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_TA5 -d /storage3/estsoi/Trihoplax/TA5 -s none -z /storage3/estsoi/Trihoplax/triadV2_030816_SP_V2_new.fasta -D /home/estsoi/juicer1.6_compact -S final                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
Sequenced Read Pairs:  32,354,642
 Normal Paired: 18,855,927 (58.28%)
 Chimeric Paired: 10,383,610 (32.09%)
 Chimeric Ambiguous: 1,884,099 (5.82%)
 Unmapped: 1,231,006 (3.80%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 29,239,537 (90.37%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-08-19T20:12:23,493]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 27,451,666 (84.85%)
PCR Duplicates: 0 (0.00%)
Optical Duplicates: 1,787,871 (5.53%)
Library Complexity Estimate: 0
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 1,021,604 (3.16% / 3.72%)
Hi-C Contacts: 26,430,062 (81.69% / 96.28%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 6% - 82% - 6% - 6%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 58%
 Cis/all (FF and RR orient): 45.1%
Inter-chromosomal: 6,066,708  (18.75% / 22.10%)
Intra-chromosomal: 20,363,354  (62.94% / 74.18%)
Short Range (<20,000bp): 16,391,547  (50.66% / 59.71%)
Long Range (>20,000bp): 3,971,807  (12.28% / 14.47%)