Experiment description: Juicer version 1.6; BWA 0.7.18-r1243-dirty; 14 threads; openjdk version "17.0.8-internal" 2023-07-18; /data/amivanov/Tools/juicer1.6_compact-main/scripts/juicer.sh -g T2T -d /data/amivanov/Projects/Embryos/2025-04-24-BGI/B/Pet1_K -s DpnII -y /data/amivanov/Databases/T2T-CHM13v2.0/juicer.rs/T2T-CHM13v2.0_DpnII.txt -p /data/amivanov/Databases/T2T-CHM13v2.0/hgT2T.chromsizes -z /data/amivanov/Databases/T2T-CHM13v2.0/hgT2T.fa -D /data/amivanov/Tools/juicer1.6_compact-main -t 14 Sequenced Read Pairs: 11,778,626 Normal Paired: 6,604,362 (56.07%) Chimeric Paired: 4,094,865 (34.77%) Chimeric Ambiguous: 929,161 (7.89%) Unmapped: 150,238 (1.28%) Ligation Motif Present: 7,242,432 (61.49%) Alignable (Normal+Chimeric Paired): 10,699,227 (90.84%) WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2025-05-17T17:14:29,200] [Globals.java:138] [main] Development mode is enabled Unique Reads: 3,960,110 (33.62%) PCR Duplicates: 6,739,117 (57.21%) Optical Duplicates: 0 (0.00%) Library Complexity Estimate: 4,324,361 Intra-fragment Reads: 361,186 (3.07% / 9.12%) Below MAPQ Threshold: 846,537 (7.19% / 21.38%) Hi-C Contacts: 3,113,573 (26.43% / 78.62%) Ligation Motif Present: 1,825,633 (15.50% / 46.10%) 3' Bias (Long Range): 65% - 35% Pair Type intra chrom %(L-I-O-R): 11% - 67% - 11% - 11% Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25% DE: 47% Cis/all (FF and RR orient): 67.3% Inter-chromosomal: 544,238 (4.62% / 13.74%) Intra-chromosomal: 2,569,335 (21.81% / 64.88%) Short Range (<20,000bp): 1,686,893 (14.32% / 42.60%) Long Range (>20,000bp): 882,442 (7.49% / 22.28%)