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/Symbiodinium/2023-09-18-Fugacium_kawagutii-Hi-C/juicer-Fugacium_kawagutii_V3-Hi-C -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2023-09-18-Fugacium_kawagutii-Hi-C/juicer-Fugacium_kawagutii_V3-Hi-C -p /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Fugacium_kawagutii_V3/Fugacium_kawagutii_V3_genome_scaffold.chrom.sizes -y none -s none -z /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Fugacium_kawagutii_V3/bwa-indexes/Fugacium_kawagutii_V3_genome_scaffold.fa                                                                                                                                                                                                                                                                                                                                                
Sequenced Read Pairs:  1,286,459,855
 Normal Paired: 1,018,372,681 (79.16%)
 Chimeric Paired: 60,074,530 (4.67%)
 Chimeric Ambiguous: 8,566,117 (0.67%)
 Unmapped: 199,446,527 (15.50%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 1,078,447,211 (83.83%)
WARN [2023-09-22T15:24:53,748]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 497,811,875 (38.70%)
PCR Duplicates: 580,635,336 (45.13%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 594,891,611
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 103,250,929 (8.03% / 20.74%)
Hi-C Contacts: 394,560,946 (30.67% / 79.26%)
 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: 64,198,890  (4.99% / 12.90%)
Intra-chromosomal: 330,362,056  (25.68% / 66.36%)
Short Range (<20Kb): 297,195,039  (23.10% / 59.70%)
Long Range (>20Kb): 33,136,363  (2.58% / 6.66%)