Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 18 threads; openjdk version "17.0.8-internal" 2023-07-18; /data/nyt/MMO/Tools/juicer1.6_compact/scripts/juicer.sh -g hg38_mm10 -d /data/nyt/Projects/Juicer-Out/2024-09-11_MGNC/Sasha_Yan/Ph-MEF-3-fixed1 -s NlaIII -y /data/nyt/Databases/4c_plasmid/hg38_mm10/juicer.rs/hg38_mm10_num3CMV_NP_NlaIII.txt -p /data/nyt/Databases/4c_plasmid/hg38_mm10/hg38_mm10_num3CMV_NP.fasta.chromsizes -z /data/nyt/Databases/4c_plasmid/hg38_mm10/hg38_mm10_num3CMV_NP.fasta -D /data/nyt/MMO/Tools/juicer1.6_compact -t 18                                                                                                                                                                                                                                                                                                                                                                                                                                                         
Sequenced Read Pairs:  1,030,468
 Normal Paired: 478,239 (46.41%)
 Chimeric Paired: 370,629 (35.97%)
 Chimeric Ambiguous: 155,519 (15.09%)
 Unmapped: 26,081 (2.53%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 848,868 (82.38%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-09-23T22:35:05,288]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 833,005 (80.84%)
PCR Duplicates: 15,753 (1.53%)
Optical Duplicates: 110 (0.01%)
Library Complexity Estimate: 22,581,369
Intra-fragment Reads: 62,370 (6.05% / 7.49%)
Below MAPQ Threshold: 100,907 (9.79% / 12.11%)
Hi-C Contacts: 732,098 (71.05% / 87.89%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 72% - 28%
 Pair Type intra chrom %(L-I-O-R): 9% - 73% - 9% - 9%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 53%
 Cis/all (FF and RR orient): 63.2%
Inter-chromosomal: 127,094  (12.33% / 15.26%)
Intra-chromosomal: 605,004  (58.71% / 72.63%)
Short Range (<20,000bp): 443,740  (43.06% / 53.27%)
Long Range (>20,000bp): 161,264  (15.65% / 19.36%)