Experiment description: Juicer version 1.6; BWA 0.7.18-r1243-dirty; 14 threads; openjdk version "17.0.8-internal" 2023-07-18; /data/amivanov/Tools/juicer1.6_compact-main/scripts/juicer.sh -g T2T -d /data/amivanov/Projects/Embryos/2025-04-24-BGI/B/Pet1_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:  11,778,626
 Normal Paired: 6,604,362 (56.07%)
 Chimeric Paired: 4,094,865 (34.77%)
 Chimeric Ambiguous: 929,161 (7.89%)
 Unmapped: 150,238 (1.28%)
 Ligation Motif Present: 7,242,432 (61.49%)
Alignable (Normal+Chimeric Paired): 10,699,227 (90.84%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-05-17T17:14:29,200]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 3,960,110 (33.62%)
PCR Duplicates: 6,739,117 (57.21%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 4,324,361
Intra-fragment Reads: 361,186 (3.07% / 9.12%)
Below MAPQ Threshold: 846,537 (7.19% / 21.38%)
Hi-C Contacts: 3,113,573 (26.43% / 78.62%)
 Ligation Motif Present: 1,825,633  (15.50% / 46.10%)
 3' Bias (Long Range): 65% - 35%
 Pair Type intra chrom %(L-I-O-R): 11% - 67% - 11% - 11%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 47%
 Cis/all (FF and RR orient): 67.3%
Inter-chromosomal: 544,238  (4.62% / 13.74%)
Intra-chromosomal: 2,569,335  (21.81% / 64.88%)
Short Range (<20,000bp): 1,686,893  (14.32% / 42.60%)
Long Range (>20,000bp): 882,442  (7.49% / 22.28%)