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/SC2_S1 -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:  47,537,027
 Normal Paired: 24,695,718 (51.95%)
 Chimeric Paired: 10,770,358 (22.66%)
 Chimeric Ambiguous: 6,555,288 (13.79%)
 Unmapped: 5,515,663 (11.60%)
 Ligation Motif Present: 27,748,407 (58.37%)
Alignable (Normal+Chimeric Paired): 35,466,076 (74.61%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2023-09-10T20:44:31,814]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 33,838,474 (71.18%)
PCR Duplicates: 1,544,150 (3.25%)
Optical Duplicates: 83,452 (0.18%)
Library Complexity Estimate: 393,496,338
Intra-fragment Reads: 1,311,705 (2.76% / 3.88%)
Below MAPQ Threshold: 12,139,990 (25.54% / 35.88%)
Hi-C Contacts: 20,386,779 (42.89% / 60.25%)
 Ligation Motif Present: 11,635,059  (24.48% / 34.38%)
 3' Bias (Long Range): 58% - 42%
 Pair Type intra chrom %(L-I-O-R): 19% - 43% - 19% - 19%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 20%
 Cis/all (FF and RR orient): 77.6%
Inter-chromosomal: 3,675,862  (7.73% / 10.86%)
Intra-chromosomal: 16,710,917  (35.15% / 49.38%)
Short Range (<20,000bp): 6,589,116  (13.86% / 19.47%)
Long Range (>20,000bp): 10,121,801  (21.29% / 29.91%)