Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 16 threads; openjdk version "17.0.8-internal" 2023-07-18; /data/nyt/MMO/Tools/juicer1.6_compact/scripts/juicer.sh -g hg19 -d /data/nyt/Projects/Juicer-Out/2022-04-19/4c_plasmid/61_1203_cmvNla -s NlaIII_CATG-ligation -y /data/nyt/Databases/4c_plasmid/mm10_hg38_plasmid_cmv_oldseq/juicer.rs/mm10_hg38_plasmid_cmv_oldseq_NlaIII.txt -p /data/nyt/Databases/4c_plasmid/mm10_hg38_plasmid_cmv_oldseq/mm10_hg38_plasmid_cmv_oldseq.fa.chromsizes -z /data/nyt/Databases/4c_plasmid/mm10_hg38_plasmid_cmv_oldseq/mm10_hg38_plasmid_cmv_oldseq.fa -D /data/nyt/MMO/Tools/juicer1.6_compact -t 16                                                                                                                                                                                                                                                                                                                                                                          
Sequenced Read Pairs:  219,126
 Normal Paired: 201,554 (91.98%)
 Chimeric Paired: 12,979 (5.92%)
 Chimeric Ambiguous: 2,285 (1.04%)
 Unmapped: 2,308 (1.05%)
 Ligation Motif Present: 120,466 (54.98%)
Alignable (Normal+Chimeric Paired): 214,533 (97.90%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2023-12-26T12:31:54,795]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 213,955 (97.64%)
PCR Duplicates: 372 (0.17%)
Optical Duplicates: 206 (0.09%)
Library Complexity Estimate: 61,670,557
Intra-fragment Reads: 88,965 (40.60% / 41.58%)
Below MAPQ Threshold: 11,361 (5.18% / 5.31%)
Hi-C Contacts: 113,629 (51.86% / 53.11%)
 Ligation Motif Present: 108,788  (49.65% / 50.85%)
 3' Bias (Long Range): 67% - 33%
 Pair Type intra chrom %(L-I-O-R): 2% - 93% - 2% - 2%
 Pair Type inter chrom %(L-I-O-R): 23% - 27% - 23% - 28%
 DE: 88%
 Cis/all (FF and RR orient): 77.9%
Inter-chromosomal: 3,005  (1.37% / 1.40%)
Intra-chromosomal: 110,624  (50.48% / 51.70%)
Short Range (<20,000bp): 103,598  (47.28% / 48.42%)
Long Range (>20,000bp): 7,026  (3.21% / 3.28%)