8. Annotate SNP List

Next thing we want to do is to look for candidate genes within the QTL region in Nipponbare, go to “Search”-> “Gene Loci”.

Set “Japonica nipponbare” as reference genome.

Set “SNP Annotator (My SNP List)” in Search.

Set “All” to search all Gene models available.

Tick the box to “Include gene interactions (RiceNetv2, PRIN)” and “Gene Ontology” annotations. You may choose to add more to gather more annotations for this region.

The result should be a table which contains the annotations that can be grouped by marker position, gene locus, or by QTL.