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/Trih_4/ -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:  138,431,124
 Normal Paired: 78,250,335 (56.53%)
 Chimeric Paired: 13,548,600 (9.79%)
 Chimeric Ambiguous: 1,478,640 (1.07%)
 Unmapped: 45,153,549 (32.62%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 91,798,935 (66.31%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2026-03-30T03:48:27,954]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 77,486,576 (55.97%)
PCR Duplicates: 0 (0.00%)
Optical Duplicates: 14,312,359 (10.34%)
Library Complexity Estimate: 0
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 4,751,428 (3.43% / 6.13%)
Hi-C Contacts: 72,735,148 (52.54% / 93.87%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 3% - 92% - 2% - 3%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 83%
 Cis/all (FF and RR orient): 57.8%
Inter-chromosomal: 5,067,192  (3.66% / 6.54%)
Intra-chromosomal: 67,667,956  (48.88% / 87.33%)
Short Range (<20,000bp): 62,294,105  (45.00% / 80.39%)
Long Range (>20,000bp): 5,373,851  (3.88% / 6.94%)