Experiment description: Juicer version 1.5.6; BWA 0.7.12-r1039; 60 threads; java version "1.8.0_40"; scripts/juicer.sh -t 60 -D /srv/scratch/marinovg/juicer-L1113-Haloferax_volcanii_Hi-C-all_reads -d /srv/scratch/marinovg/juicer-L1113-Haloferax_volcanii_Hi-C-all_reads -p /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/all.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bwa-indexes/Haloferax_volcanii_DS2_uid46845_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bwa-indexes/all.fa                                                                                                                                                                                                                                                                                                                                            
Sequenced Read Pairs:  157,863,614
 Normal Paired: 132,291,234 (83.80%)
 Chimeric Paired: 0 (0.00%)
 Chimeric Ambiguous: 0 (0.00%)
 Unmapped: 25,572,380 (16.20%)
 Ligation Motif Present: 20,263,910 (12.84%)
Alignable (Normal+Chimeric Paired): 132,291,234 (83.80%)
Unique Reads: 110,326,760 (69.89%)
PCR Duplicates: 21,901,236 (13.87%)
Optical Duplicates: 63,238 (0.04%)
Library Complexity Estimate: 353,747,347
Intra-fragment Reads: 10,035,724 (6.36% / 9.10%)
Below MAPQ Threshold: 15,840,452 (10.03% / 14.36%)
Hi-C Contacts: 84,450,584 (53.50% / 76.55%)
 Ligation Motif Present: 3,185,586  (2.02% / 2.89%)
 3' Bias (Long Range): 90% - 10%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 39,970,247  (25.32% / 36.23%)
Intra-chromosomal: 44,480,337  (28.18% / 40.32%)
Short Range (<20Kb): 7,144,165  (4.53% / 6.48%)
Long Range (>20Kb): 37,335,964  (23.65% / 33.84%)