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 -d /storage3/estsoi/Trihoplax -s none -z /storage3/estsoi/Trihoplax/triadV2_030816_SP_new.fasta -D /home/estsoi/juicer1.6_compact                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
Sequenced Read Pairs:  27,407,019
 Normal Paired: 12,351,739 (45.07%)
 Chimeric Paired: 7,128,137 (26.01%)
 Chimeric Ambiguous: 1,085,393 (3.96%)
 Unmapped: 6,841,750 (24.96%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 19,479,876 (71.08%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-08-17T22:12:55,133]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 18,093,637 (66.02%)
PCR Duplicates: 0 (0.00%)
Optical Duplicates: 1,386,239 (5.06%)
Library Complexity Estimate: 0
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 1,261,071 (4.60% / 6.97%)
Hi-C Contacts: 16,832,566 (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% - 83% - 5% - 6%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 66%
 Cis/all (FF and RR orient): 57.3%
Inter-chromosomal: 2,443,519  (8.92% / 13.50%)
Intra-chromosomal: 14,389,047  (52.50% / 79.53%)
Short Range (<20,000bp): 12,175,762  (44.43% / 67.29%)
Long Range (>20,000bp): 2,213,285  (8.08% / 12.23%)