Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 18 threads; openjdk version "17.0.8-internal" 2023-07-18; /data/nyt/MMO/Tools/juicer1.6_compact/scripts/juicer.sh -g hg38_mm10 -d /data/nyt/Projects/Juicer-Out/2024-09-11_MGNC/Sasha_Yan/Ph-MEF-4-fixed2 -s NlaIII -y /data/nyt/Databases/4c_plasmid/hg38_mm10/juicer.rs/hg38_mm10_num3CMV_NP_NlaIII.txt -p /data/nyt/Databases/4c_plasmid/hg38_mm10/hg38_mm10_num3CMV_NP.fasta.chromsizes -z /data/nyt/Databases/4c_plasmid/hg38_mm10/hg38_mm10_num3CMV_NP.fasta -D /data/nyt/MMO/Tools/juicer1.6_compact -t 18                                                                                                                                                                                                                                                                                                                                                                                                                                                         
Sequenced Read Pairs:  640,664
 Normal Paired: 315,293 (49.21%)
 Chimeric Paired: 218,505 (34.11%)
 Chimeric Ambiguous: 93,834 (14.65%)
 Unmapped: 13,032 (2.03%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 533,798 (83.32%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-09-23T22:39:16,386]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 525,777 (82.07%)
PCR Duplicates: 7,931 (1.24%)
Optical Duplicates: 90 (0.01%)
Library Complexity Estimate: 17,779,302
Intra-fragment Reads: 51,670 (8.07% / 9.83%)
Below MAPQ Threshold: 59,280 (9.25% / 11.27%)
Hi-C Contacts: 466,497 (72.81% / 88.73%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 66% - 34%
 Pair Type intra chrom %(L-I-O-R): 8% - 75% - 8% - 8%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 54%
 Cis/all (FF and RR orient): 56.8%
Inter-chromosomal: 92,606  (14.45% / 17.61%)
Intra-chromosomal: 373,891  (58.36% / 71.11%)
Short Range (<20,000bp): 289,344  (45.16% / 55.03%)
Long Range (>20,000bp): 84,547  (13.20% / 16.08%)