Info • Sidera vulgaris OMC 1730 v1.0


[August 2020] The Sidera vulgaris OMC 1730 v1.0 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.

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 Sidera vulgaris OMC 1730 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 67.25
Sequencing read coverage depth 267.64x
# of contigs 243
# of scaffolds 243
# of scaffolds >= 2Kbp 243
Scaffold N50 19
Scaffold L50 (Mbp) 0.98
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.89, 2.77, 2.76

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 70562 67855 96.2%
Ests est.fasta 156938189 155808939 99.3%

Gene Models FilteredModels2
length (bp) of: average median
gene 1929 1695
transcript 1583 1388
exon 251 150
intron 67 57
protein length (aa) 469 392
exons per gene 6.30 5
# of gene models 13089



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.