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/ALK8 -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:  611,209
 Normal Paired: 379,005 (62.01%)
 Chimeric Paired: 175,266 (28.68%)
 Chimeric Ambiguous: 48,251 (7.89%)
 Unmapped: 8,687 (1.42%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 554,271 (90.68%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-06-20T16:08:49,731]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 547,992 (89.66%)
PCR Duplicates: 6,136 (1.00%)
Optical Duplicates: 143 (0.02%)
Library Complexity Estimate: 24,835,958
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 74,578 (12.20% / 13.61%)
Hi-C Contacts: 473,414 (77.46% / 86.39%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 7% - 79% - 7% - 7%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 67%
 Cis/all (FF and RR orient): 80.1%
Inter-chromosomal: 31,167  (5.10% / 5.69%)
Intra-chromosomal: 442,247  (72.36% / 80.70%)
Short Range (<20,000bp): 368,510  (60.29% / 67.25%)
Long Range (>20,000bp): 73,737  (12.06% / 13.46%)