Thanks. Based on this discussion, I decided to switch to Nipponbare, as it may be easier to analyse.

Thanks. This is from 2006, I hoped for something newer.

See my edit. May be that is the latest one.

This looks very good, but isnt Nipponbare a strain of subspecies japonica, as SES wrote?

I am not so familiar with rice genomes, but the website says (according to SES also), it is commonly used as the rice reference. As in humans, there is hg18, hg19 etc commonly used as reference genome.

Thanks for help. I decided to analyse Nipponbare instead of Indica, because as you write, it is often used as reference.

Note that indica and japonica are considered subspecies of O. sativa and are phenotypically distinct (indica is long-grain rice, japonica is short-grain rice). The cultivated line (I used the term strain before, but cultivar or line is more common) Nipponbare of subsp. japonica was chosen by the International Rice Genome Sequencing Project to serve as the reference. The difference between these assemblies is not a matter of versioning (hg18 vs. hg19), but these are distinct subspecies and you should the appropriate one for your study (use Nipponbare if you only need one "rice" genome).