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/ncaph2_merged_comp -s none -z /home/estsoi/mm10.fasta -D /home/estsoi/juicer1.6_compact -t 13 -c ncaph2_merged_comp.cool -q 1000                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
Sequenced Read Pairs:  96,083,900
 Normal Paired: 41,752,826 (43.45%)
 Chimeric Paired: 39,973,177 (41.60%)
 Chimeric Ambiguous: 12,197,810 (12.69%)
 Unmapped: 2,160,087 (2.25%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 81,726,003 (85.06%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-06-03T20:51:00,258]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 79,315,833 (82.55%)
PCR Duplicates: 0 (0.00%)
Optical Duplicates: 2,410,170 (2.51%)
Library Complexity Estimate: 0
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 13,211,073 (13.75% / 16.66%)
Hi-C Contacts: 66,104,760 (68.80% / 83.34%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type intra chrom %(L-I-O-R): 13% - 62% - 13% - 13%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 43%
 Cis/all (FF and RR orient): 79.5%
Inter-chromosomal: 7,698,253  (8.01% / 9.71%)
Intra-chromosomal: 58,406,507  (60.79% / 73.64%)
Short Range (<20,000bp): 37,780,150  (39.32% / 47.63%)
Long Range (>20,000bp): 20,626,357  (21.47% / 26.01%)