Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 16 threads; openjdk version "17.0.12" 2024-07-16; /home/estsoi/juicer1.6_compact/scripts/juicer.sh -g triadV2_T1 -d /storage3/estsoi/Trihoplax/T1 -s none -z /storage3/estsoi/Trihoplax/triadV2_030816_SP_V2_new.fasta -D /home/estsoi/juicer1.6_compact                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
Sequenced Read Pairs:  27,407,019
 Normal Paired: 12,351,748 (45.07%)
 Chimeric Paired: 7,128,114 (26.01%)
 Chimeric Ambiguous: 1,085,408 (3.96%)
 Unmapped: 6,841,749 (24.96%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 19,479,862 (71.08%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-08-18T18:18:35,260]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 18,093,621 (66.02%)
PCR Duplicates: 0 (0.00%)
Optical Duplicates: 1,386,241 (5.06%)
Library Complexity Estimate: 0
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 1,261,050 (4.60% / 6.97%)
Hi-C Contacts: 16,832,571 (61.42% / 93.03%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 6% - 84% - 5% - 6%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 66%
 Cis/all (FF and RR orient): 55.7%
Inter-chromosomal: 2,532,315  (9.24% / 14.00%)
Intra-chromosomal: 14,300,256  (52.18% / 79.03%)
Short Range (<20,000bp): 12,175,767  (44.43% / 67.29%)
Long Range (>20,000bp): 2,124,489  (7.75% / 11.74%)