Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 10 threads; openjdk version "17.0.8-internal" 2023-07-18; /data/nyt/MMO/Tools/juicer1.6_compact/scripts/juicer.sh -g T2T -d /data/nyt/Projects/Juicer-Out/2024-03-04_ENC/Hepatocytes/7007_treat -s DpnII -y /data/nyt/Databases/T2T-CHM13v2.0/juicer.rs/T2T-CHM13v2.0_DpnII.txt -p /data/nyt/Databases/T2T-CHM13v2.0/hgT2T.chromsizes -z /data/nyt/Databases/T2T-CHM13v2.0/hgT2T.fa -D /data/nyt/MMO/Tools/juicer1.6_compact -t 10                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
Sequenced Read Pairs:  2,771,426
 Normal Paired: 1,753,128 (63.26%)
 Chimeric Paired: 738,438 (26.64%)
 Chimeric Ambiguous: 260,731 (9.41%)
 Unmapped: 19,129 (0.69%)
 Ligation Motif Present: 1,896,137 (68.42%)
Alignable (Normal+Chimeric Paired): 2,491,566 (89.90%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-03-26T16:39:00,031]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 1,926,796 (69.52%)
PCR Duplicates: 543,371 (19.61%)
Optical Duplicates: 21,399 (0.77%)
Library Complexity Estimate: 4,756,955
Intra-fragment Reads: 164,630 (5.94% / 8.54%)
Below MAPQ Threshold: 331,173 (11.95% / 17.19%)
Hi-C Contacts: 1,595,623 (57.57% / 82.81%)
 Ligation Motif Present: 1,063,534  (38.37% / 55.20%)
 3' Bias (Long Range): 76% - 24%
 Pair Type intra chrom %(L-I-O-R): 9% - 72% - 9% - 9%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 41%
 Cis/all (FF and RR orient): 39.7%
Inter-chromosomal: 568,156  (20.50% / 29.49%)
Intra-chromosomal: 1,027,467  (37.07% / 53.33%)
Short Range (<20,000bp): 716,394  (25.85% / 37.18%)
Long Range (>20,000bp): 311,073  (11.22% / 16.14%)