Experiment description: Juicer version 1.6; BWA 0.7.18-r1243-dirty; 14 threads; openjdk version "17.0.8-internal" 2023-07-18; /data/amivanov/Tools/juicer1.6_compact-main/scripts/juicer.sh -g T2T -d /data/amivanov/Projects/Embryos/2025-04-24-BGI/B/Shur2_K -s DpnII -y /data/amivanov/Databases/T2T-CHM13v2.0/juicer.rs/T2T-CHM13v2.0_DpnII.txt -p /data/amivanov/Databases/T2T-CHM13v2.0/hgT2T.chromsizes -z /data/amivanov/Databases/T2T-CHM13v2.0/hgT2T.fa -D /data/amivanov/Tools/juicer1.6_compact-main -t 14                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
Sequenced Read Pairs:  6,527,976
 Normal Paired: 3,317,491 (50.82%)
 Chimeric Paired: 2,433,422 (37.28%)
 Chimeric Ambiguous: 489,554 (7.50%)
 Unmapped: 287,509 (4.40%)
 Ligation Motif Present: 4,268,085 (65.38%)
Alignable (Normal+Chimeric Paired): 5,750,913 (88.10%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-05-17T17:29:27,799]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 1,650,442 (25.28%)
PCR Duplicates: 4,100,471 (62.81%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 1,709,593
Intra-fragment Reads: 125,059 (1.92% / 7.58%)
Below MAPQ Threshold: 377,019 (5.78% / 22.84%)
Hi-C Contacts: 1,273,423 (19.51% / 77.16%)
 Ligation Motif Present: 768,160  (11.77% / 46.54%)
 3' Bias (Long Range): 66% - 34%
 Pair Type intra chrom %(L-I-O-R): 13% - 61% - 13% - 13%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 41%
 Cis/all (FF and RR orient): 73.3%
Inter-chromosomal: 200,675  (3.07% / 12.16%)
Intra-chromosomal: 1,072,748  (16.43% / 65.00%)
Short Range (<20,000bp): 712,882  (10.92% / 43.19%)
Long Range (>20,000bp): 359,866  (5.51% / 21.80%)