Info • Cortinarius saniosus 2018PMI107 v1.1
Please note that this organism is for archival use only. Please see the current Cortinarius saniosus 2018PMI107 v2.0 site for the latest data and information.

Status

[April 2022] The Cortinarius saniosus 2018PMI107 v1.1 genome was sequenced with PacBio, assembled with Flye, and annotated with the JGI Annotation Pipeline. Due to limited material, the genome assembly and annotation are fragmented. Mitochondrial genome was assembled separately and is available in the downloads 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.

Genome Assembly
Genome Assembly size (Mbp) 209.77
Sequencing read coverage depth 46.10x
# of contigs 6661
# of scaffolds 6661
# of scaffolds >= 2Kbp 6619
Scaffold N50 1473
Scaffold L50 (Mbp) 0.04
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.34, 0.32, 0.28


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 80351 71232 88.7%
Ests est.fasta 181295837 179886987 99.2%


Gene Models FilteredModels1
length (bp) of: average median
gene 1639 1302
transcript 1293 1044
exon 239 148
intron 80 58
description:
protein length (aa) 391 301
exons per gene 5.42 4
# of gene models 26292


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.