Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 13 threads; openjdk version "17.0.15" 2025-04-15; /home/estsoi/juicer1.6_compact/scripts/juicer.sh -g mm10 -d /storage3/estsoi/ncaph1_merged_comp -s none -z /home/estsoi/mm10.fasta -D /home/estsoi/juicer1.6_compact -t 13 -c ncaph1_merged_comp.cool -q 1000                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
Sequenced Read Pairs:  75,821,391
 Normal Paired: 32,829,516 (43.30%)
 Chimeric Paired: 31,818,689 (41.97%)
 Chimeric Ambiguous: 9,344,792 (12.32%)
 Unmapped: 1,828,394 (2.41%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 64,648,205 (85.26%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-06-01T23:20:55,244]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 62,970,285 (83.05%)
PCR Duplicates: 0 (0.00%)
Optical Duplicates: 1,677,920 (2.21%)
Library Complexity Estimate: 0
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 10,814,004 (14.26% / 17.17%)
Hi-C Contacts: 52,156,281 (68.79% / 82.83%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 13% - 61% - 13% - 13%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 43%
 Cis/all (FF and RR orient): 82.2%
Inter-chromosomal: 5,242,654  (6.91% / 8.33%)
Intra-chromosomal: 46,913,627  (61.87% / 74.50%)
Short Range (<20,000bp): 29,709,524  (39.18% / 47.18%)
Long Range (>20,000bp): 17,204,103  (22.69% / 27.32%)