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#!/usr/bin/perl
use strict;
...
foreach my $k (keys %sum){
    print $OUT "$sum{$k}\n";
}

CREATE DATABASE kmers;
CREATE TABLE matrix (file int, number int, key (file), key (number));

use DBI; 
my $dbh = DBI->new('DBI:mysql:database=kmers;host=127.0.0.1','mysql_us
+er','');
...
}
$sth->finish();

my $count_query = "SELECT number,COUNT(number) FROM matrix GROUP BY nu
+mber ORDER BY number";
$sth = $dbh->prepare($count_query);

#sum up
#foreach my $k (keys %sum){
...
while (my $res = $sth->fetchrow_arrayref()) {
   print $OUT $res->[1]\n";
}