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Info • Caecomyces churrovis A v1.0

Status

[December 2017] The Caecomyces churrovis A genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline.

Caecomyces churrovis A is likely a diploid or polymorphic heterokaryon, and this is reflected in an assembly and annotation with significant separation of alleles. 6615 of the 7737 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 Caecomyces churrovis A v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 165.50
Sequencing read coverage depth 88.81x
# of contigs 7737
# of scaffolds 7737
# of scaffolds >= 2Kbp 7550
Scaffold N50 783
Scaffold L50 (Mbp) 0.03
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.63, 0.59, 0.56


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 40186 33100 82.4%
Ests est.fasta 111540536 109474417 98.1%


Gene Models FilteredModels3
length (bp) of: average median
gene 2372 1900
transcript 1669 1303
exon 354 156
intron 192 138
description:
protein length (aa) 497 368
exons per gene 4.71 3
# of gene models 15009


Funding

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.