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/Bag3_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:  6,058,072
 Normal Paired: 2,587,949 (42.72%)
 Chimeric Paired: 2,220,421 (36.65%)
 Chimeric Ambiguous: 482,596 (7.97%)
 Unmapped: 767,106 (12.66%)
 Ligation Motif Present: 4,090,857 (67.53%)
Alignable (Normal+Chimeric Paired): 4,808,370 (79.37%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-05-14T19:45:12,239]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 632,134 (10.43%)
PCR Duplicates: 4,171,642 (68.86%)
Optical Duplicates: 4,594 (0.08%)
Library Complexity Estimate: 632,451
Intra-fragment Reads: 23,356 (0.39% / 3.69%)
Below MAPQ Threshold: 210,980 (3.48% / 33.38%)
Hi-C Contacts: 421,154 (6.95% / 66.62%)
 Ligation Motif Present: 285,092  (4.71% / 45.10%)
 3' Bias (Long Range): 69% - 31%
 Pair Type intra chrom %(L-I-O-R): 15% - 54% - 15% - 15%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 35%
 Cis/all (FF and RR orient): 83.3%
Inter-chromosomal: 45,616  (0.75% / 7.22%)
Intra-chromosomal: 375,538  (6.20% / 59.41%)
Short Range (<20,000bp): 205,821  (3.40% / 32.56%)
Long Range (>20,000bp): 169,717  (2.80% / 26.85%)