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/2023-12-21-Amphidinium_carteri_Hi-C/juicer-Amphidinium_carterae-Acart.genome.v1-Hi-C -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2023-12-21-Amphidinium_carteri_Hi-C/juicer-Amphidinium_carterae-Acart.genome.v1-Hi-C -p /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Amphidinium_carterae-Acart.genome.v1/Acart.genome.v1.chrom.sizes -y none -s none -z /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Amphidinium_carterae-Acart.genome.v1/bwa-indexes/Acart.genome.v1.fa                                                                                                                                                                                                                                                                                                                              
Sequenced Read Pairs:  747,098,834
 Normal Paired: 473,229,288 (63.34%)
 Chimeric Paired: 141,425,785 (18.93%)
 Chimeric Ambiguous: 99,529,749 (13.32%)
 Unmapped: 32,914,012 (4.41%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 614,655,073 (82.27%)
WARN [2023-12-24T05:27:19,643]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 461,913,658 (61.83%)
PCR Duplicates: 152,741,415 (20.44%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 1,022,009,457
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 216,121,263 (28.93% / 46.79%)
Hi-C Contacts: 245,792,395 (32.90% / 53.21%)
 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: 57,563,192  (7.70% / 12.46%)
Intra-chromosomal: 188,229,203  (25.19% / 40.75%)
Short Range (<20Kb): 174,524,767  (23.36% / 37.78%)
Long Range (>20Kb): 13,670,189  (1.83% / 2.96%)