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Current Release: OMAP Chromosome 3 Short Arm (AA genome type)
A minimum tiling path of BAC clones was selected across the short arm of chromosome 3 of Oryza rufipogon using a heavily manually edited physical map. The BACs were divided into two 9Mb pools and Roche GSFLX sequenced (Titanium and paired-end reads) to a depth of 35X. Sequence reads were assembled with Newbler (454) and Bambus (Pop et al. 2004), followed by manual inspection of the assembly (Rounsley et al. 2009). The assembly resulted in a total of 532 scaffolds with a scaffold N50 of 45,715bp
Reference:
"Hierarchical scaffolding with Bambus." Pop M, Kosack DS, Salzberg SL, Genome Research, 2004. 14(1):149-59.
Additional annotations generated by the Gramene project include:
- Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see more.
- Identification of various repeat features from MIPS and AGI repeat libraries
- Ab initio gene prediction with program fgenesh
- Pairwise Whole genome alignments (blastz-chain-net) with Oryza sativa Japonica
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