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Info • Volvox carteri v2.1

Status

The genome sequence and gene models of Volvox carteri were downloaded from Phytozome, the Joint Genome Institute (JGI) plant genomics portal. In order to allow comparative analyses with other algal genomes sequenced by the JGI, a copy of this genome is incorporated into PhycoCosm.

We applied filters to remove if present: 1) transposable elements, 2) pseudogenes, 3) alternative transcripts and overlapping models, and 4) unsupported short models. This resulted in removal of 2,999 models from V. carteri v2.1 and generation of the FilteredModels1 gene track. All published models are available in the ExternalModels track. JGI tools were used to automatically annotate predicted proteins.

Summary statistics for the Volvox carteri v2.1 release are below.
Genome Assembly
Genome Assembly size (Mbp) 131.16
Sequencing read coverage depth 8x
# of contigs 4100
# of scaffolds 434
# of scaffolds >= 2Kbp 408
Scaffold N50 15
Scaffold L50 (Mbp) 2.60
# of gaps 3666
% of scaffold length in gaps 4.4%
Three largest Scaffolds (Mbp) 14.15, 5.17, 5.14


Gene Models FilteredModels1
length (bp) of: average median
gene 6265 5132
transcript 3220 2663
exon 387 167
intron 418 345
description:
protein length (aa) 684 487
exons per gene 8.31 7
# of gene models 13076


Genome Reference(s)

Links

Funding

The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.