27 -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:  8,499,940
 Normal Paired: 3,722,263 (43.79%)
 Chimeric Paired: 3,465,185 (40.77%)
 Chimeric Ambiguous: 664,132 (7.81%)
 Unmapped: 648,360 (7.63%)
 Ligation Motif Present: 5,501,017 (64.72%)
Alignable (Normal+Chimeric Paired): 7,187,448 (84.56%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-05-14T20:25:01,765]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 881,001 (10.36%)
PCR Duplicates: 6,298,098 (74.10%)
Optical Duplicates: 8,349 (0.10%)
Library Complexity Estimate: 881,256
Intra-fragment Reads: 50,847 (0.60% / 5.77%)
Below MAPQ Threshold: 351,406 (4.13% / 39.89%)
Hi-C Contacts: 529,595 (6.23% / 60.11%)
 Ligation Motif Present: 316,378  (3.72% / 35.91%)
 3' Bias (Long Range): 69% - 31%
 Pair Type intra chrom %(L-I-O-R): 13% - 62% - 13% - 13%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 37%
 Cis/all (FF and RR orient): 59.4%
Inter-chromosomal: 135,916  (1.60% / 15.43%)
Intra-chromosomal: 393,679  (4.63% / 44.69%)
Short Range (<20,000bp): 255,563  (3.01% / 29.01%)
Long Range (>20,000bp): 138,116  (1.62% / 15.68%)