haven't had a chance to read the code but wouldn't something like this do what you want?

Untested

#!/usr/bin/perl

use strict;
use warnings;
my %dups;

while (<DATA>) {
   my $col = (split /\t/)[1];  # get the second col
   $dups{$col}++;  # put the text into a hash and increment counter.
}

print +($_ , " : ", $dups{$_},$/) for (keys %dups); # print the counts
[download]