Info • Mycena filopes CBHHK001 v1.0


[December 2017] The Mycena filopes CBHHK001 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 filopes CBHHK001 is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. 197 of the 277scaffolds 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 filopes CBHHK001 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 112.00
Sequencing read coverage depth 58.23x
# of contigs 277
# of scaffolds 277
# of scaffolds >= 2Kbp 277
Scaffold N50 26
Scaffold L50 (Mbp) 1.61
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 4.09, 3.16, 3.05

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 76576 73197 95.6%
Ests est.fasta 80092499 79702529 99.5%

Gene Models FilteredModels1
length (bp) of: average median
gene 1741 1492
transcript 1384 1194
exon 223 137
intron 71 55
protein length (aa) 414 346
exons per gene 6.20 5
# of gene models 29152


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.