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/Trih2/ -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:  150,885,100
 Normal Paired: 100,217,958 (66.42%)
 Chimeric Paired: 27,611,229 (18.30%)
 Chimeric Ambiguous: 3,295,420 (2.18%)
 Unmapped: 19,760,493 (13.10%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 127,829,187 (84.72%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2026-01-22T23:16:56,444]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 107,271,631 (71.09%)
PCR Duplicates: 82,569 (0.05%)
Optical Duplicates: 20,474,987 (13.57%)
Library Complexity Estimate: 69,753,866,950
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 3,946,676 (2.62% / 3.68%)
Hi-C Contacts: 103,324,955 (68.48% / 96.32%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 3% - 90% - 3% - 3%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 74%
 Cis/all (FF and RR orient): 45.4%
Inter-chromosomal: 14,430,299  (9.56% / 13.45%)
Intra-chromosomal: 88,894,656  (58.92% / 82.87%)
Short Range (<20,000bp): 78,896,756  (52.29% / 73.55%)
Long Range (>20,000bp): 9,997,900  (6.63% / 9.32%)