You want to count the number of instances of each character (hash) for each column (array), so you want a AoH.

my @counts;
while (<>) {
   my ($id, @fields) = split;
   for my $col_num (0..$#fields) {
      ++$counts[$col_num]{ $fields[$col_num] };
   }
}
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Outputting in the desired format (sorted by descending count) is tricky, though.

for my $col_num (1..$#counts) {         # for my $col_num (0, 8) { ??
   my $col_counts = $counts[$col_num];

   say("column ", $col_num+2);

   my %by_count;
   for keys(%$col_counts) {
      my $count = $col_counts->{$_};
      push @{ $by_count{$count} }, $_;
   }

   say
      join ' ',
         map { join(',', @{ $by_count{$_} }) }
            keys(%by_count);
}
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Update: Fixed off-by-one in column number.