Assembly v1 ((28 July 2010) is a draft assembly of 454 gDNA reads. A total of 153 scaffolds and 56.1 Mbp were assembled using Newbler:
Nuclear Genome Assembly: | v1.0 |
Scaffold count: | 153 |
All Contig count: | 970 |
Scaffold sequence bases total: | 56.1 Mbp |
Scaffolded (Large) Contig sequence bases total: | 55.8 Mbp |
Estimated % sequence bases in gaps: | 0.7% |
Scaffold N50 / L50: | 25 / 784.9 kbp |
Contig N50 / L50: | 138 / 119.5 kbp |
Number of scaffolds > 50.0 Kb: | 109 |
% in scaffolds > 50.0 Kb: | 99.2% |
% assembly masked by repeats: | 0.1% |
Annotation v1 (28 July 2010) of the v1.0 assembly was produced by the JGI Annotation Pipeline, using a variety of protein-based and ab initio gene predictors. After filtering for protein homology support, a total of 7159 genes were structurally and functionally annotated:
Nuclear Genome Annotation: | v1.0 |
# gene models: | 7159 |
Gene density: | 128 genes per Mbp scaffold |
Avg.gene length: | 4549 nt |
Avg. protein length: | 465 aa |
Avg. exon frequency: | 9.26 exons per gene |
% genes with intron: | 96 % |
% complete gene models (with start and stop codons): | 74% |
% genes with NR support: | 93% |
% genes with Pfam domains: | 73% |
% genes with transmembrane domain: | 15% |
% genes in multigene family: | 60% |
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.