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-5-fixed2 -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:  837,871
 Normal Paired: 452,609 (54.02%)
 Chimeric Paired: 270,246 (32.25%)
 Chimeric Ambiguous: 96,070 (11.47%)
 Unmapped: 18,946 (2.26%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 722,855 (86.27%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-09-23T22:43:18,234]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 712,035 (84.98%)
PCR Duplicates: 10,705 (1.28%)
Optical Duplicates: 115 (0.01%)
Library Complexity Estimate: 24,156,110
Intra-fragment Reads: 79,833 (9.53% / 11.21%)
Below MAPQ Threshold: 118,846 (14.18% / 16.69%)
Hi-C Contacts: 593,189 (70.80% / 83.31%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 69% - 31%
 Pair Type intra chrom %(L-I-O-R): 7% - 78% - 7% - 7%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 62%
 Cis/all (FF and RR orient): 65.8%
Inter-chromosomal: 77,506  (9.25% / 10.89%)
Intra-chromosomal: 515,683  (61.55% / 72.42%)
Short Range (<20,000bp): 417,570  (49.84% / 58.64%)
Long Range (>20,000bp): 98,113  (11.71% / 13.78%)