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_KO_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:  12,077,226
 Normal Paired: 6,822,485 (56.49%)
 Chimeric Paired: 4,153,578 (34.39%)
 Chimeric Ambiguous: 1,055,100 (8.74%)
 Unmapped: 46,063 (0.38%)
 Ligation Motif Present: 10,041,864 (83.15%)
Alignable (Normal+Chimeric Paired): 10,976,063 (90.88%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-10-29T01:25:07,061]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 10,774,018 (89.21%)
PCR Duplicates: 0 (0.00%)
Optical Duplicates: 202,045 (1.67%)
Library Complexity Estimate: 0
Intra-fragment Reads: 925,363 (7.66% / 8.59%)
Below MAPQ Threshold: 1,015,861 (8.41% / 9.43%)
Hi-C Contacts: 9,758,157 (80.80% / 90.57%)
 Ligation Motif Present: 7,951,756  (65.84% / 73.80%)
 3' Bias (Long Range): 81% - 19%
 Pair Type intra chrom %(L-I-O-R): 4% - 89% - 4% - 4%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 63%
 Cis/all (FF and RR orient): 29.4%
Inter-chromosomal: 2,555,241  (21.16% / 23.72%)
Intra-chromosomal: 7,202,916  (59.64% / 66.85%)
Short Range (<20,000bp): 6,257,018  (51.81% / 58.08%)
Long Range (>20,000bp): 945,898  (7.83% / 8.78%)