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/62_1203_emptyNla -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:  177,536
 Normal Paired: 172,734 (97.30%)
 Chimeric Paired: 2,239 (1.26%)
 Chimeric Ambiguous: 615 (0.35%)
 Unmapped: 1,948 (1.10%)
 Ligation Motif Present: 98,357 (55.40%)
Alignable (Normal+Chimeric Paired): 174,973 (98.56%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2023-12-26T12:33:23,906]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 174,063 (98.04%)
PCR Duplicates: 737 (0.42%)
Optical Duplicates: 173 (0.10%)
Library Complexity Estimate: 20,671,027
Intra-fragment Reads: 74,585 (42.01% / 42.85%)
Below MAPQ Threshold: 7,622 (4.29% / 4.38%)
Hi-C Contacts: 91,856 (51.74% / 52.77%)
 Ligation Motif Present: 88,546  (49.87% / 50.87%)
 3' Bias (Long Range): 69% - 31%
 Pair Type intra chrom %(L-I-O-R): 0% - 99% - 0% - 0%
 Pair Type inter chrom %(L-I-O-R): 21% - 30% - 22% - 27%
 DE: 97%
 Cis/all (FF and RR orient): 44.7%
Inter-chromosomal: 1,340  (0.75% / 0.77%)
Intra-chromosomal: 90,516  (50.98% / 52.00%)
Short Range (<20,000bp): 89,855  (50.61% / 51.62%)
Long Range (>20,000bp): 661  (0.37% / 0.38%)