Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 20 threads; java version "1.8.0_131"; scripts/juicer.sh -t 20 -D /oak/stanford/groups/akundaje/marinovg/ENCODE4/DNAzoo/2023-09-26-Novogene-NovaSeq/juicer-L2874-HEPES_Hi-C -d /oak/stanford/groups/akundaje/marinovg/ENCODE4/DNAzoo/2023-09-26-Novogene-NovaSeq/juicer-L2874-HEPES_Hi-C -p /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/bwa-indexes/scaffolds.chrom.sizes -y none -s none -z /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/bwa-indexes/scaffolds.fa                                                                                                                                                                                                                                                          
Sequenced Read Pairs:  65,255,303
 Normal Paired: 29,500,337 (45.21%)
 Chimeric Paired: 30,512,661 (46.76%)
 Chimeric Ambiguous: 5,054,657 (7.75%)
 Unmapped: 187,648 (0.29%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 60,012,998 (91.97%)
WARN [2023-09-28T01:00:55,625]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 35,756,968 (54.80%)
PCR Duplicates: 21,896,426 (33.56%)
Optical Duplicates: 2,359,604 (3.62%)
Library Complexity Estimate: 55,132,780
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 289,742 (0.44% / 0.81%)
Hi-C Contacts: 35,467,226 (54.35% / 99.19%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 363,097  (0.56% / 1.02%)
Intra-chromosomal: 35,104,129  (53.80% / 98.17%)
Short Range (<20Kb): 5,346,435  (8.19% / 14.95%)
Long Range (>20Kb): 29,755,600  (45.60% / 83.22%)