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 T2T -d /data/nyt/Projects/Juicer-Out/2024-07-29_ENC/Hepatocytes/87c_Rep2 -s DpnII -y /data/nyt/Databases/T2T-CHM13v2.0/juicer.rs/T2T-CHM13v2.0_DpnII.txt -p /data/nyt/Databases/T2T-CHM13v2.0/hgT2T.chromsizes -z /data/nyt/Databases/T2T-CHM13v2.0/hgT2T.fa -D /data/nyt/MMO/Tools/juicer1.6_compact -t 20 Sequenced Read Pairs: 84,676 Normal Paired: 48,777 (57.60%) Chimeric Paired: 28,444 (33.59%) Chimeric Ambiguous: 6,296 (7.44%) Unmapped: 1,159 (1.37%) Ligation Motif Present: 44,905 (53.03%) Alignable (Normal+Chimeric Paired): 77,221 (91.20%) WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2024-08-01T16:39:14,290] [Globals.java:138] [main] Development mode is enabled Unique Reads: 68,299 (80.66%) PCR Duplicates: 8,555 (10.10%) Optical Duplicates: 367 (0.43%) Library Complexity Estimate: 319,085 Intra-fragment Reads: 14,102 (16.65% / 20.65%) Below MAPQ Threshold: 11,075 (13.08% / 16.22%) Hi-C Contacts: 57,224 (67.58% / 83.78%) Ligation Motif Present: 27,052 (31.95% / 39.61%) 3' Bias (Long Range): 64% - 36% Pair Type intra chrom %(L-I-O-R): 3% - 88% - 7% - 3% Pair Type inter chrom %(L-I-O-R): 25% - 24% - 25% - 25% DE: 64% Cis/all (FF and RR orient): 20.3% Inter-chromosomal: 16,343 (19.30% / 23.93%) Intra-chromosomal: 40,881 (48.28% / 59.86%) Short Range (<20,000bp): 39,758 (46.95% / 58.21%) Long Range (>20,000bp): 1,123 (1.33% / 1.64%)