Info • Suillus pictus EM44 v1.0

Status

Assembly v1 (January 2016) is a standard draft assembly, using Pacbio and Illumina gDNAs assembled with Falcon, improved with finisherSC, and polished with quiver.

Suillua pictus EM44 is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. 716 of the 1400 scaffolds are very similar to larger scaffolds and are predicted to constitute an alternate or secondary haplotype. To represent these primary and secondary haplotypes in the Portal, we have created 'primary alleles' and 'secondary alleles' gene model tracks, comprising the models found on each haplotype. The goal of the GeneCatalog (GC) is to produce a non-redundant set of models which captures the full functional repertiore of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.

Summary statistics for the Suillus pictus EM44 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 87.09
Sequencing read coverage depth 73.85x
# of contigs 1400
# of scaffolds 1400
# of scaffolds >= 2Kbp 1395
Scaffold N50 186
Scaffold L50 (Mbp) 0.13
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.77, 0.75, 0.71


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 67526 43614 64.6%
Ests est.fasta 193436861 188087975 97.2%


Gene Models FilteredModels2
length (bp) of: average median
gene 1481 1196
transcript 1187 939
exon 214 139
intron 67 55
description:
protein length (aa) 342 261
exons per gene 5.54 4
# of gene models 19349


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.