Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 20 threads; openjdk version "11.0.21" 2023-10-17; /data/nyt/MMO/Tools/juicer1.6_compact/scripts/juicer.sh -g hg19 -d /data/nyt/Projects/Juicer-Out/2024-02-14_MGNC/Ph_Sasha_Yan/Ph_Dpn -s DpnII -y /data/nyt/Databases/hg38/juicer.rs/GRCh38_no_alt_analysis_set_GCA_000001405.15_DpnII.txt -p /data/nyt/Databases/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.chromsizes -z /data/nyt/Databases/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta -D /data/nyt/MMO/Tools/juicer1.6_compact -t 20                                                                                                                                                                                                                                                                                                                                                                                                                                                         
Sequenced Read Pairs:  2,274,136
 Normal Paired: 1,016,834 (44.71%)
 Chimeric Paired: 903,960 (39.75%)
 Chimeric Ambiguous: 321,518 (14.14%)
 Unmapped: 31,824 (1.40%)
 Ligation Motif Present: 2,021,245 (88.88%)
Alignable (Normal+Chimeric Paired): 1,920,794 (84.46%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-02-15T15:53:13,665]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 1,895,764 (83.36%)
PCR Duplicates: 24,863 (1.09%)
Optical Duplicates: 167 (0.01%)
Library Complexity Estimate: 73,541,082
Intra-fragment Reads: 104,970 (4.62% / 5.54%)
Below MAPQ Threshold: 399,641 (17.57% / 21.08%)
Hi-C Contacts: 1,496,123 (65.79% / 78.92%)
 Ligation Motif Present: 1,297,051  (57.03% / 68.42%)
 3' Bias (Long Range): 82% - 18%
 Pair Type intra chrom %(L-I-O-R): 9% - 74% - 9% - 9%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 55%
 Cis/all (FF and RR orient): 67.3%
Inter-chromosomal: 217,478  (9.56% / 11.47%)
Intra-chromosomal: 1,278,645  (56.23% / 67.45%)
Short Range (<20,000bp): 968,746  (42.60% / 51.10%)
Long Range (>20,000bp): 309,899  (13.63% / 16.35%)