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/Lam1_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 10                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
Sequenced Read Pairs:  11,353,701
 Normal Paired: 8,071,801 (71.09%)
 Chimeric Paired: 473,328 (4.17%)
 Chimeric Ambiguous: 98,881 (0.87%)
 Unmapped: 2,709,691 (23.87%)
 Ligation Motif Present: 759,020 (6.69%)
Alignable (Normal+Chimeric Paired): 8,545,129 (75.26%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-04-26T16:22:52,823]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 3,223,545 (28.39%)
PCR Duplicates: 0 (0.00%)
Optical Duplicates: 5,321,584 (46.87%)
Library Complexity Estimate: 0
Intra-fragment Reads: 301,900 (2.66% / 9.37%)
Below MAPQ Threshold: 436,105 (3.84% / 13.53%)
Hi-C Contacts: 2,787,440 (24.55% / 86.47%)
 Ligation Motif Present: 270,376  (2.38% / 8.39%)
 3' Bias (Long Range): 38% - 62%
 Pair Type intra chrom %(L-I-O-R): 3% - 91% - 3% - 3%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 86%
 Cis/all (FF and RR orient): 84.4%
Inter-chromosomal: 60,886  (0.54% / 1.89%)
Intra-chromosomal: 2,726,554  (24.01% / 84.58%)
Short Range (<20,000bp): 2,523,875  (22.23% / 78.30%)
Long Range (>20,000bp): 202,679  (1.79% / 6.29%)