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_1-2 -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:  1,003,210
 Normal Paired: 592,387 (59.05%)
 Chimeric Paired: 144,148 (14.37%)
 Chimeric Ambiguous: 258,123 (25.73%)
 Unmapped: 8,552 (0.85%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 736,535 (73.42%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2023-12-16T14:26:35,301]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 599,297 (59.74%)
PCR Duplicates: 130,213 (12.98%)
Optical Duplicates: 7,025 (0.70%)
Library Complexity Estimate: 1,792,329
Intra-fragment Reads: 242,416 (24.16% / 40.45%)
Below MAPQ Threshold: 78,434 (7.82% / 13.09%)
Hi-C Contacts: 278,447 (27.76% / 46.46%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 68% - 32%
 Pair Type intra chrom %(L-I-O-R): 4% - 89% - 4% - 4%
 Pair Type inter chrom %(L-I-O-R): 18% - 32% - 18% - 32%
 DE: 60%
 Cis/all (FF and RR orient): 26.5%
Inter-chromosomal: 81,891  (8.16% / 13.66%)
Intra-chromosomal: 196,556  (19.59% / 32.80%)
Short Range (<20,000bp): 173,842  (17.33% / 29.01%)
Long Range (>20,000bp): 22,714  (2.26% / 3.79%)