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/32cell/ -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:  136,779,099
 Normal Paired: 45,489,774 (33.26%)
 Chimeric Paired: 17,364,290 (12.70%)
 Chimeric Ambiguous: 9,926,261 (7.26%)
 Unmapped: 63,998,774 (46.79%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 62,854,064 (45.95%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2026-04-02T06:13:20,784]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 33,776,930 (24.69%)
PCR Duplicates: 29,077,134 (21.26%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 44,779,144
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 17,080,951 (12.49% / 50.57%)
Hi-C Contacts: 16,695,979 (12.21% / 49.43%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 9% - 73% - 9% - 9%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 47%
 Cis/all (FF and RR orient): 47.5%
Inter-chromosomal: 4,677,191  (3.42% / 13.85%)
Intra-chromosomal: 12,018,788  (8.79% / 35.58%)
Short Range (<20,000bp): 8,264,781  (6.04% / 24.47%)
Long Range (>20,000bp): 3,754,007  (2.74% / 11.11%)