Info • Phytophthora capsici LT1534 v11.0

Status

Assembly v11 (20 Aug 2010) is a hybrid assembly of 454 and Sanger gDNA reads. A total of 917 scaffolds and 64.0 Mbp were assembled using Arachne:

Nuclear Genome Assembly: v11.0 v1.0
Scaffold count: 917 1406
All Contig count: 10760 36297
Scaffold sequence bases total(Mbp): 64.0 107.8
Scaffolded Contig sequence bases total(Mbp): 56.0 Mb 63.2 Mb
Estimated % sequence bases in gaps: 12.5% 40.9%
Scaffold N50 / L50 (# / kbp): 29 / 706 28 / 439
Contig N50 / L50 (# / kbp): 397 / 35 1574 / 10
Number of scaffolds > 50.0 Kb: 140 302
% in scaffolds > 50.0 Kb: 91.9% 79.7%
% assembly masked by repeats: 14.4% 0.2%
# finished cDNAs: 1260 1260
% finished cDNAs that align with assembly: 97.1% 83.1%

Annotation v11 (20 August 2010) of the v11.0 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 19805 genes were structurally and functionally annotated.

Nuclear Genome Annotation: v11.0 v1.0
# gene models: 19805 17414
Gene density(# / Mbp scaffold): 309 162
Avg.gene length (nt): 1253 1625
Avg. protein length (aa) : 314 381
Avg. exon frequency (# / gene): 2.20 2.62
% genes with intron: 50% 58%
% complete models (with start+stop codons): 69% 72%
% genes with EST support: 50% 53%
% genes with nr support: 75% 76%
% genes with Pfam domains: 47% 42%
% genes with transmembrane domain: 15% 18%
% genes in multigene family: 78% 79%

Genome Reference(s)

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.