Info • Mycocalia denudata CBS 494.85 v1.0


The Mycocalia denudata CBS 494.85 v1.0 genome was sequenced with PacBio, assembled with HiCanu, and annotated with the JGI Annotation Pipeline. 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) 72.67
Sequencing read coverage depth 123.42x
# of contigs 194
# of scaffolds 194
# of scaffolds >= 2Kbp 194
Scaffold N50 11
Scaffold L50 (Mbp) 2.72
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 4.82, 4.76, 4.31

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 63563 61827 97.3%
Ests est.fasta 135580684 133721399 98.6%

Gene Models FilteredModels1
length (bp) of: average median
gene 1885 1618
transcript 1538 1320
exon 240 148
intron 66 57
protein length (aa) 444 358
exons per gene 6.42 5
# of gene models 13474


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.