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-L2875-LB_Hi-C -d /oak/stanford/groups/akundaje/marinovg/ENCODE4/DNAzoo/2023-09-26-Novogene-NovaSeq/juicer-L2875-LB_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:  44,698,509
 Normal Paired: 33,956,085 (75.97%)
 Chimeric Paired: 10,118,145 (22.64%)
 Chimeric Ambiguous: 446,334 (1.00%)
 Unmapped: 177,945 (0.40%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 44,074,230 (98.60%)
WARN [2023-09-27T23:58:00,381]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 13,438,170 (30.06%)
PCR Duplicates: 29,706,108 (66.46%)
Optical Duplicates: 929,952 (2.08%)
Library Complexity Estimate: 14,099,218
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 278,185 (0.62% / 2.07%)
Hi-C Contacts: 13,159,985 (29.44% / 97.93%)
 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: 301,340  (0.67% / 2.24%)
Intra-chromosomal: 12,858,645  (28.77% / 95.69%)
Short Range (<20Kb): 6,545,811  (14.64% / 48.71%)
Long Range (>20Kb): 6,311,852  (14.12% / 46.97%)