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/2019-03-03-NextSeq-run/juicer-L530-Haloferax_45C_Hi-C -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-03-03-NextSeq-run/juicer-L530-Haloferax_45C_Hi-C -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:  8,533,052
 Normal Paired: 6,003,338 (70.35%)
 Chimeric Paired: 1,983,357 (23.24%)
 Chimeric Ambiguous: 383,180 (4.49%)
 Unmapped: 163,177 (1.91%)
 Ligation Motif Present: 6,666,783 (78.13%)
Alignable (Normal+Chimeric Paired): 7,986,695 (93.60%)
Unique Reads: 4,883,430 (57.23%)
PCR Duplicates: 3,097,550 (36.30%)
Optical Duplicates: 5,715 (0.07%)
Library Complexity Estimate: 7,400,621
Intra-fragment Reads: 719,393 (8.43% / 14.73%)
Below MAPQ Threshold: 752,314 (8.82% / 15.41%)
Hi-C Contacts: 3,411,723 (39.98% / 69.86%)
 Ligation Motif Present: 2,233,623  (26.18% / 45.74%)
 3' Bias (Long Range): 93% - 7%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 1,722,452  (20.19% / 35.27%)
Intra-chromosomal: 1,689,271  (19.80% / 34.59%)
Short Range (<20Kb): 676,000  (7.92% / 13.84%)
Long Range (>20Kb): 1,013,265  (11.87% / 20.75%)