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: 16,717,957 (6.04% / 8.04%)
Hi-C Contacts: 136,942,096 (49.50% / 65.84%)
 Ligation Motif Present: 62,942,760  (22.75% / 30.26%)
 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: 29%
 Cis/all (FF and RR orient): 86.2%
Inter-chromosomal: 13,352,779  (4.83% / 6.42%)
Intra-chromosomal: 123,589,317  (44.67% / 59.42%)
Short Range (<20,000bp): 63,918,354  (23.10% / 30.73%)
Long Range (>20,000bp): 59,670,963  (21.57% / 28.69%)