Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 20 threads; openjdk version "1.8.0_152-release"; /home/aapopov/tool/juicer1.6_compact-main/scripts/juicer.sh -g GalGal_T2T -d /home/aapopov/Projects/ChickenOocyt -s HindIII -y /home/aapopov/Projects/ChickenOocyt/genome/GalGal_T2T_HindIII.txt -p /home/aapopov/Projects/ChickenOocyt/genome/GalGal_T2T.chrom.sizes -z /home/aapopov/Projects/ChickenOocyt/genome/GalGal_T2T.fa -D /home/aapopov/tool/juicer1.6_compact-main -t 20                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
Sequenced Read Pairs:  276,677,613
 Normal Paired: 223,140,465 (80.65%)
 Chimeric Paired: 44,852,117 (16.21%)
 Chimeric Ambiguous: 2,568,178 (0.93%)
 Unmapped: 6,116,853 (2.21%)
 Ligation Motif Present: 89,631,283 (32.40%)
Alignable (Normal+Chimeric Paired): 267,992,582 (96.86%)
Unique Reads: 207,983,127 (75.17%)
PCR Duplicates: 60,009,455 (21.69%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 505,271,678
Intra-fragment Reads: 54,323,074 (19.63% / 26.12%)
Below MAPQ Threshold: 18,224,090 (6.59% / 8.76%)
Hi-C Contacts: 135,435,963 (48.95% / 65.12%)
 Ligation Motif Present: 62,554,314  (22.61% / 30.08%)
 3' Bias (Long Range): 90% - 10%
 Pair Type intra chrom %(L-I-O-R): 17% - 50% - 16% - 17%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 30%
 Cis/all (FF and RR orient): 86.7%
Inter-chromosomal: 12,720,891  (4.60% / 6.12%)
Intra-chromosomal: 122,715,072  (44.35% / 59.00%)
Short Range (<20,000bp): 63,588,497  (22.98% / 30.57%)
Long Range (>20,000bp): 59,126,575  (21.37% / 28.43%)