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/OPO227 -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:  797,470
 Normal Paired: 454,643 (57.01%)
 Chimeric Paired: 232,142 (29.11%)
 Chimeric Ambiguous: 88,402 (11.09%)
 Unmapped: 22,283 (2.79%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 686,785 (86.12%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-06-20T16:18:54,618]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 679,604 (85.22%)
PCR Duplicates: 7,068 (0.89%)
Optical Duplicates: 113 (0.01%)
Library Complexity Estimate: 33,126,574
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 64,304 (8.06% / 9.46%)
Hi-C Contacts: 615,300 (77.16% / 90.54%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 7% - 80% - 7% - 7%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 64%
 Cis/all (FF and RR orient): 65.9%
Inter-chromosomal: 75,430  (9.46% / 11.10%)
Intra-chromosomal: 539,870  (67.70% / 79.44%)
Short Range (<20,000bp): 454,636  (57.01% / 66.90%)
Long Range (>20,000bp): 85,234  (10.69% / 12.54%)