Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 16 threads; openjdk version "17.0.8-internal" 2023-07-18; /data/nyt/MMO/Tools/juicer1.6_compact/scripts/juicer.sh -g hg19 -d /data/nyt/Projects/Juicer-Out/2023-12-4-Sirius/4c_plasmid/Pct_2-2 -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 16                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
Sequenced Read Pairs:  989,511
 Normal Paired: 584,919 (59.11%)
 Chimeric Paired: 130,471 (13.19%)
 Chimeric Ambiguous: 264,822 (26.76%)
 Unmapped: 9,299 (0.94%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 715,390 (72.30%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2023-12-16T14:32:15,185]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 556,038 (56.19%)
PCR Duplicates: 150,967 (15.26%)
Optical Duplicates: 8,385 (0.85%)
Library Complexity Estimate: 1,410,342
Intra-fragment Reads: 219,708 (22.20% / 39.51%)
Below MAPQ Threshold: 61,873 (6.25% / 11.13%)
Hi-C Contacts: 274,457 (27.74% / 49.36%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 66% - 34%
 Pair Type intra chrom %(L-I-O-R): 4% - 89% - 4% - 4%
 Pair Type inter chrom %(L-I-O-R): 17% - 33% - 17% - 33%
 DE: 61%
 Cis/all (FF and RR orient): 26.9%
Inter-chromosomal: 78,680  (7.95% / 14.15%)
Intra-chromosomal: 195,777  (19.79% / 35.21%)
Short Range (<20,000bp): 173,571  (17.54% / 31.22%)
Long Range (>20,000bp): 22,206  (2.24% / 3.99%)