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: 1,897,619 (5.87% / 6.91%)
Hi-C Contacts: 25,554,047 (78.98% / 93.09%)
 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: 59%
 Cis/all (FF and RR orient): 45.7%
Inter-chromosomal: 5,729,594  (17.71% / 20.87%)
Intra-chromosomal: 19,824,453  (61.27% / 72.22%)
Short Range (<20,000bp): 15,985,090  (49.41% / 58.23%)
Long Range (>20,000bp): 3,839,363  (11.87% / 13.99%)