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_3/ -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:  203,123,703
 Normal Paired: 71,473,927 (35.19%)
 Chimeric Paired: 11,829,737 (5.82%)
 Chimeric Ambiguous: 1,370,149 (0.67%)
 Unmapped: 118,449,890 (58.31%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 83,303,664 (41.01%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2026-03-29T23:12:38,365]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 71,925,358 (35.41%)
PCR Duplicates: 0 (0.00%)
Optical Duplicates: 11,378,306 (5.60%)
Library Complexity Estimate: 0
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 2,837,626 (1.40% / 3.95%)
Hi-C Contacts: 69,087,732 (34.01% / 96.05%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 3% - 92% - 3% - 3%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 83%
 Cis/all (FF and RR orient): 62.0%
Inter-chromosomal: 4,480,689  (2.21% / 6.23%)
Intra-chromosomal: 64,607,043  (31.81% / 89.83%)
Short Range (<20,000bp): 58,923,203  (29.01% / 81.92%)
Long Range (>20,000bp): 5,683,840  (2.80% / 7.90%)