Info • Sistotrema muscicola OMC 1658 v1.0


[June 2020] The Sistotrema muscicola OMC 1658 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 Sistotrema muscicola OMC 1658 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 43.67
Sequencing read coverage depth 319.27x
# of contigs 215
# of scaffolds 215
# of scaffolds >= 2Kbp 215
Scaffold N50 7
Scaffold L50 (Mbp) 2.75
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 4.01, 3.51, 3.31

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 67024 61270 91.4%
Ests est.fasta 202353817 200430894 99.0%

Gene Models FilteredModels1
length (bp) of: average median
gene 1944 1670
transcript 1558 1323
exon 235 145
intron 71 62
protein length (aa) 452 367
exons per gene 6.63 5
# of gene models 10463



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.