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-2-1-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:  804,737
 Normal Paired: 322,661 (40.10%)
 Chimeric Paired: 303,244 (37.68%)
 Chimeric Ambiguous: 161,059 (20.01%)
 Unmapped: 17,773 (2.21%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 625,905 (77.78%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-09-23T22:26:08,280]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 614,054 (76.30%)
PCR Duplicates: 11,743 (1.46%)
Optical Duplicates: 108 (0.01%)
Library Complexity Estimate: 16,465,436
Intra-fragment Reads: 38,180 (4.74% / 6.22%)
Below MAPQ Threshold: 119,681 (14.87% / 19.49%)
Hi-C Contacts: 494,373 (61.43% / 80.51%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 70% - 30%
 Pair Type intra chrom %(L-I-O-R): 10% - 69% - 10% - 10%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 47%
 Cis/all (FF and RR orient): 61.8%
Inter-chromosomal: 99,301  (12.34% / 16.17%)
Intra-chromosomal: 395,072  (49.09% / 64.34%)
Short Range (<20,000bp): 276,767  (34.39% / 45.07%)
Long Range (>20,000bp): 118,305  (14.70% / 19.27%)