Info • Paraphoma fimeti UNK v1.0

Status

[October 2022] The Paraphoma fimeti UNK genome is one of two metagenome-extracted genomes from a set of contaminated samples. Sequenced by Illumina, binned DNA reads for Paraphoma fimeti UNK and Penicillium rubens UNK were assembled separately by SPAdes, and a shared transcriptome library was assembled by Trinity. Subsequently, the JGI Annotation Pipeline produced structural and functional annotations. The P. fimeti UNK mitochondrial genome was assembled separately and is available in the downloads section.

Genome Assembly
Genome Assembly size (Mbp) 36.16
Sequencing read coverage depth 121.51x
# of contigs 144
# of scaffolds 132
# of scaffolds >= 2Kbp 132
Scaffold N50 17
Scaffold L50 (Mbp) 0.71
# of gaps 12
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.90, 1.60, 1.59


Note: this transcriptome library was determined to be a sample heavily contaminated with Penicillium rubens UNK. Therefore, mapping to Paraphoma fimeti UNK is low compared to typical axenic RNAseq libaries.
ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 92950 57336 61.7%
Ests est.fasta 150172547 79577907 53.0%


Gene Models FilteredModels1
length (bp) of: average median
gene 1863 1587
transcript 1714 1469
exon 618 393
intron 86 55
description:
protein length (aa) 489 398
exons per gene 2.78 2
# of gene models 13045


Collaborators

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.