Info • Hymenopellis radicata IJFM A160 v1.0

Status

(Mar 2016) The Hymenopellis radicata IJFM A160 genome was sequenced using PacBio, assembled with Falcon, improved with finisherSC, polished with Quiver, and annotated with the JGI annotation pipeline.

The JGI annotation pipeline identified 6,316 gene models as possible diploid alleles, and excluded them from the filtered model/gene catalog set. These models are shown in the track "secondary_alleles", and are available from the download page.

Summary statistics for the Hymenopellis radicata v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 78.59
Sequencing read coverage depth
# of contigs 1968
# of scaffolds 1968
# of scaffolds >= 2Kbp 1877
Scaffold N50 195
Scaffold L50 (Mbp) 0.10
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.28, 0.93, 0.74


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 55564 48816 87.9%


Gene Models FilteredModels1
length (bp) of: average median
gene 1454 1212
transcript 1179 982
exon 223 142
intron 66 53
description:
protein length (aa) 345 277
exons per gene 5.29 4
# of gene models 27481


Collaborators

José María Barrasa, Universidad de Alcalá, Spain

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.