Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 12 threads; openjdk version "17.0.15" 2025-04-15; juicer.sh -d /storage3/artem/Trichoplax/Trih1/ -p /storage3/artem/Trichoplax/Genome/file.chrom.sizes -z /storage3/artem/Trichoplax/Genome/H1pacbio_consensus.fa -t 12 -D /storage3/artem/Software/juicer1.6_compact/                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
Sequenced Read Pairs:  123,138,321
 Normal Paired: 73,396,172 (59.60%)
 Chimeric Paired: 37,481,419 (30.44%)
 Chimeric Ambiguous: 10,067,989 (8.18%)
 Unmapped: 2,192,741 (1.78%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 110,877,591 (90.04%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2026-01-22T17:29:46,311]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 100,723,849 (81.80%)
PCR Duplicates: 35,280 (0.03%)
Optical Duplicates: 10,118,462 (8.22%)
Library Complexity Estimate: 143,849,661,098
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 3,776,352 (3.07% / 3.75%)
Hi-C Contacts: 96,947,497 (78.73% / 96.25%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 6% - 81% - 6% - 6%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 61%
 Cis/all (FF and RR orient): 51.1%
Inter-chromosomal: 18,728,312  (15.21% / 18.59%)
Intra-chromosomal: 78,219,185  (63.52% / 77.66%)
Short Range (<20,000bp): 62,465,028  (50.73% / 62.02%)
Long Range (>20,000bp): 15,754,157  (12.79% / 15.64%)