Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 16 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/Hepatocytes/Prime_contr -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 16                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
Sequenced Read Pairs:  127,609,520
 Normal Paired: 67,692,945 (53.05%)
 Chimeric Paired: 44,891,059 (35.18%)
 Chimeric Ambiguous: 13,364,628 (10.47%)
 Unmapped: 1,660,888 (1.30%)
 Ligation Motif Present: 81,373,047 (63.77%)
Alignable (Normal+Chimeric Paired): 112,584,004 (88.23%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-05-31T16:40:19,241]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 94,197,806 (73.82%)
PCR Duplicates: 17,236,209 (13.51%)
Optical Duplicates: 1,149,989 (0.90%)
Library Complexity Estimate: 322,026,235
Intra-fragment Reads: 12,205,522 (9.56% / 12.96%)
Below MAPQ Threshold: 15,102,305 (11.83% / 16.03%)
Hi-C Contacts: 79,095,501 (61.98% / 83.97%)
 Ligation Motif Present: 47,350,012  (37.11% / 50.27%)
 3' Bias (Long Range): 65% - 35%
 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: 43%
 Cis/all (FF and RR orient): 64.0%
Inter-chromosomal: 16,107,153  (12.62% / 17.10%)
Intra-chromosomal: 62,988,348  (49.36% / 66.87%)
Short Range (<20,000bp): 40,766,763  (31.95% / 43.28%)
Long Range (>20,000bp): 22,221,585  (17.41% / 23.59%)