I was aiming to identify outlier loci under selection for populations of a South African bee species using RAD-Seq. Overall, I got 1,119 outliers using various outlier approaches. However, I was able to annotate only a small proportion (12 %, i.e. 136) in BLAST2GO and even less could be associated with GO terms, i.e. 59 loci. Thus, I was wondering how meaningful is it do GO term enrichment when most of the outliers are anyways not captured in the list of annonated locu?! Moreover, there is no reference genome existing for my species which complicates things even more.
Please let me know what you think.