Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 10 threads; openjdk version "17.0.8.1" 2023-08-24; /storage2/dreamworld/Tools/juicer1.6_compact/scripts/juicer.sh -g hg19 -d /storage3/nyt/Projects/Juicer-Out/2023-08-HiC-data_Sciara_less/SC5_S9 -s DpnII -y /storage/nyt/Data/Genomes/Sciara/juicer.rs/sciara_merged_Prim_on_Gerbi_soft_WG.rawchrom.assembly_DpnII.txt -p /storage/nyt/Data/Genomes/Sciara/sciara_merged_Prim_on_Gerbi_soft_WG.rawchrom.assembly.chromsizes -z /storage/nyt/Data/Genomes/Sciara/sciara_merged_Prim_on_Gerbi_soft_WG.rawchrom.assembly.fasta -D /storage2/dreamworld/Tools/juicer1.6_compact -t 10                                                                                                                                                                                                                                                                                                                                                                                      
Sequenced Read Pairs:  41,725,958
 Normal Paired: 19,988,201 (47.90%)
 Chimeric Paired: 10,312,875 (24.72%)
 Chimeric Ambiguous: 5,812,069 (13.93%)
 Unmapped: 5,612,813 (13.45%)
 Ligation Motif Present: 25,526,977 (61.18%)
Alignable (Normal+Chimeric Paired): 30,301,076 (72.62%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2023-09-10T23:07:09,951]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 28,886,846 (69.23%)
PCR Duplicates: 1,325,585 (3.18%)
Optical Duplicates: 88,645 (0.21%)
Library Complexity Estimate: 334,151,189
Intra-fragment Reads: 1,205,800 (2.89% / 4.17%)
Below MAPQ Threshold: 7,753,178 (18.58% / 26.84%)
Hi-C Contacts: 19,927,868 (47.76% / 68.99%)
 Ligation Motif Present: 12,027,407  (28.82% / 41.64%)
 3' Bias (Long Range): 57% - 43%
 Pair Type intra chrom %(L-I-O-R): 19% - 44% - 18% - 19%
 Pair Type inter chrom %(L-I-O-R): 24% - 25% - 25% - 26%
 DE: 20%
 Cis/all (FF and RR orient): 76.2%
Inter-chromosomal: 3,781,219  (9.06% / 13.09%)
Intra-chromosomal: 16,146,649  (38.70% / 55.90%)
Short Range (<20,000bp): 6,777,038  (16.24% / 23.46%)
Long Range (>20,000bp): 9,369,611  (22.46% / 32.44%)