Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 20 threads; openjdk version "17.0.8-internal" 2023-07-18; /data/nyt/MMO/Tools/juicer1.6_compact/scripts/juicer.sh -g T2T -d /data/nyt/Projects/Juicer-Out/2024-06-18_MGNC/FFPE/LpS3 -s none -p /data/nyt/Databases/T2T-CHM13v2.0/hgT2T.chromsizes -z /data/nyt/Databases/T2T-CHM13v2.0/hgT2T.fa -D /data/nyt/MMO/Tools/juicer1.6_compact -t 20                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
Sequenced Read Pairs:  668,749
 Normal Paired: 408,189 (61.04%)
 Chimeric Paired: 202,035 (30.21%)
 Chimeric Ambiguous: 45,721 (6.84%)
 Unmapped: 12,804 (1.91%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 610,224 (91.25%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-06-20T16:15:53,289]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 603,668 (90.27%)
PCR Duplicates: 6,456 (0.97%)
Optical Duplicates: 100 (0.01%)
Library Complexity Estimate: 28,626,135
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 47,714 (7.13% / 7.90%)
Hi-C Contacts: 555,954 (83.13% / 92.10%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 7% - 78% - 7% - 7%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 64%
 Cis/all (FF and RR orient): 73.1%
Inter-chromosomal: 53,890  (8.06% / 8.93%)
Intra-chromosomal: 502,064  (75.08% / 83.17%)
Short Range (<20,000bp): 414,963  (62.05% / 68.74%)
Long Range (>20,000bp): 87,101  (13.02% / 14.43%)