Gbrowse and blast datasets
Details of tracks currently loaded onto GBrowse:
Putative gene models - The transcriptome assembly was mapped to the genome assembly using the software, GMAP, to generate putative gene models. Transcript IDs have the following convention: version-kmer-ID (e.g. Nbv3K605753726 is version Nbv3, kmer of 60, and ID of 5753726).
Transcriptome profile - RNAseq read distribution profile from 12 different samples are shown. Reads were aligned to the transcriptome assembly using the software, RSEM. Read depth at a position were normalized to the post-processed library size, and multiplied by 10 million. Sample profiles can be over-layed (and auto-scaled) by clicking on 'Showing X of 12 tracks', and checking 'Semi-transparent overlap' at the bottom left corner. Symbols: L - Lab line, QLD - Queensland line, WA - Western Australia line. Sample names are self explanatory, except for: Dstress - drought stressed leaves , Caps - capsules, T_C - tissue cultures of callus.
miRNAs - Small RNA reads from leaf samples were analyzed by the software, miRCAT from the UEA sRNA workbench.
Single/Paired end RNAseq reads - Tracks showing the RSEM alignment of individual RNAseq reads onto the transcriptome assembly. These are combined reads from all the 'L' RNAseq samples, used also for the transcriptome assembly. Paired end tracks display mate information of the single end read data.
Coverage - Read depth profile of all 'L' RNAseq samples combined (from RSEM alignment). Red regions indicate depth below 20 reads, blue regions indicates depth above 20 reads.
For details about these assemblies, see Sequencing Strategy.
Genome assembly - There are currently two formats of the assembly: scaff+contigs - contigs that are scaffolded by paired-end/mate-pair information, containing N's for yet unresolved gaps; contigs - scaffolds are split into individual contigs, removing N's. The current assembly (v0.3) scaffold IDs have the following convention: version-scaffoldID (e.g. Nbv0.3scaffold18718 is version Nbv0.3, and ID of scaffold18718).
Transcriptome assembly - Blast-like descriptions of contigs were added by an in-house annotation pipeline at the PFR institute. Transcript IDs have the following convention: version-kmer-ID (e.g. Nbv3K605753726 is version Nbv3, kmer of 60, and ID of 5753726).