Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 6 threads; openjdk version "17.0.10" 2024-01-16; juicer.sh -g Trichoplax -d /storage3/artem/Trichoplax/TA3 -s DpnII -p /storage3/artem/Genomes/Trichoplax/triadV2_030816_SP.sizes -y /storage3/artem/Genomes/Trichoplax/Trichoplax_DpnII.txt -z /storage3/artem/Genomes/Trichoplax/triadV2_030816_SP.fasta -t 6 -D /storage3/artem/Software/juicer1.6_compact/                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
Sequenced Read Pairs:  1,654,751
 Normal Paired: 1,233,213 (74.53%)
 Chimeric Paired: 282,015 (17.04%)
 Chimeric Ambiguous: 44,553 (2.69%)
 Unmapped: 94,970 (5.74%)
 Ligation Motif Present: 4,475 (0.27%)
Alignable (Normal+Chimeric Paired): 1,515,228 (91.57%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-03-04T20:56:37,924]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 1,156,018 (69.86%)
PCR Duplicates: 346,329 (20.93%)
Optical Duplicates: 12,881 (0.78%)
Library Complexity Estimate: 2,735,701
Intra-fragment Reads: 612,032 (36.99% / 52.94%)
Below MAPQ Threshold: 45,121 (2.73% / 3.90%)
Hi-C Contacts: 1,110,897 (67.13% / 96.10%)
 Ligation Motif Present: 2,733  (0.17% / 0.24%)
 3' Bias (Long Range): 46% - 54%
 Pair Type intra chrom %(L-I-O-R): 2% - 92% - 4% - 2%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 73%
 Cis/all (FF and RR orient): 23.9%
Inter-chromosomal: 229,854  (13.89% / 19.88%)
Intra-chromosomal: 881,043  (53.24% / 76.21%)
Short Range (<20,000bp): 859,660  (51.95% / 74.36%)
Long Range (>20,000bp): 21,383  (1.29% / 1.85%)