#!/usr/bin/perl
use warnings;
use strict;
use 5.010;

{	# Within this block because of the next line
	local $/ = undef;
	for(<DATA> =~ /(Data_Set.*?Count= 0)/gs) {

    	my $counter = 0;
    	my $total_aligned_reads = 0;
    	my $mtDNA;

    	for(split /\n/) {
        	## my $line = $_; #### Unnecessary; see next comment
        	next if /(Data_Set_\d+: |^NoCoordinateCount|^$)/;
        	## next if /^NoCoordinateCount/;
        	## next if /^$/;
			my($chr, $lenLabel, $lengNumbers, $AlignedLabel, $alignedNumbers) = split /\s/; ####, $line; split operates on $_ by default
        	$total_aligned_reads +=  $alignedNumbers;
        	$mtDNA = $alignedNumbers if $chr eq "chrM";
    	}

    say "total aligned reads = $total_aligned_reads";
    say "mtDNA = $mtDNA";
    say "mtDNA percentage = ", $mtDNA/$total_aligned_reads*100;
	}
}

__DATA__