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Info • Cladonia grayi Cgr/DA2myc/ss v2.0


Assembly v3 (25 September 2011) is a draft assembly of 454 and Solexa gDNA reads. A total of 414 scaffolds and 34.6 Mbp were assembled using Velvet and then Newbler.

This genome sequence and gene prediction of the Cladonia grayi mycobiont were not determined by the JGI, but were acquired from Olaf Mueller at Duke U. on September 25 2011. This copy of the genome does not include the mitochondrial chromosomes or genes. The JGI Annotation Pipeline was used to add additional functional annotation to Duke's scaffolds and gene models.

Summary statistics for the Cladonia grayi Cgr/DA2myc/ss v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp} 34.62
Sequencing read coverage depth 15x
# of contigs 519
# of scaffolds 414
# of scaffolds >= 2Kbp 414
Scaffold N50 43
Scaffold L50 (Mbp) 0.24
# of gaps 105
% of scaffold length in gaps 0.2%
Three largest Scaffolds (Mbp) 0.96, 0.83, 0.76

ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests 454_ESTs 740680 564099 76.2%
Other Newbler_contigs 17471 12252 70.1%
Other Velvet_and_Trinity_contigs 17986 17878 99.4%

Gene Models Maker
length (bp) of: average median
gene 1807 1525
transcript 1651 1385
exon 545 320
intron 79 58
protein length (aa) 477 388
exons per gene 3.03 3
# of gene models 11389

Genome Reference(s)


This project was not sequenced at the JGI.