Generate SNP/indel annotation in Arabidopsis
The Ensembl Variant Effect Predictor will annotate your A. thaliana variants:
http://plants.ensembl.org/Oryza_sativa/Tools/VEP

The web based tool will use the reference genome assembly and gene annotation used in the Ensembl browser:
http://plants.ensembl.org/Arabidopsis_thaliana/Info/Annotation/#assembly

However, if you use the command-line version of VEP, you can provide your own reference genome assembly and gene annotation files to be used as a reference.

You can find all of the documentation here:
http://www.ensembl.org/info/index.html

Best wishes

Ben
Ensembl Helpdesk