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/Mal3_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:  4,456,179
 Normal Paired: 2,313,919 (51.93%)
 Chimeric Paired: 1,663,680 (37.33%)
 Chimeric Ambiguous: 356,839 (8.01%)
 Unmapped: 121,741 (2.73%)
 Ligation Motif Present: 2,956,696 (66.35%)
Alignable (Normal+Chimeric Paired): 3,977,599 (89.26%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-04-26T16:35:10,004]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 802,973 (18.02%)
PCR Duplicates: 0 (0.00%)
Optical Duplicates: 3,174,626 (71.24%)
Library Complexity Estimate: 0
Intra-fragment Reads: 42,183 (0.95% / 5.25%)
Below MAPQ Threshold: 201,403 (4.52% / 25.08%)
Hi-C Contacts: 601,570 (13.50% / 74.92%)
 Ligation Motif Present: 357,765  (8.03% / 44.56%)
 3' Bias (Long Range): 66% - 34%
 Pair Type intra chrom %(L-I-O-R): 13% - 60% - 14% - 13%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 39%
 Cis/all (FF and RR orient): 74.8%
Inter-chromosomal: 91,956  (2.06% / 11.45%)
Intra-chromosomal: 509,614  (11.44% / 63.47%)
Short Range (<20,000bp): 318,454  (7.15% / 39.66%)
Long Range (>20,000bp): 191,160  (4.29% / 23.81%)