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: 304,312 (4.66% / 18.44%)
Hi-C Contacts: 1,346,130 (20.62% / 81.56%)
 Ligation Motif Present: 823,213  (12.61% / 49.88%)
 3' Bias (Long Range): 67% - 33%
 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: 40%
 Cis/all (FF and RR orient): 72.6%
Inter-chromosomal: 222,192  (3.40% / 13.46%)
Intra-chromosomal: 1,123,938  (17.22% / 68.10%)
Short Range (<20,000bp): 738,775  (11.32% / 44.76%)
Long Range (>20,000bp): 385,163  (5.90% / 23.34%)