We will now use the Geneious variant finder to find SNPs in our mapped data. Select the contig document and go to Annotate and Predict → Find Variations/SNPs. Reset to the default settings using the Settings cog at the bottom left.
The options in the top ("Find Polymorphisms") panel allow you to set the parameters for when SNPs are called, so that disagreements that result from sequencing errors are filtered out. We will use the default settings as they are normally appropriate for identifying real SNPs - if you want more information on these settings click the "?" button or mouse over the option.
Ensure that the option to Analyze effect of polymorphisms on translations is checked, and change the Default Genetic Code to "Bacterial". This uses the CDS annotation on our reference sequence to determine the coding sequence of our mapped reads, and calculates whether observed SNPs will result in a change in the amino acid sequence.
Leave the other options as they are and click OK
You should now see an annotation track called "Variants: yghJ paired Illumina reads" added to the reference sequence. Click Save and choose "Yes" when asked if you want to apply changes to the original sequence. This will load your SNP track onto the original reference document.
Scroll along the contig document to a position containing a SNP annotation (denoted by a vertical yellow bar). Mouse over the annotation and you'll see a popup window containing information about that SNP. This includes the base change, variant frequency, SNP type, and information about the protein and CDS changes.
To display this information in a table, click the Annotations tab above the sequence viewer. This will bring up a table of all the annotations on your sequence. Click Type and choose "Polymorphism" to display only polymorphism annotations. The table should automatically be showing the relevant columns, such as Polymorphism Type, Variant Frequency, Amino acid/Codon/base change etc. To bring up additional columns or remove existing columns click the Columns button and add/remove the columns you want.
Once you have the table looking the way you want it to, you can export it to a spread sheet by clicking Export table. This will export your table in comma-separated (.csv) format.