Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 20 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/2024-03-05_MGNC/Sasha_Yan/MEF -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 20 Sequenced Read Pairs: 1,727,987 Normal Paired: 894,307 (51.75%) Chimeric Paired: 606,798 (35.12%) Chimeric Ambiguous: 185,761 (10.75%) Unmapped: 41,121 (2.38%) Ligation Motif Present: 0 (0.00%) Alignable (Normal+Chimeric Paired): 1,501,105 (86.87%) WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2024-03-06T13:53:07,241] [Globals.java:138] [main] Development mode is enabled Unique Reads: 1,444,090 (83.57%) PCR Duplicates: 56,701 (3.28%) Optical Duplicates: 314 (0.02%) Library Complexity Estimate: 19,358,372 Intra-fragment Reads: 172,091 (9.96% / 11.92%) Below MAPQ Threshold: 177,559 (10.28% / 12.30%) Hi-C Contacts: 1,266,531 (73.30% / 87.70%) Ligation Motif Present: 0 (0.00% / 0.00%) 3' Bias (Long Range): 68% - 32% Pair Type intra chrom %(L-I-O-R): 8% - 76% - 8% - 8% Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25% DE: 56% Cis/all (FF and RR orient): 58.4% Inter-chromosomal: 231,716 (13.41% / 16.05%) Intra-chromosomal: 1,034,815 (59.89% / 71.66%) Short Range (<20,000bp): 780,550 (45.17% / 54.05%) Long Range (>20,000bp): 254,265 (14.71% / 17.61%)