my $snp_covered{$mismatch}= $snp_chip_covered; ...doesn't make sense.

You'll need to declare your hash as a lexical (my) variable outside the loop, so it won't get clobbered each time through. Then you can add keys to it in the normal way.

However, I don't quite understand what you're trying to do with %snp_covered. You're using the same key each time ($mismatch, which is 3) and overwriting the previous value each time there's a match. If you just want to keep track of the total number of matches, you can use a plain scalar and just increment it each time: 

my $count;
while(<INPUT2>){
         chomp;
          my @current_line  = split /\t/;
          my $mismatch =3;
          next unless $current_line[5] == 1 && 
            $current_line[14] >= $mismatch;

          $count++;
}

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In reply to Re: Hash making by friedo
in thread Hash making by sesemin

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