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/Sach1_e -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:  8,039,959
 Normal Paired: 4,277,332 (53.20%)
 Chimeric Paired: 2,668,336 (33.19%)
 Chimeric Ambiguous: 606,063 (7.54%)
 Unmapped: 488,228 (6.07%)
 Ligation Motif Present: 4,122,670 (51.28%)
Alignable (Normal+Chimeric Paired): 6,945,668 (86.39%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-05-14T20:39:30,377]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 592,707 (7.37%)
PCR Duplicates: 6,348,395 (78.96%)
Optical Duplicates: 4,566 (0.06%)
Library Complexity Estimate: 592,711
Intra-fragment Reads: 81,946 (1.02% / 13.83%)
Below MAPQ Threshold: 263,585 (3.28% / 44.47%)
Hi-C Contacts: 329,122 (4.09% / 55.53%)
 Ligation Motif Present: 148,927  (1.85% / 25.13%)
 3' Bias (Long Range): 62% - 38%
 Pair Type intra chrom %(L-I-O-R): 11% - 66% - 12% - 11%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 49%
 Cis/all (FF and RR orient): 75.4%
Inter-chromosomal: 41,460  (0.52% / 7.00%)
Intra-chromosomal: 287,662  (3.58% / 48.53%)
Short Range (<20,000bp): 203,237  (2.53% / 34.29%)
Long Range (>20,000bp): 84,425  (1.05% / 14.24%)