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-2-2-fixed1 -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:  779,051
 Normal Paired: 334,493 (42.94%)
 Chimeric Paired: 301,517 (38.70%)
 Chimeric Ambiguous: 122,119 (15.68%)
 Unmapped: 20,922 (2.69%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 636,010 (81.64%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-09-23T22:30:33,228]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 624,743 (80.19%)
PCR Duplicates: 11,126 (1.43%)
Optical Duplicates: 141 (0.02%)
Library Complexity Estimate: 17,957,893
Intra-fragment Reads: 52,420 (6.73% / 8.39%)
Below MAPQ Threshold: 75,243 (9.66% / 12.04%)
Hi-C Contacts: 549,500 (70.53% / 87.96%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 67% - 33%
 Pair Type intra chrom %(L-I-O-R): 11% - 66% - 11% - 11%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 45%
 Cis/all (FF and RR orient): 65.9%
Inter-chromosomal: 103,440  (13.28% / 16.56%)
Intra-chromosomal: 446,060  (57.26% / 71.40%)
Short Range (<20,000bp): 298,728  (38.35% / 47.82%)
Long Range (>20,000bp): 147,332  (18.91% / 23.58%)