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Info • Serpula lacrymans S7.9 v1.0
Please note that this organism is for archival use only. Please see the current Serpula lacrymans S7.9 v2.0 site for the latest data and information.

Status

Assembly v1.0 (December 2009): The assembly release version 1.0 of whole genome shotgun reads was constructed with Arachne, using paired end sequencing reads at an average coverage of ~8.01X. After trimming for vector and quality, 494,556 reads assembled into 46 main genome scaffolds totaling 42.8 MB. Roughly half of the genome is contained in 6 scaffolds all at least 2.9 MB in length.

Nuclear Genome Assembly: v1.0
Scaffold count: 46
All Contig count: 434
Scaffold sequence bases total: 42.8 Mb
Scaffolded (Large) Contig sequence bases total: 42.4 Mb
Estimated % sequence bases in gaps: 0.9%
Scaffold N50: 6.0 Mb
Contig N50: 0.6 Mb
Number of scaffolds > 50.0 Kb: 24
% in scaffolds > 50.0 Kb: 99.6%

Annotation v1.0 (December 2009) of the v1.0 assembly was produced by the JGI Annotation Pipeline, using a variety of homology-based and ab initio gene predictors. After filtering for EST support, completeness and homology support, a total of 12917 genes were structurally and functionally annotated.

Nuclear Genome Annotation: v1.0
# gene models: 12917
Gene density: 301.80 genes per Mbp scaffold
Ave.gene length: 1599.71 nt
Ave. protein length: 339.18 aa
Ave. exon frequency: 5.63 exons/gene
Ave. exon length: 222.22 nt
Ave. intron length: 77.19 nt
% complete gene models (with start and stop codons): 87%
% genes with homology support: 69%
% genes with Pfam domains: 42%

Collaborators

  • Daniel Eastwood,Warwick HRI, University of Warwick, Wellesbourne, UK.
  • Nils Hogberg, Department of Forest Mycology & Pathology, Swedish University of Agricultural Sciences, UPPSALA, Sweden.
  • Olaf Schmidt, Department of Wood Biology, University of Hamburg, Hamburg, Germany.

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.