Mycena sp. CBHHK59/15 v1.0


[July 2017] The Mycena sp. CBHHK59/15 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

Mycena sp. CBHHK59/15 is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. 883 of the 1786 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 Mycena sp. CBHHK59/15 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 177.78
Sequencing read coverage depth 44.7x
# of contigs 1786
# of scaffolds 1786
# of scaffolds >= 2Kbp 1775
Scaffold N50 242
Scaffold L50 (Mbp) 0.20
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 3.22, 1.27, 1.10

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 107199 99271 92.6%
Ests est.fasta 163960522 161239866 98.3%

Gene Models FilteredModels1
length (bp) of: average median
gene 1463 1188
transcript 1135 923
exon 212 143
intron 77 55
protein length (aa) 338 259
exons per gene 5.34 4
# of gene models 38334


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.