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/Darevska/DU1 -p /sf/storage/gmo/mirmir/data/Darevska/daUn.hap1.fa.scf.sizes -q 30 -y /sf/storage/gmo/mirmir/data/Darevska/daUn.hap1.fa.DpnII.juicer.txt -n daUn.hap1 -l 2500000,1000000,500000,250000,100000,50000,25000,10000 -z /sf/storage/gmo/mirmir/data/Darevska/daUn.hap1.fa -o /sf/storage/gmo/mirmir/out/Darevska/DU1 -D /home/mirmir/work/progs/juicer-master/CPU                                                                                                                                                                                                                                                                                                                                                                                                      
Sequenced Read Pairs:  572,282,981
 Normal Paired: 376,519,247 (65.79%)
 Chimeric Paired: 30,287,975 (5.29%)
 Chimeric Ambiguous: 13,573,035 (2.37%)
 Unmapped: 151,902,724 (26.54%)
 Ligation Motif Present: 46,464,528 (8.12%)
Alignable (Normal+Chimeric Paired): 406,807,222 (71.08%)
Unique Reads: 26,842,343 (4.69%)
PCR Duplicates: 379,696,799 (66.35%)
Optical Duplicates: 268,080 (0.05%)
Library Complexity Estimate: 26,842,350
Intra-fragment Reads: 2,507,475 (0.44% / 9.34%)
Below MAPQ Threshold: 21,002,299 (3.67% / 78.24%)
Hi-C Contacts: 5,840,044 (1.02% / 21.76%)
 Ligation Motif Present: 361,605  (0.06% / 1.35%)
 3' Bias (Long Range): 50% - 50%
 Pair Type intra chrom %(L-I-O-R): 3% - 88% - 5% - 3%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 76%
 Cis/all (FF and RR orient): 50.5%
Inter-chromosomal: 686,293  (0.12% / 2.56%)
Intra-chromosomal: 5,153,751  (0.90% / 19.20%)
Short Range (<20,000bp): 4,730,970  (0.83% / 17.63%)
Long Range (>20,000bp): 422,781  (0.07% / 1.58%)