Info • Amanita rubescens Přilba v1.0


[March 2019] The genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity.i The mitochondrial genome was assembled separately and is available on the Download page.

The DNA sample source is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. Many of the smaller 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 Amanita rubescens Přilba v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 76.59
Sequencing read coverage depth 573.53x
# of contigs 817
# of scaffolds 817
# of scaffolds >= 2Kbp 816
Scaffold N50 102
Scaffold L50 (Mbp) 0.16
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.67, 1.65, 1.50

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 82560 66516 80.6%
Ests est.fasta 165207273 163555703 99.0%

Gene Models FilteredModels1
length (bp) of: average median
gene 1715 1448
transcript 1404 1182
exon 235 147
intron 64 54
protein length (aa) 418 336
exons per gene 5.98 5
# of gene models 16076

Genome Reference(s)


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.