Info • Raphidocelis subcapitata NIES-35


The genome sequence and gene models of Raphidocelis subcapitata NIES-35 were not determined by the JGI, but were downloaded from NCBI, on November 14, 2019. In order to ensure this genome is comparable to those sequenced by the JGI, we applied filters to remove if present: 1) transposable elements, 2) pseudogenes, 3) alternative transcripts and overlapping models, 4) alleles on secondary scaffolds and 5) unsupported short models. This resulted in the removal of 295 models and the generation of the FilteredModels1 (GeneCatalog) gene track. All published models are available in the ExternalModels track. Please note that this copy of the genome is not maintained by NCBI and is therefore not automatically updated. In order to allow comparative analyses with other algal genomes sequenced by the JGI, a copy of this genome is incorporated into PhycoCosm. The JGI Annotation Pipeline was used to add functional annotation to this genome.

Genome Assembly
Genome Assembly size (Mbp) 51.16
Sequencing read coverage depth 80x
# of contigs 1480
# of scaffolds 300
# of scaffolds >= 2Kbp 300
Scaffold N50 46
Scaffold L50 (Mbp) 0.34
# of gaps 1180
% of scaffold length in gaps 2.2%
Three largest Scaffolds (Mbp) 1.44, 1.07, 1.03

Gene Models FilteredModels1
length (bp) of: average median
gene 3019 2390
transcript 1705 1356
exon 251 141
intron 229 205
protein length (aa) 568 452
exons per gene 6.78 5
# of gene models 13088

Genome Reference(s)



This project was not sequenced at the JGI.