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-scaffold.FINAL-debris-merged -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2023-09-18-Fugacium_kawagutii-Hi-C/juicer-Fugacium_kawagutii_V3-Hi-C-scaffold.FINAL-debris-merged -p /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2023-09-18-Fugacium_kawagutii-Hi-C/juicer-Fugacium_kawagutii_V3-Hi-C-3D_DNA-r20/Fugacium_kawagutii_V3_genome_scaffold.FINAL.debris-merged.chrom.sizes -y none -s none -z /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2023-09-18-Fugacium_kawagutii-Hi-C/juicer-Fugacium_kawagutii_V3-Hi-C-3D_DNA-r20/bwa-indexes/Fugacium_kawagutii_V3_genome_scaffold.FINAL.debris-merged.fa                                                                                                                                              
Sequenced Read Pairs:  1,286,459,855
 Normal Paired: 1,018,073,529 (79.14%)
 Chimeric Paired: 59,847,375 (4.65%)
 Chimeric Ambiguous: 9,102,983 (0.71%)
 Unmapped: 199,435,968 (15.50%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 1,077,920,904 (83.79%)
WARN [2023-10-21T04:03:28,914]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 497,599,528 (38.68%)
PCR Duplicates: 580,321,376 (45.11%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 594,657,851
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 103,031,172 (8.01% / 20.71%)
Hi-C Contacts: 394,568,356 (30.67% / 79.29%)
 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: 61,266,753  (4.76% / 12.31%)
Intra-chromosomal: 333,301,603  (25.91% / 66.98%)
Short Range (<20Kb): 296,855,010  (23.08% / 59.66%)
Long Range (>20Kb): 36,416,024  (2.83% / 7.32%)