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Info • Sistotrema raduloides OMC1660 v1.0

Status

[November 2018] The Sistotrema raduloides OMC1660 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 Sistotrema raduloides OMC1660 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 53.93
Sequencing read coverage depth 242.04x
# of contigs 378
# of scaffolds 378
# of scaffolds >= 2Kbp 374
Scaffold N50 36
Scaffold L50 (Mbp) 0.34
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.33, 2.24, 1.38


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 78164 74315 95.1%
Ests est.fasta 211969621 209815159 99.0%


Gene Models FilteredModels1
length (bp) of: average median
gene 1957 1692
transcript 1555 1335
exon 228 142
intron 71 63
description:
protein length (aa) 454 372
exons per gene 6.82 6
# of gene models 12046


Collaborators

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.