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: 286,356 (3.56% / 48.31%)
Hi-C Contacts: 306,351 (3.81% / 51.69%)
 Ligation Motif Present: 135,467  (1.68% / 22.86%)
 3' Bias (Long Range): 61% - 39%
 Pair Type intra chrom %(L-I-O-R): 11% - 68% - 11% - 11%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 51%
 Cis/all (FF and RR orient): 77.8%
Inter-chromosomal: 33,273  (0.41% / 5.61%)
Intra-chromosomal: 273,078  (3.40% / 46.07%)
Short Range (<20,000bp): 195,501  (2.43% / 32.98%)
Long Range (>20,000bp): 77,577  (0.96% / 13.09%)