Experiment description: Juicer version 1.5.6; BWA 0.7.17-r1188; 4 threads; /home/mirmir/work/progs/juicer-master/CPU/juicer.sh: line 338: java: command not found; /home/mirmir/work/progs/juicer-master/CPU/juicer.sh -t 4 -d /home/mirmir/work/fastq/miAr/ -p /sf/storage/gmo/mirmir/data/miAr/miAr.fa.scf.sizes -q 30 -y /sf/storage/gmo/mirmir/data/miAr/miAr.fa.DpnII.juicer.txt -n miAr -l 2500000,1000000,500000,250000,100000,50000,25000,10000 -z /sf/storage/gmo/mirmir/data/miAr/miAr.fa -o /sf/storage/gmo/mirmir/out/miAr -D /home/mirmir/work/progs/juicer-master/CPU                                                                                                                                                                                                                                                                                                                                                                                                                                                     
Sequenced Read Pairs:  10,648
 Normal Paired: 5,623 (52.81%)
 Chimeric Paired: 3,700 (34.75%)
 Chimeric Ambiguous: 1,242 (11.66%)
 Unmapped: 83 (0.78%)
 Ligation Motif Present: 8,889 (83.48%)
Alignable (Normal+Chimeric Paired): 9,323 (87.56%)
Unique Reads: 9,271 (87.07%)
PCR Duplicates: 14 (0.13%)
Optical Duplicates: 38 (0.36%)
Library Complexity Estimate: 3,075,876
Intra-fragment Reads: 873 (8.20% / 9.42%)
Below MAPQ Threshold: 1,026 (9.64% / 11.07%)
Hi-C Contacts: 8,245 (77.43% / 88.93%)
 Ligation Motif Present: 6,619  (62.16% / 71.39%)
 3' Bias (Long Range): 82% - 18%
 Pair Type intra chrom %(L-I-O-R): 5% - 83% - 6% - 5%
 Pair Type inter chrom %(L-I-O-R): 25% - 24% - 24% - 26%
 DE: 60%
 Cis/all (FF and RR orient): 41.5%
Inter-chromosomal: 1,898  (17.82% / 20.47%)
Intra-chromosomal: 6,347  (59.61% / 68.46%)
Short Range (<20,000bp): 5,248  (49.29% / 56.61%)
Long Range (>20,000bp): 1,099  (10.32% / 11.85%)