Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 10 threads; openjdk version "17.0.14" 2025-01-21; juicer.sh -g T2T -d /storage3/artem/MGNC_Feb2025/mCherry-sR -s DpnII -p /storage3/artem/Genomes/T2T-CHM13v2.0/hgT2T.chromsizes -y /storage3/artem/Genomes/T2T-CHM13v2.0/juicer.rs/T2T-CHM13v2.0_DpnII.txt -z /storage3/artem/Genomes/T2T-CHM13v2.0/hgT2T.fa -t 10 -D /storage2/dreamworld/Tools/juicer1.6_compact/                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
Sequenced Read Pairs:  1,634,664
 Normal Paired: 587,782 (35.96%)
 Chimeric Paired: 610,464 (37.34%)
 Chimeric Ambiguous: 405,909 (24.83%)
 Unmapped: 30,509 (1.87%)
 Ligation Motif Present: 474,292 (29.01%)
Alignable (Normal+Chimeric Paired): 1,198,246 (73.30%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-02-19T02:52:28,118]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 1,180,407 (72.21%)
PCR Duplicates: 3,574 (0.22%)
Optical Duplicates: 14,265 (0.87%)
Library Complexity Estimate: 195,717,481
Intra-fragment Reads: 265,597 (16.25% / 22.50%)
Below MAPQ Threshold: 442,832 (27.09% / 37.52%)
Hi-C Contacts: 737,575 (45.12% / 62.48%)
 Ligation Motif Present: 194,814  (11.92% / 16.50%)
 3' Bias (Long Range): 60% - 40%
 Pair Type intra chrom %(L-I-O-R): 8% - 77% - 7% - 8%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 64%
 Cis/all (FF and RR orient): 80.1%
Inter-chromosomal: 52,696  (3.22% / 4.46%)
Intra-chromosomal: 684,879  (41.90% / 58.02%)
Short Range (<20,000bp): 532,322  (32.56% / 45.10%)
Long Range (>20,000bp): 152,557  (9.33% / 12.92%)