Info • Chroogomphus vinicolor CA002 v1.0


The nuclear genome was sequenced with PacBio, assembled with Flye, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity. The mitochondrial genome was assembled separately and is available on the Download page.

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) 495.70
Sequencing read coverage depth 11.46x
# of contigs 1868
# of scaffolds 1868
# of scaffolds >= 2Kbp 1868
Scaffold N50 161
Scaffold L50 (Mbp) 0.90
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 5.89, 5.51, 4.82

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 103603 91815 88.6%
Ests est.fasta 138105329 105842287 76.6%

Gene Models FilteredModels2
length (bp) of: average median
gene 1409 1134
transcript 1097 849
exon 213 141
intron 77 56
protein length (aa) 336 253
exons per gene 5.16 4
# of gene models 21397



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.