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_05_29_ENC_2024-07-29_ENC/Hepatocytes/Prime_contr_concatenated -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:  149,272,079
 Normal Paired: 79,185,562 (53.05%)
 Chimeric Paired: 52,559,123 (35.21%)
 Chimeric Ambiguous: 15,617,570 (10.46%)
 Unmapped: 1,909,824 (1.28%)
 Ligation Motif Present: 95,273,740 (63.83%)
Alignable (Normal+Chimeric Paired): 131,744,685 (88.26%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-08-01T21:25:46,786]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 110,657,794 (74.13%)
PCR Duplicates: 19,829,583 (13.28%)
Optical Duplicates: 1,257,308 (0.84%)
Library Complexity Estimate: 384,635,244
Intra-fragment Reads: 14,381,868 (9.63% / 13.00%)
Below MAPQ Threshold: 17,710,597 (11.86% / 16.00%)
Hi-C Contacts: 92,947,197 (62.27% / 84.00%)
 Ligation Motif Present: 55,721,156  (37.33% / 50.35%)
 3' Bias (Long Range): 65% - 35%
 Pair Type intra chrom %(L-I-O-R): 11% - 66% - 11% - 11%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 44%
 Cis/all (FF and RR orient): 64.0%
Inter-chromosomal: 18,876,863  (12.65% / 17.06%)
Intra-chromosomal: 74,070,334  (49.62% / 66.94%)
Short Range (<20,000bp): 48,043,672  (32.19% / 43.42%)
Long Range (>20,000bp): 26,026,662  (17.44% / 23.52%)