Experiment description: Juicer version 1.6; BWA 0.7.19-r1273; 18 threads; openjdk version "17.0.8-internal" 2023-07-18; /data/emkabirova/Tools/juicer1.6_compact/scripts/juicer.sh -g hg38 -d /data/emkabirova/Juicer_out/2025-10-23-BGI/PARP_WT_r1 -s DpnII -y /data/nyt/Databases/hg38_canonical/juicer.rs/hg38_canonical_DpnII.txt -p /data/nyt/Databases/hg38_canonical/GRCh38_no_alt_analysis_set_GCA_000001405.15.canonical.fasta.chromsizes -z /data/nyt/Databases/hg38_canonical/GRCh38_no_alt_analysis_set_GCA_000001405.15.canonical.fasta -D /data/emkabirova/Tools/juicer1.6_compact -t 18                                                                                                                                                                                                                                                                                                                                                                                                                                  
Sequenced Read Pairs:  11,728,867
 Normal Paired: 7,151,398 (60.97%)
 Chimeric Paired: 3,528,632 (30.09%)
 Chimeric Ambiguous: 985,413 (8.40%)
 Unmapped: 63,424 (0.54%)
 Ligation Motif Present: 9,338,337 (79.62%)
Alignable (Normal+Chimeric Paired): 10,680,030 (91.06%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-10-29T01:56:23,600]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 10,474,258 (89.30%)
PCR Duplicates: 0 (0.00%)
Optical Duplicates: 205,772 (1.75%)
Library Complexity Estimate: 0
Intra-fragment Reads: 1,336,658 (11.40% / 12.76%)
Below MAPQ Threshold: 1,034,358 (8.82% / 9.88%)
Hi-C Contacts: 9,439,900 (80.48% / 90.12%)
 Ligation Motif Present: 7,307,114  (62.30% / 69.76%)
 3' Bias (Long Range): 81% - 19%
 Pair Type intra chrom %(L-I-O-R): 4% - 87% - 4% - 4%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 68%
 Cis/all (FF and RR orient): 44.4%
Inter-chromosomal: 1,700,611  (14.50% / 16.24%)
Intra-chromosomal: 7,739,289  (65.98% / 73.89%)
Short Range (<20,000bp): 6,506,945  (55.48% / 62.12%)
Long Range (>20,000bp): 1,232,344  (10.51% / 11.77%)