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: 2,216 (12.64% / 19.87%) Hi-C Contacts: 8,399 (47.91% / 75.31%) Ligation Motif Present: 6,590 (37.59% / 59.09%) 3' Bias (Long Range): 60% - 40% Pair Type intra chrom %(L-I-O-R): 17% - 48% - 17% - 18% Pair Type inter chrom %(L-I-O-R): 24% - 26% - 27% - 24% DE: 25% Cis/all (FF and RR orient): 78.3% Inter-chromosomal: 1,435 (8.19% / 12.87%) Intra-chromosomal: 6,964 (39.72% / 62.44%) Short Range (<20,000bp): 3,226 (18.40% / 28.92%) Long Range (>20,000bp): 3,738 (21.32% / 33.52%)