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/single-cell/2024-10-18-NextSeq-run/juicer-L3100+L3105+L3110-pooled-Symbiodinium_microadriaticum_v1.0 -d /oak/stanford/groups/akundaje/marinovg/ENCODE4/single-cell/2024-10-18-NextSeq-run/juicer-L3100+L3105+L3110-pooled-Symbiodinium_microadriaticum_v1.0 -p /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes -y none -s none -z /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bwa-indexes/Smic.genome.scaffold.final.fa                                                                                                                                                                                                                                                                                        
Sequenced Read Pairs:  47,773,046
 Normal Paired: 1,044,217 (2.19%)
 Chimeric Paired: 0 (0.00%)
 Chimeric Ambiguous: 0 (0.00%)
 Unmapped: 46,728,829 (97.81%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 1,044,217 (2.19%)
WARN [2024-10-20T21:48:51,269]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 798,097 (1.67%)
PCR Duplicates: 246,063 (0.52%)
Optical Duplicates: 57 (0.00%)
Library Complexity Estimate: 1,851,659
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 277,834 (0.58% / 34.81%)
Hi-C Contacts: 520,263 (1.09% / 65.19%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type %(L-I-O-R): 27% - 24% - 25% - 24%
Inter-chromosomal: 16,679  (0.03% / 2.09%)
Intra-chromosomal: 503,584  (1.05% / 63.10%)
Short Range (<20Kb): 501,008  (1.05% / 62.78%)
Long Range (>20Kb): 1,853  (0.00% / 0.23%)