Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 20 threads; openjdk version "11.0.21" 2023-10-17; /data/nyt/MMO/Tools/juicer1.6_compact/scripts/juicer.sh -g hg19 -d /data/nyt/Projects/Juicer-Out/2024-02-14_MGNC/Ph_Sasha_Yan/Ph_Nla_CS -s NlaIII -y /data/nyt/Databases/hg38/juicer.rs/GRCh38_no_alt_analysis_set_GCA_000001405.15_NlaIII.txt -p /data/nyt/Databases/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.chromsizes -z /data/nyt/Databases/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta -D /data/nyt/MMO/Tools/juicer1.6_compact -t 20                                                                                                                                                                                                                                                                                                                                                                                                                                                    
Sequenced Read Pairs:  949,319
 Normal Paired: 481,103 (50.68%)
 Chimeric Paired: 352,756 (37.16%)
 Chimeric Ambiguous: 102,778 (10.83%)
 Unmapped: 12,682 (1.34%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 833,859 (87.84%)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-02-15T15:38:02,941]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 823,647 (86.76%)
PCR Duplicates: 10,113 (1.07%)
Optical Duplicates: 99 (0.01%)
Library Complexity Estimate: 34,090,927
Intra-fragment Reads: 79,874 (8.41% / 9.70%)
Below MAPQ Threshold: 120,172 (12.66% / 14.59%)
Hi-C Contacts: 703,475 (74.10% / 85.41%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 70% - 30%
 Pair Type intra chrom %(L-I-O-R): 8% - 76% - 8% - 8%
 Pair Type inter chrom %(L-I-O-R): 25% - 25% - 25% - 25%
 DE: 59%
 Cis/all (FF and RR orient): 67.3%
Inter-chromosomal: 94,459  (9.95% / 11.47%)
Intra-chromosomal: 609,016  (64.15% / 73.94%)
Short Range (<20,000bp): 489,575  (51.57% / 59.44%)
Long Range (>20,000bp): 119,441  (12.58% / 14.50%)