Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 20 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/2024-03-05_MGNC/Sasha_Yan/Ph_Pct -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 20                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
Sequenced Read Pairs:  1,642,041
 Normal Paired: 708,829 (43.17%)
 Chimeric Paired: 729,047 (44.40%)
 Chimeric Ambiguous: 178,013 (10.84%)
 Unmapped: 26,152 (1.59%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 1,437,876 (87.57%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-03-06T13:40:36,111]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 1,421,871 (86.59%)
PCR Duplicates: 15,701 (0.96%)
Optical Duplicates: 304 (0.02%)
Library Complexity Estimate: 65,331,448
Intra-fragment Reads: 80,721 (4.92% / 5.68%)
Below MAPQ Threshold: 137,951 (8.40% / 9.70%)
Hi-C Contacts: 1,283,920 (78.19% / 90.30%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 70% - 30%
 Pair Type intra chrom %(L-I-O-R): 11% - 68% - 11% - 11%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 47%
 Cis/all (FF and RR orient): 66.0%
Inter-chromosomal: 231,561  (14.10% / 16.29%)
Intra-chromosomal: 1,052,359  (64.09% / 74.01%)
Short Range (<20,000bp): 701,661  (42.73% / 49.35%)
Long Range (>20,000bp): 350,698  (21.36% / 24.66%)