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/MEF -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:  1,727,987
 Normal Paired: 894,307 (51.75%)
 Chimeric Paired: 606,798 (35.12%)
 Chimeric Ambiguous: 185,761 (10.75%)
 Unmapped: 41,121 (2.38%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 1,501,105 (86.87%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-03-06T13:53:07,241]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 1,444,090 (83.57%)
PCR Duplicates: 56,701 (3.28%)
Optical Duplicates: 314 (0.02%)
Library Complexity Estimate: 19,358,372
Intra-fragment Reads: 172,091 (9.96% / 11.92%)
Below MAPQ Threshold: 255,641 (14.79% / 17.70%)
Hi-C Contacts: 1,188,449 (68.78% / 82.30%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 68% - 32%
 Pair Type intra chrom %(L-I-O-R): 8% - 77% - 8% - 8%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 58%
 Cis/all (FF and RR orient): 60.2%
Inter-chromosomal: 199,556  (11.55% / 13.82%)
Intra-chromosomal: 988,893  (57.23% / 68.48%)
Short Range (<20,000bp): 754,006  (43.63% / 52.21%)
Long Range (>20,000bp): 234,887  (13.59% / 16.27%)