Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 10 threads; openjdk version "11.0.18" 2023-01-17; /storage2/dreamworld/Tools/juicer1.6_compact/scripts/juicer.sh -g hg19 -d /storage/nyt/Projects/Juicer-Out/2023-04-11_Hic_Sci/HiC-Sc-2 -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: 11,213 Normal Paired: 2,966 (26.45%) Chimeric Paired: 4,321 (38.54%) Chimeric Ambiguous: 2,329 (20.77%) Unmapped: 1,597 (14.24%) Ligation Motif Present: 8,235 (73.44%) Alignable (Normal+Chimeric Paired): 7,287 (64.99%) WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-04-11T19:18:45,320] [Globals.java:138] [main] Development mode is enabled Unique Reads: 7,286 (64.98%) PCR Duplicates: 0 (0.00%) Optical Duplicates: 1 (0.01%) Library Complexity Estimate: 0 Intra-fragment Reads: 320 (2.85% / 4.39%) Below MAPQ Threshold: 2,099 (18.72% / 28.81%) Hi-C Contacts: 4,867 (43.40% / 66.80%) Ligation Motif Present: 3,815 (34.02% / 52.36%) 3' Bias (Long Range): 60% - 40% Pair Type intra chrom %(L-I-O-R): 18% - 48% - 17% - 17% Pair Type inter chrom %(L-I-O-R): 24% - 25% - 24% - 26% DE: 25% Cis/all (FF and RR orient): 76.6% Inter-chromosomal: 853 (7.61% / 11.71%) Intra-chromosomal: 4,014 (35.80% / 55.09%) Short Range (<20,000bp): 1,711 (15.26% / 23.48%) Long Range (>20,000bp): 2,303 (20.54% / 31.61%)