Experiment description: Juicer version 1.5.6; BWA 0.7.17-r1198-dirty; 16 threads; openjdk version "11.0.1" 2018-10-16 LTS; /home/numiab/distributive/juicer-master/CPU/juicer.sh -t 16 -d /home/numiab/temporary/fastq/miAr/hic -p /home/numiab/mydata/genome/miAr/miAr.fa.scf.sizes -y /home/numiab/mydata/genome/miAr/miAr.DpnII.juicer.txt -n miAr -l 2500000,1000000,500000,250000,100000,50000,25000,10000,5000 -z /home/numiab/mydata/genome/miAr/miAr.fa -o /home/numiab/temporary/hic/miAr -D /home/numiab/distributive/juicer-master/CPU                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
Sequenced Read Pairs:  85,307
 Normal Paired: 55,754 (65.36%)
 Chimeric Paired: 20,683 (24.25%)
 Chimeric Ambiguous: 6,912 (8.10%)
 Unmapped: 1,958 (2.30%)
 Ligation Motif Present: 67,778 (79.45%)
Alignable (Normal+Chimeric Paired): 76,437 (89.60%)
Unique Reads: 69,739 (81.75%)
PCR Duplicates: 6,411 (7.52%)
Optical Duplicates: 287 (0.34%)
Library Complexity Estimate: 426,499
Intra-fragment Reads: 5,158 (6.05% / 7.40%)
Below MAPQ Threshold: 13,327 (15.62% / 19.11%)
Hi-C Contacts: 56,412 (66.13% / 80.89%)
 Ligation Motif Present: 39,416  (46.20% / 56.52%)
 3' Bias (Long Range): 79% - 21%
 Pair Type intra chrom %(L-I-O-R): 7% - 78% - 7% - 7%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 54%
 Cis/all (FF and RR orient): 48.0%
Inter-chromosomal: 13,389  (15.70% / 19.20%)
Intra-chromosomal: 43,023  (50.43% / 61.69%)
Short Range (<20,000bp): 33,644  (39.44% / 48.24%)
Long Range (>20,000bp): 9,379  (10.99% / 13.45%)