Info • Mycena leptocephala CBHHK5/15 v1.0


[June 2018] The Mycena leptocephala CBHHK5/15 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.

M. leptocephala is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. 2044 of the 4647 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 leptocephala CBHHK5/15 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 377.32
Sequencing read coverage depth 66.46x
# of contigs 4647
# of scaffolds 4647
# of scaffolds >= 2Kbp 4577
Scaffold N50 593
Scaffold L50 (Mbp) 0.16
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.91, 1.82, 1.61

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 134599 121145 90.0%
Ests est.fasta 119969725 118831207 99.1%

Gene Models FilteredModels1
length (bp) of: average median
gene 1469 1219
transcript 1110 917
exon 206 135
intron 84 55
protein length (aa) 344 278
exons per gene 5.39 4
# of gene models 75907


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.