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-5 -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: 17,532 Normal Paired: 4,539 (25.89%) Chimeric Paired: 6,625 (37.79%) Chimeric Ambiguous: 3,657 (20.86%) Unmapped: 2,711 (15.46%) Ligation Motif Present: 12,686 (72.36%) Alignable (Normal+Chimeric Paired): 11,164 (63.68%) WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-04-11T19:19:14,762] [Globals.java:138] [main] Development mode is enabled Unique Reads: 11,153 (63.62%) PCR Duplicates: 2 (0.01%) Optical Duplicates: 9 (0.05%) Library Complexity Estimate: 31,104,787 Intra-fragment Reads: 538 (3.07% / 4.82%) Below MAPQ Threshold: 3,119 (17.79% / 27.97%) Hi-C Contacts: 7,496 (42.76% / 67.21%) Ligation Motif Present: 5,888 (33.58% / 52.79%) 3' Bias (Long Range): 60% - 40% Pair Type intra chrom %(L-I-O-R): 17% - 49% - 16% - 18% Pair Type inter chrom %(L-I-O-R): 23% - 26% - 27% - 24% DE: 25% Cis/all (FF and RR orient): 80.0% Inter-chromosomal: 1,183 (6.75% / 10.61%) Intra-chromosomal: 6,313 (36.01% / 56.60%) Short Range (<20,000bp): 2,979 (16.99% / 26.71%) Long Range (>20,000bp): 3,334 (19.02% / 29.89%)