Data sets available for RefBeet-1.1, annotations as of February 2013
====================================================================

Assembly
--------
- RefBeet-1.1.fna: The genome assembly of reference genotype KWS2320 (Beta 
vulgaris ssp. vulgaris) integrated with genetic and physical maps
- RefBeet-1.1.masked.fna: Masked genome assembly, repeats determined by 
RepeatModeler based on RefBeet-1.1, masked by RepeatMasker

Protein coding genes
--------------------
- RefBeet.genes.1302.cds.fa: CDS of 27,421 predicted gene models supported 
by mRNA evidence and filtered for transposable elements
- RefBeet.genes.1302.mrna.fa: mRNA sequences of these genes
- RefBeet.genes.1302.pep.fa: Translated protein sequences of these genes
- RefBeet.funct_anno.1302.txt: List of functional annotations for these 
genes. The longest protein sequence per gene was used for sequence 
similarity searches.
- RefBeet.unfiltered_genes.1302.gff3: Positions of all protein coding genes 
predicted including genes which are not supported by mRNA evidence

Non-coding RNA genes
--------------------
- RefBeet.ncgenes.1302.fa: Sequences of predicted non-coding RNA genes
- RefBeet.ncgenes.1302.gff3: Positions of predicted non-coding RNA genes

Repeats
-------
- RefBeet.repeats.1302.gff3: Positions and annotation of repeats determined 
by RepeatModeler based on RefBeet-1.1, repeat classification was manually 
revised

Variants
--------
- RefBeet.variants.1302.gff3: All variant positions of RefBeet-1.1 after
comparison with double haploid sugar beet accessions KDHBv, UMSBv, YMoBv, 
YTiBv, as well as sea beet (DeKBm). Differences between RefBeet-1.1 and 
RefBv (same genotype) may represent errors in the reference assembly. 
Variants were determined by read mapping and by scaffold alignment. Variants 
of sea beet (DeKBm) were determined by read mapping only.