Data sets available for RefBeet-1.2 =================================== Assembly -------- - RefBeet-1.2.fna: The genome assembly of reference genotype KWS2320 (Beta vulgaris ssp. vulgaris) integrated with genetic and physical maps as well as GBS data (genotyping by sequencing) - RefBeet-1.2.masked.fna: Masked genome assembly, repeats determined by RepeatModeler based on RefBeet-1.2, masked by RepeatMasker Protein coding genes -------------------- - *.genes.1408.cds.fa: CDS of predicted gene models supported by mRNA evidence - *.genes.1408.mrna.fa: mRNA sequences of these genes - *.genes.1408.pep.fa: Translated protein sequences of these genes - *.unfiltered_genes.1408.gff3: Positions of all protein coding genes predicted including genes which are not supported by mRNA evidence Validated gene models --------------------- - validated-genes.SMRT.RefBeet-1.2.gff3: 2267 gene models predicted by Augustus and validated by SMRT full-insert sequences; additional 665 gene models solely inferred from full-insert SMRT sequences - validated-genes.manually.RefBeet-1.1.gff3: 400 manually validated gene models Corrected SMRT sequences ------------------------ - SMRT.KWS2320.corrected.fasta.gz: SMRT sequences corrected with Illumina short reads using the proovread software. Augustus hints and anchors ------------------------ - Augustus-hints-anchors.RefBeet-1.2.gff.gz: Gene models were calculated using these mRNA-seq exon and intron hints, intron anchors, repeat hints, SMRT anchors, hints from Sanger ESTs and Roche/454 sequences.