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: 665,052 (5.65% / 16.79%)
Hi-C Contacts: 3,295,058 (27.97% / 83.21%)
 Ligation Motif Present: 1,962,871  (16.66% / 49.57%)
 3' Bias (Long Range): 65% - 35%
 Pair Type intra chrom %(L-I-O-R): 11% - 66% - 11% - 11%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 45%
 Cis/all (FF and RR orient): 66.6%
Inter-chromosomal: 603,029  (5.12% / 15.23%)
Intra-chromosomal: 2,692,029  (22.86% / 67.98%)
Short Range (<20,000bp): 1,742,515  (14.79% / 44.00%)
Long Range (>20,000bp): 949,514  (8.06% / 23.98%)