Experiment description: Juicer version 1.6; BWA 0.7.18-r1243-dirty; 14 threads; openjdk version "17.0.11-internal" 2024-04-16; /data/amivanov/Tools/juicer1.6_compact-main/scripts/juicer.sh -g T2T -d /data/amivanov/Projects/Embryos/2025-04-25_Orlov/Kur3_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:  19,101,958
 Normal Paired: 11,818,080 (61.87%)
 Chimeric Paired: 1,826,046 (9.56%)
 Chimeric Ambiguous: 416,030 (2.18%)
 Unmapped: 5,041,802 (26.39%)
 Ligation Motif Present: 2,561,930 (13.41%)
Alignable (Normal+Chimeric Paired): 13,644,126 (71.43%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-05-14T20:09:13,811]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 2,057,098 (10.77%)
PCR Duplicates: 11,572,497 (60.58%)
Optical Duplicates: 14,531 (0.08%)
Library Complexity Estimate: 2,059,853
Intra-fragment Reads: 303,060 (1.59% / 14.73%)
Below MAPQ Threshold: 581,623 (3.04% / 28.27%)
Hi-C Contacts: 1,475,475 (7.72% / 71.73%)
 Ligation Motif Present: 105,185  (0.55% / 5.11%)
 3' Bias (Long Range): 39% - 61%
 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: 90%
 Cis/all (FF and RR orient): 44.8%
Inter-chromosomal: 78,778  (0.41% / 3.83%)
Intra-chromosomal: 1,396,697  (7.31% / 67.90%)
Short Range (<20,000bp): 1,357,660  (7.11% / 66.00%)
Long Range (>20,000bp): 39,037  (0.20% / 1.90%)