Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 18 threads; openjdk version "17.0.8-internal" 2023-07-18; /data/nyt/MMO/Tools/juicer1.6_compact/scripts/juicer.sh -g hg38_mm10 -d /data/nyt/Projects/Juicer-Out/2024-04-25_MGNC/Sasha_Yan_new/Ph-MEF-2-Hi-C-4 -s NlaIII -y /data/nyt/Databases/4c_plasmid/hg38_mm10/juicer.rs/hg38_mm10_num3CMV_NP_NlaIII.txt -p /data/nyt/Databases/4c_plasmid/hg38_mm10/hg38_mm10_num3CMV_NP.fasta.chromsizes -z /data/nyt/Databases/4c_plasmid/hg38_mm10/hg38_mm10_num3CMV_NP.fasta -D /data/nyt/MMO/Tools/juicer1.6_compact -t 18 Sequenced Read Pairs: 652,425 Normal Paired: 323,526 (49.59%) Chimeric Paired: 246,817 (37.83%) Chimeric Ambiguous: 68,224 (10.46%) Unmapped: 13,858 (2.12%) Ligation Motif Present: 0 (0.00%) Alignable (Normal+Chimeric Paired): 570,343 (87.42%) WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2024-05-05T05:23:33,765] [Globals.java:138] [main] Development mode is enabled Unique Reads: 554,224 (84.95%) PCR Duplicates: 16,018 (2.46%) Optical Duplicates: 101 (0.02%) Library Complexity Estimate: 9,959,344 Intra-fragment Reads: 42,423 (6.50% / 7.65%) Below MAPQ Threshold: 98,433 (15.09% / 17.76%) Hi-C Contacts: 455,791 (69.86% / 82.24%) Ligation Motif Present: 0 (0.00% / 0.00%) 3' Bias (Long Range): 69% - 31% Pair Type intra chrom %(L-I-O-R): 9% - 73% - 9% - 9% Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25% DE: 55% Cis/all (FF and RR orient): 67.5% Inter-chromosomal: 66,708 (10.22% / 12.04%) Intra-chromosomal: 389,083 (59.64% / 70.20%) Short Range (<20,000bp): 290,825 (44.58% / 52.47%) Long Range (>20,000bp): 98,258 (15.06% / 17.73%)