Experiment description: Juicer version 1.6; BWA 0.7.18-r1243-dirty; 14 threads; openjdk version "17.0.11-internal" 2024-04-16; /data/amivanov/Tools/juicer1.6_compact-main/scripts/juicer.sh -g T2T -d /data/amivanov/Projects/Embryos/2025-04-25_Orlov/Sach1_e -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: 8,039,959 Normal Paired: 4,277,332 (53.20%) Chimeric Paired: 2,668,336 (33.19%) Chimeric Ambiguous: 606,063 (7.54%) Unmapped: 488,228 (6.07%) Ligation Motif Present: 4,122,670 (51.28%) Alignable (Normal+Chimeric Paired): 6,945,668 (86.39%) WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2025-05-14T20:39:30,377] [Globals.java:138] [main] Development mode is enabled Unique Reads: 592,707 (7.37%) PCR Duplicates: 6,348,395 (78.96%) Optical Duplicates: 4,566 (0.06%) Library Complexity Estimate: 592,711 Intra-fragment Reads: 81,946 (1.02% / 13.83%) Below MAPQ Threshold: 263,585 (3.28% / 44.47%) Hi-C Contacts: 329,122 (4.09% / 55.53%) Ligation Motif Present: 148,927 (1.85% / 25.13%) 3' Bias (Long Range): 62% - 38% Pair Type intra chrom %(L-I-O-R): 11% - 66% - 12% - 11% Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25% DE: 49% Cis/all (FF and RR orient): 75.4% Inter-chromosomal: 41,460 (0.52% / 7.00%) Intra-chromosomal: 287,662 (3.58% / 48.53%) Short Range (<20,000bp): 203,237 (2.53% / 34.29%) Long Range (>20,000bp): 84,425 (1.05% / 14.24%)