"I appreciate your response, but I believe that it should be much more simpler than this, check the FINAL OUT portion in the post that I've just added, it explains it much more. Thanks!"

So, two days after you posted your question you decide to tell us the exact output format you want. You then have a problem with my sample output which, in the absence of any other information, I had to guess at.

If you're incapable of modifying

    print join(',' => @$row[2,3,4]),
        "\n\tfound in '$gen_file':\n\t\t", join ', ' => @$row;
[download]

which outputs

34787800,A,G
    found in 'pm_1079751_source1.gen':
        C1, M4, 34787800, A, G, ... source1 info ...
[download]

to code which just outputs the first line of that, i.e.

34787800,A,G
[download]

I suggest you read "Perl introduction for beginners".