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: 76,955 (9.18% / 10.81%)
Hi-C Contacts: 635,080 (75.80% / 89.19%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 69% - 31%
 Pair Type intra chrom %(L-I-O-R): 8% - 78% - 7% - 7%
 Pair Type inter chrom %(L-I-O-R): 24% - 25% - 25% - 26%
 DE: 60%
 Cis/all (FF and RR orient): 64.4%
Inter-chromosomal: 90,610  (10.81% / 12.73%)
Intra-chromosomal: 544,470  (64.98% / 76.47%)
Short Range (<20,000bp): 436,392  (52.08% / 61.29%)
Long Range (>20,000bp): 108,078  (12.90% / 15.18%)