You say your problem is with extracting a column and summing it. That only takes one line (three without a module), so why did you present so much code? 

use List::Util qw( sum );

my $sum = sum map { $array[$_][$col] } 0..$#array;

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my $sum = 0;
for my $row (0..$#array) {
   $sum += $array[$row][$col];
}

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Please locate your problem, then come back if you can't fix it once you locate it.

By the way, 

      my $nextline = <FASTA>;
      if($nextline =~ /^(\S+)$/) {
        my $nextline = <FASTA>;
        if($nextline =~ /^\+(.*)\s/) {
          my $nextline = <FASTA>;
          if($nextline =~ /^(\S+)$/) {
            $qual = $1;

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causes lines to be skipped if an "if" is ever false. You want redo. And the unused captures needlessly slow down your matches. 
      my $nextline = <FASTA>;
      redo if $nextline !~ /^\S+$/;

      $nextline = <FASTA>;
      redo if $nextline !~ /^\+/;

      $nextline = <FASTA>;
      redo if $nextline !~ /^\S+$/;

      chomp( my $qual = $nextline );

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In reply to Re: 2d Array - making an array for the column then adding the values by ikegami
in thread 2d Array - making an array for the column then adding the values by hansoffate

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