Info • Cladonia grayi Cgr/DA2myc/ss v1.0
Please note that this organism is for archival use only. Please see the current Cladonia grayi Cgr/DA2myc/ss v2.0 site for the latest data and information.


Assembly v1 (28 July 2010) is a draft assembly of 454 gDNA reads and shredded Velvet contigs. The latter were assembled from Solexa gDNA reads. A total of 1506 scaffolds and 39.6 Mbp were assembled using Newbler:

Nuclear Genome Assembly: v1.0
Scaffold count: 1506
All Contig count: 5214
Scaffold sequence bases total: 39.6 Mbp
Scaffolded (Large) Contig sequence bases total: 38.4 Mbp
Estimated % sequence bases in gaps: 3.0%
Scaffold N50 / L50: 45 / 219.1 kbp
Contig N50 / L50: 342 / 14.9 kbp
Number of scaffolds > 50.0 Kb: 140
% in scaffolds > 50.0 Kb: 77.6%
% assembly masked by repeats: 7.2%
# ESTs: 740680
% ESTs that align with assembly: 65%

Annotation v1 (28 July 2010) of the v1.0 assembly was produced by the JGI Annotation Pipeline, using a variety of cDNA-based, protein-based, and ab initio gene predictors. After filtering for EST and protein homology support, a total of 11415 genes were structurally and functionally annotated.

Nuclear Genome Annotation: v1.0
# gene models: 11415
Gene density: 288 genes per Mbp scaffold
Avg.gene length: 1832 nt
Avg. protein length: 441 aa
Avg. exon frequency: 3.25 exons per gene
% genes with intron: 81 %
% complete gene models (with start and stop codons): 83%
% genes with NR support: 87%
% genes with Pfam domains: 53%
% genes with transmembrane domain: 19%
% genes in multigene family: 60%
% genes with EST support: 83%





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.