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-1-Hi-C-1 -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:  687,820
 Normal Paired: 348,206 (50.62%)
 Chimeric Paired: 253,441 (36.85%)
 Chimeric Ambiguous: 74,087 (10.77%)
 Unmapped: 12,086 (1.76%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 601,647 (87.47%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-05-05T05:09:35,626]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 589,079 (85.64%)
PCR Duplicates: 12,444 (1.81%)
Optical Duplicates: 124 (0.02%)
Library Complexity Estimate: 14,337,121
Intra-fragment Reads: 50,937 (7.41% / 8.65%)
Below MAPQ Threshold: 66,444 (9.66% / 11.28%)
Hi-C Contacts: 522,635 (75.98% / 88.72%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 71% - 29%
 Pair Type intra chrom %(L-I-O-R): 8% - 75% - 9% - 8%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 56%
 Cis/all (FF and RR orient): 65.2%
Inter-chromosomal: 80,052  (11.64% / 13.59%)
Intra-chromosomal: 442,583  (64.35% / 75.13%)
Short Range (<20,000bp): 331,228  (48.16% / 56.23%)
Long Range (>20,000bp): 111,355  (16.19% / 18.90%)