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/gastrula/ -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:  100,186,189
 Normal Paired: 47,096,502 (47.01%)
 Chimeric Paired: 26,016,800 (25.97%)
 Chimeric Ambiguous: 13,290,640 (13.27%)
 Unmapped: 13,782,247 (13.76%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 73,113,302 (72.98%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2026-04-03T04:21:44,433]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 53,385,845 (53.29%)
PCR Duplicates: 19,727,457 (19.69%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 109,824,821
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 22,478,714 (22.44% / 42.11%)
Hi-C Contacts: 30,907,131 (30.85% / 57.89%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 16% - 53% - 15% - 16%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 33%
 Cis/all (FF and RR orient): 81.5%
Inter-chromosomal: 3,833,461  (3.83% / 7.18%)
Intra-chromosomal: 27,073,670  (27.02% / 50.71%)
Short Range (<20,000bp): 16,174,439  (16.14% / 30.30%)
Long Range (>20,000bp): 10,899,231  (10.88% / 20.42%)