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/Trih1/ -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:  258,968
 Normal Paired: 153,090 (59.12%)
 Chimeric Paired: 77,036 (29.75%)
 Chimeric Ambiguous: 21,911 (8.46%)
 Unmapped: 6,931 (2.68%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 230,126 (88.86%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-12-13T21:31:59,175]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 230,020 (88.82%)
PCR Duplicates: 72 (0.03%)
Optical Duplicates: 34 (0.01%)
Library Complexity Estimate: 367,578,357
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 8,400 (3.24% / 3.65%)
Hi-C Contacts: 221,620 (85.58% / 96.35%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 6% - 83% - 6% - 6%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 64%
 Cis/all (FF and RR orient): 51.4%
Inter-chromosomal: 38,789  (14.98% / 16.86%)
Intra-chromosomal: 182,831  (70.60% / 79.48%)
Short Range (<20,000bp): 149,891  (57.88% / 65.16%)
Long Range (>20,000bp): 32,940  (12.72% / 14.32%)