I am new to Perl, would you show me an example of the code I would need to add to my existing code?

Hi,

this is a simplified version checking 3 files:

use strict;
use warnings;

my %result;

open my $A, "<", "file1" or die "could not open file1 $!";
while (<$A>) {
    chomp;
    my $key = (split /\t/, $_)[0];
    $result{$key} = 1;
}
close $A;
open my $B, "<", "file2" or die "could not open file2 $!";
while (<$B>) {
    chomp;
    my $key = (split /\t/, $_)[0];
    $result{$key}++;
}
close $B;
open my $C, "<", "file3" or die "could not open file3 $!";
while (<$C>) {
    chomp;
    my $key = (split /\t/, $_)[0];
    if ($result{$key} == 2) { # this key has been seen in both previou
+s files
        print "Line with $key is present in all three files\n";
    }
}    
close $C;
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The value in the %result hash is basically a counter saying how many times you've seen the key. If you find in file3 a key that has already been seen twice, then the key is present in all 3 files. Please note that this assumes that the key cannot be more than once in file2, but only rather small changes would be required to take this possibility into account.

Update: when reading your answer, I only reread the narrative of your original post, without looking at the file samples. I assumed above that all your three files had the same structure, but only see now that they don't. A few minor changes are needed to cope with the actual structure of your files, but I guess that I still gave you the general idea of the solution.