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/2024-04-25_MGNC/Sasha_Yan_new/Ph-MEF-1-Hi-C-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 18                                                                                                                                                                                                                                                                                                                                                                                                                                                     
Sequenced Read Pairs:  752,730
 Normal Paired: 376,139 (49.97%)
 Chimeric Paired: 279,867 (37.18%)
 Chimeric Ambiguous: 82,637 (10.98%)
 Unmapped: 14,087 (1.87%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 656,006 (87.15%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-05-05T05:14:29,144]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 641,677 (85.25%)
PCR Duplicates: 14,201 (1.89%)
Optical Duplicates: 128 (0.02%)
Library Complexity Estimate: 14,926,549
Intra-fragment Reads: 55,834 (7.42% / 8.70%)
Below MAPQ Threshold: 112,748 (14.98% / 17.57%)
Hi-C Contacts: 528,929 (70.27% / 82.43%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 70% - 30%
 Pair Type intra chrom %(L-I-O-R): 8% - 75% - 8% - 8%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 57%
 Cis/all (FF and RR orient): 66.8%
Inter-chromosomal: 75,322  (10.01% / 11.74%)
Intra-chromosomal: 453,607  (60.26% / 70.69%)
Short Range (<20,000bp): 343,185  (45.59% / 53.48%)
Long Range (>20,000bp): 110,422  (14.67% / 17.21%)