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-Fugacium_kawagutii_V3-Hi-C-scaffold.FINAL-debris-merged -d /oak/stanford/groups/akundaje/marinovg/ENCODE4/single-cell/2024-10-18-NextSeq-run/juicer-L3100+L3105+L3110-pooled-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:  47,773,046
 Normal Paired: 872,303 (1.83%)
 Chimeric Paired: 0 (0.00%)
 Chimeric Ambiguous: 0 (0.00%)
 Unmapped: 46,900,743 (98.17%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 872,303 (1.83%)
WARN [2024-10-20T22:00:15,830]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 666,103 (1.39%)
PCR Duplicates: 206,162 (0.43%)
Optical Duplicates: 38 (0.00%)
Library Complexity Estimate: 1,541,334
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 220,410 (0.46% / 33.09%)
Hi-C Contacts: 445,693 (0.93% / 66.91%)
 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: 11,960  (0.03% / 1.80%)
Intra-chromosomal: 433,733  (0.91% / 65.12%)
Short Range (<20Kb): 425,034  (0.89% / 63.81%)
Long Range (>20Kb): 7,527  (0.02% / 1.13%)