Experiment description: Juicer version 1.6; BWA 0.7.18-r1243-dirty; 10 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/A/6069_plus -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 10                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
Sequenced Read Pairs:  16,055,725
 Normal Paired: 10,159,732 (63.28%)
 Chimeric Paired: 3,688,502 (22.97%)
 Chimeric Ambiguous: 2,066,254 (12.87%)
 Unmapped: 141,237 (0.88%)
 Ligation Motif Present: 107,101 (0.67%)
Alignable (Normal+Chimeric Paired): 13,848,234 (86.25%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-04-26T15:58:11,693]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 5,137,453 (32.00%)
PCR Duplicates: 0 (0.00%)
Optical Duplicates: 8,710,781 (54.25%)
Library Complexity Estimate: 0
Intra-fragment Reads: 2,216,171 (13.80% / 43.14%)
Below MAPQ Threshold: 1,113,411 (6.93% / 21.67%)
Hi-C Contacts: 4,024,042 (25.06% / 78.33%)
 Ligation Motif Present: 20,625  (0.13% / 0.40%)
 3' Bias (Long Range): 47% - 53%
 Pair Type intra chrom %(L-I-O-R): 1% - 96% - 2% - 1%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 73%
 Cis/all (FF and RR orient): 13.9%
Inter-chromosomal: 924,761  (5.76% / 18.00%)
Intra-chromosomal: 3,099,281  (19.30% / 60.33%)
Short Range (<20,000bp): 3,031,270  (18.88% / 59.00%)
Long Range (>20,000bp): 68,011  (0.42% / 1.32%)