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_1/ -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:  107,904,810
 Normal Paired: 69,975,520 (64.85%)
 Chimeric Paired: 13,832,426 (12.82%)
 Chimeric Ambiguous: 1,756,322 (1.63%)
 Unmapped: 22,340,542 (20.70%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 83,807,946 (77.67%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2026-03-29T06:00:05,096]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 72,800,811 (67.47%)
PCR Duplicates: 23,265 (0.02%)
Optical Duplicates: 10,983,870 (10.18%)
Library Complexity Estimate: 113,952,643,137
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 2,837,453 (2.63% / 3.90%)
Hi-C Contacts: 69,963,358 (64.84% / 96.10%)
 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: 80%
 Cis/all (FF and RR orient): 58.2%
Inter-chromosomal: 5,911,981  (5.48% / 8.12%)
Intra-chromosomal: 64,051,377  (59.36% / 87.98%)
Short Range (<20,000bp): 57,453,336  (53.24% / 78.92%)
Long Range (>20,000bp): 6,598,041  (6.11% / 9.06%)