How To Use Geneious 5.4 To Do The Snp Detection?

Question

[arkilis]

I make use of the inner-built tool from Geneious Pro 5.4. to do SNP detect. The dataset I get are seperated into two parts FWD and REV. I drag and drop all the ab1 files into Geneious. and put the ref I get from ensembl into Geneious too.

I do Tools-> Algin/Assemble -> Map to Reference. The outcome is like in the following pic, am I doing something wrong? Thanks