Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 6 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 6 -D /storage3/artem/Software/juicer1.6_compact/                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
Sequenced Read Pairs:  343,199
 Normal Paired: 224,599 (65.44%)
 Chimeric Paired: 60,582 (17.65%)
 Chimeric Ambiguous: 7,760 (2.26%)
 Unmapped: 50,258 (14.64%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 285,181 (83.09%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-12-13T21:33:34,517]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 284,969 (83.03%)
PCR Duplicates: 167 (0.05%)
Optical Duplicates: 45 (0.01%)
Library Complexity Estimate: 243,325,719
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 9,735 (2.84% / 3.42%)
Hi-C Contacts: 275,234 (80.20% / 96.58%)
 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: 79%
 Cis/all (FF and RR orient): 45.7%
Inter-chromosomal: 31,611  (9.21% / 11.09%)
Intra-chromosomal: 243,623  (70.99% / 85.49%)
Short Range (<20,000bp): 221,715  (64.60% / 77.80%)
Long Range (>20,000bp): 21,908  (6.38% / 7.69%)