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-4 -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:  652,425
 Normal Paired: 323,526 (49.59%)
 Chimeric Paired: 246,817 (37.83%)
 Chimeric Ambiguous: 68,224 (10.46%)
 Unmapped: 13,858 (2.12%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 570,343 (87.42%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-05-05T05:23:33,765]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 554,224 (84.95%)
PCR Duplicates: 16,018 (2.46%)
Optical Duplicates: 101 (0.02%)
Library Complexity Estimate: 9,959,344
Intra-fragment Reads: 42,423 (6.50% / 7.65%)
Below MAPQ Threshold: 66,821 (10.24% / 12.06%)
Hi-C Contacts: 487,403 (74.71% / 87.94%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 69% - 31%
 Pair Type intra chrom %(L-I-O-R): 9% - 72% - 9% - 9%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 53%
 Cis/all (FF and RR orient): 66.0%
Inter-chromosomal: 77,359  (11.86% / 13.96%)
Intra-chromosomal: 410,044  (62.85% / 73.99%)
Short Range (<20,000bp): 303,342  (46.49% / 54.73%)
Long Range (>20,000bp): 106,702  (16.35% / 19.25%)