Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 8 threads; openjdk version "17.0.15" 2025-04-15; juicer.sh -t 8 -d /storage3/artem/Lancelet/BrFloridae/64cell/ -p /storage3/artem/Genomes/BrFloridae/Bfl_VNyyK.chrom.sizes -z /storage3/artem/Genomes/BrFloridae/GCF_000003815.2_Bfl_VNyyK_genomic.fna -D /storage3/artem/Software/juicer1.6_compact/                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
Sequenced Read Pairs:  154,347,440
 Normal Paired: 70,754,523 (45.84%)
 Chimeric Paired: 29,937,632 (19.40%)
 Chimeric Ambiguous: 16,687,767 (10.81%)
 Unmapped: 36,967,518 (23.95%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 100,692,155 (65.24%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2026-04-02T23:13:26,383]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 63,463,994 (41.12%)
PCR Duplicates: 37,228,161 (24.12%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 99,993,207
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 29,627,975 (19.20% / 46.68%)
Hi-C Contacts: 33,836,019 (21.92% / 53.32%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 11% - 66% - 11% - 11%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 42%
 Cis/all (FF and RR orient): 59.8%
Inter-chromosomal: 7,905,657  (5.12% / 12.46%)
Intra-chromosomal: 25,930,362  (16.80% / 40.86%)
Short Range (<20,000bp): 16,962,928  (10.99% / 26.73%)
Long Range (>20,000bp): 8,967,434  (5.81% / 14.13%)