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: 229,042,029 (28.11% / 60.59%)
Hi-C Contacts: 148,962,018 (18.28% / 39.41%)
 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: 46,211,984  (5.67% / 12.23%)
Intra-chromosomal: 102,750,034  (12.61% / 27.18%)
Short Range (<20Kb): 33,404,144  (4.10% / 8.84%)
Long Range (>20Kb): 69,340,430  (8.51% / 18.34%)