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-1-fixed22 -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:  549,477
 Normal Paired: 304,013 (55.33%)
 Chimeric Paired: 163,603 (29.77%)
 Chimeric Ambiguous: 66,948 (12.18%)
 Unmapped: 14,913 (2.71%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 467,616 (85.10%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-09-23T22:21:43,954]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 461,862 (84.05%)
PCR Duplicates: 5,685 (1.03%)
Optical Duplicates: 69 (0.01%)
Library Complexity Estimate: 19,069,883
Intra-fragment Reads: 61,814 (11.25% / 13.38%)
Below MAPQ Threshold: 78,076 (14.21% / 16.90%)
Hi-C Contacts: 383,786 (69.85% / 83.10%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 68% - 32%
 Pair Type intra chrom %(L-I-O-R): 6% - 81% - 6% - 6%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 64%
 Cis/all (FF and RR orient): 61.2%
Inter-chromosomal: 53,481  (9.73% / 11.58%)
Intra-chromosomal: 330,305  (60.11% / 71.52%)
Short Range (<20,000bp): 273,075  (49.70% / 59.12%)
Long Range (>20,000bp): 57,230  (10.42% / 12.39%)