Exporting nt's differences from MEGA alignment
You don't say which version of MEGA you are using, but this works for MEGA X on Linux:


Open your alignment with the "Sequence data explorer"
At the "Highlight" menu, select "Variable sites".
Then at the menu "Statistics", select "Use only highlighted sites" and select what you consider an appropriate output - I choose "Display results as CSV".
Now at the menu "Data" select "Export data"; at the "Sequence data export options window" if necessary select the data format again, and select "For each site" at "Writing site numbers", and select "Only highlighted sites" at "Selected sites to include".


This will result in a comma-separated values file, showing only positions with variable sites.