Experiment description: Juicer version 1.5.6; 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/2019-12-14-NextSeq-run-2/juicer-L1274-Aureococcus_anophagefferens-Hi-C -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-12-14-NextSeq-run-2/juicer-L1274-Aureococcus_anophagefferens-Hi-C -p /oak/stanford/groups/akundaje/marinovg/genomes/Pelagophyta/Aureococcus_anophagefferens-v1.0/GCA_000186865.1_v_1.0_genomic+chrM+chrC.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Pelagophyta/Aureococcus_anophagefferens-v1.0/bwa-indexes/GCA_000186865.1_v_1.0_genomic+chrM+chrC_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Pelagophyta/Aureococcus_anophagefferens-v1.0/bwa-indexes/GCA_000186865.1_v_1.0_genomic+chrM+chrC.fa                                                                                                                                                                          
Sequenced Read Pairs:  29,027,688
 Normal Paired: 25,364,610 (87.38%)
 Chimeric Paired: 0 (0.00%)
 Chimeric Ambiguous: 0 (0.00%)
 Unmapped: 3,663,078 (12.62%)
 Ligation Motif Present: 97,887 (0.34%)
Alignable (Normal+Chimeric Paired): 25,364,610 (87.38%)
Unique Reads: 12,513,643 (43.11%)
PCR Duplicates: 12,843,130 (44.24%)
Optical Duplicates: 7,837 (0.03%)
Library Complexity Estimate: 15,567,200
Intra-fragment Reads: 585,908 (2.02% / 4.68%)
Below MAPQ Threshold: 3,426,463 (11.80% / 27.38%)
Hi-C Contacts: 8,501,272 (29.29% / 67.94%)
 Ligation Motif Present: 18,335  (0.06% / 0.15%)
 3' Bias (Long Range): 32% - 68%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 816,491  (2.81% / 6.52%)
Intra-chromosomal: 7,684,781  (26.47% / 61.41%)
Short Range (<20Kb): 7,494,190  (25.82% / 59.89%)
Long Range (>20Kb): 190,495  (0.66% / 1.52%)