Experiment description: Juicer version 1.5.6; BWA 0.7.17-r1188; 20 threads; java version "1.8.0_131"; scripts/juicer.sh -t 20 -D /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-03-07-NextSeq-run/juicer-L530-Haloferax_45C_Hi-C-all_reads -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-03-07-NextSeq-run/juicer-L530-Haloferax_45C_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:  40,393,847
 Normal Paired: 29,525,933 (73.10%)
 Chimeric Paired: 1,983,867 (4.91%)
 Chimeric Ambiguous: 382,674 (0.95%)
 Unmapped: 8,501,373 (21.05%)
 Ligation Motif Present: 16,367,343 (40.52%)
Alignable (Normal+Chimeric Paired): 31,509,800 (78.01%)
Unique Reads: 20,524,196 (50.81%)
PCR Duplicates: 10,975,791 (27.17%)
Optical Duplicates: 9,813 (0.02%)
Library Complexity Estimate: 33,942,978
Intra-fragment Reads: 2,064,333 (5.11% / 10.06%)
Below MAPQ Threshold: 3,857,910 (9.55% / 18.80%)
Hi-C Contacts: 14,601,953 (36.15% / 71.15%)
 Ligation Motif Present: 3,122,064  (7.73% / 15.21%)
 3' Bias (Long Range): 92% - 8%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 8,388,448  (20.77% / 40.87%)
Intra-chromosomal: 6,213,505  (15.38% / 30.27%)
Short Range (<20Kb): 1,357,343  (3.36% / 6.61%)
Long Range (>20Kb): 4,856,103  (12.02% / 23.66%)