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/MGNC_2025-04-26/Ask_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:  3,368,772
 Normal Paired: 2,136,822 (63.43%)
 Chimeric Paired: 807,150 (23.96%)
 Chimeric Ambiguous: 208,587 (6.19%)
 Unmapped: 216,213 (6.42%)
 Ligation Motif Present: 1,219,317 (36.19%)
Alignable (Normal+Chimeric Paired): 2,943,972 (87.39%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-05-17T14:35:06,051]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 1,491,279 (44.27%)
PCR Duplicates: 122,794 (3.65%)
Optical Duplicates: 1,329,899 (39.48%)
Library Complexity Estimate: 10,063,001
Intra-fragment Reads: 241,695 (7.17% / 16.21%)
Below MAPQ Threshold: 197,280 (5.86% / 13.23%)
Hi-C Contacts: 1,293,999 (38.41% / 86.77%)
 Ligation Motif Present: 478,532  (14.20% / 32.09%)
 3' Bias (Long Range): 61% - 39%
 Pair Type intra chrom %(L-I-O-R): 7% - 78% - 8% - 7%
 Pair Type inter chrom %(L-I-O-R): 24% - 25% - 25% - 26%
 DE: 64%
 Cis/all (FF and RR orient): 75.3%
Inter-chromosomal: 115,856  (3.44% / 7.77%)
Intra-chromosomal: 1,178,143  (34.97% / 79.00%)
Short Range (<20,000bp): 898,235  (26.66% / 60.23%)
Long Range (>20,000bp): 279,908  (8.31% / 18.77%)