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-2-Hi-C-3 -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:  607,611
 Normal Paired: 317,164 (52.20%)
 Chimeric Paired: 220,341 (36.26%)
 Chimeric Ambiguous: 58,571 (9.64%)
 Unmapped: 11,535 (1.90%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 537,505 (88.46%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-05-05T05:19:05,456]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 523,095 (86.09%)
PCR Duplicates: 14,322 (2.36%)
Optical Duplicates: 88 (0.01%)
Library Complexity Estimate: 9,903,039
Intra-fragment Reads: 58,298 (9.59% / 11.14%)
Below MAPQ Threshold: 87,244 (14.36% / 16.68%)
Hi-C Contacts: 435,851 (71.73% / 83.32%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 66% - 34%
 Pair Type intra chrom %(L-I-O-R): 9% - 74% - 9% - 9%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 57%
 Cis/all (FF and RR orient): 69.2%
Inter-chromosomal: 58,334  (9.60% / 11.15%)
Intra-chromosomal: 377,517  (62.13% / 72.17%)
Short Range (<20,000bp): 285,195  (46.94% / 54.52%)
Long Range (>20,000bp): 92,322  (15.19% / 17.65%)