Info • Conocybe apala SZMC-NL-8967 v1.0


[November 2018] The Conocybe apala SZMC-NL-8967 genome was sequenced with PacBio, assembled with Falcon (v1.8.8), and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the Download 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.

Summary statistics for the Conocybe apala SZMC-NL-8967 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 64.08
Sequencing read coverage depth 190.11x
# of contigs 2441
# of scaffolds 2441
# of scaffolds >= 2Kbp 2187
Scaffold N50 227
Scaffold L50 (Mbp) 0.06
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.95, 0.70, 0.66

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 139754 91516 65.5%
Ests est.fasta 158815777 142374791 89.6%
  • Please note: Using BLAST, unmapped RNA reads and contigs were found to hit plant (Selaginella moellendorffii), as well as some Agaricomycetes (target organism, Chondrostereum purpureum, Rhizoctonia sp), suggesting that the RNA library was contaminated.

Gene Models FilteredModels2
length (bp) of: average median
gene 1783 1535
transcript 1427 1229
exon 240 148
intron 74 60
protein length (aa) 421 351
exons per gene 5.95 5
# of gene models 17284



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.