for my $penta (keys %totalProbability) {
    print "$totalProbability{$penta}, $totalCounts{$penta}, ...\n";
}

##</code><code>##

my %stats;
while (<FREQ>) {
   chomp;
   my ($pent, $pentExpected, $pentObserved, $pentTotal) = split("\t", $_);
   next if !defined $pentTotal; # skip malformed lines and end line

   my $h =  { 
        pent=>$pent, count=>$pentObserved, prob=>$pentExpected,
        pentTotal=>$pentTotal
   };
   push @data,$h;

   if (exists $stats{$pent}) {
      $stats{$pent} = {
          probTotal  => $$h{prob},
          countTotal => $$h{count},
          pentTotal  => $$h{pentTotal},
      };
   }
   else {
      $stats{$pent}{probTotal} += $$h{prob};
      $stats{$pent}{countTotal} += $$h{count};
      $stats{$pent}{pentTotal}  += $$h{pentTotal};
   }
}