Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 60 threads; java version "1.8.0_40"; scripts/juicer.sh -t 60 -D /srv/scratch/marinovg/juicer-L1523-Killifish-Hi-C-additional_reads-against_scaffolding -d /srv/scratch/marinovg/juicer-L1523-Killifish-Hi-C-additional_reads-against_scaffolding -p /srv/scratch/marinovg/juicer-L1523-Killifish-Hi-C-additional_reads-3D_DNA-repeat-editor-coverage100-rounds5-manual-MND/final-post-review/GCA_001465895.2_Nfu_20140520_genomic.FINAL.against_scaffolding.chrom.sizes -y none -s none -z /srv/scratch/marinovg/juicer-L1523-Killifish-Hi-C-additional_reads-3D_DNA-repeat-editor-coverage100-rounds5-manual-MND/final-post-review/bwa-indexes/GCA_001465895.2_Nfu_20140520_genomic.FINAL.fasta                                                                                                                                                                                                                                                                          
Sequenced Read Pairs:  814,717,494
 Normal Paired: 501,989,199 (61.62%)
 Chimeric Paired: 0 (0.00%)
 Chimeric Ambiguous: 0 (0.00%)
 Unmapped: 312,728,295 (38.38%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 501,989,199 (61.62%)
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 266,374,269 (32.70% / 70.47%)
Hi-C Contacts: 111,629,778 (13.70% / 29.53%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 30,086,780  (3.69% / 7.96%)
Intra-chromosomal: 81,542,998  (10.01% / 21.57%)
Short Range (<20Kb): 27,269,766  (3.35% / 7.21%)
Long Range (>20Kb): 54,269,302  (6.66% / 14.36%)