Due to the emerging COVID-19 pandemic, JGI will not be accepting or processing any samples because of reduced onsite staffing until further notice.
Info • Amylocorticium subincarnatum OMC1654 v1.0

Status

[December 2018] The Amylocorticium subincarnatum OMC1654 genome was sequenced with PacBio, assembled with Falcon (v1.8.8), and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the Download section.

The genome is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. Many of the scaffolds are very similar to larger scaffolds and are predicted to constitute an alternate or secondary haplotype. To represent these primary and secondary haplotypes in the Portal, we have created 'primary alleles' and 'secondary alleles' gene model tracks, comprising the models found on each haplotype. The goal of the GeneCatalog (GC) is to produce a non-redundant set of models which captures the full functional repertiore of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.

Summary statistics for the Amylocorticium subincarnatum OMC1666 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 45.93
Sequencing read coverage depth 215.45x
# of contigs 364
# of scaffolds 364
# of scaffolds >= 2Kbp 360
Scaffold N50 23
Scaffold L50 (Mbp) 0.66
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.07, 1.77, 1.53


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 114348 111213 97.3%
Ests est.fasta 297182106 293851178 98.9%


Gene Models FilteredModels1
length (bp) of: average median
gene 1863 1605
transcript 1496 1283
exon 236 147
intron 71 59
description:
protein length (aa) 444 362
exons per gene 6.33 5
# of gene models 10977


Collaborators

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.