This looks like it will do what you want:

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

local $/ = ''; # use paragraph mode
while ( <DATA> ) {
    my $total_aligned_reads;
    $total_aligned_reads += $1 while /Aligned= (\d+)/g;
    my ( $mtDNA ) = /^chrM.+Aligned= (\d+)/m;
    say "total aligned reads = $total_aligned_reads";
    say "mtDNA = $mtDNA";
    say "mtDNA percentage = ", $mtDNA / $total_aligned_reads * 100;
    }

__DATA__
Data_Set_116: BAM Index Statistics_on_data 115.html
chr10 length= 135534747 Aligned= 435 Unaligned= 0
chr11 length= 135006516 Aligned= 553 Unaligned= 0
chr12 length= 133851895 Aligned= 482 Unaligned= 0
chr13 length= 115169878 Aligned= 367 Unaligned= 0
chr14 length= 107349540 Aligned= 341 Unaligned= 0
chr15 length= 102531392 Aligned= 243 Unaligned= 0
chr16 length= 90354753 Aligned= 258 Unaligned= 0
chr17 length= 81195210 Aligned= 210 Unaligned= 0
chr18 length= 78077248 Aligned= 326 Unaligned= 0
chr19 length= 59128983 Aligned= 115 Unaligned= 0
chr1 length= 249250621 Aligned= 1012 Unaligned= 0
chr20 length= 63025520 Aligned= 194 Unaligned= 0
chr21 length= 48129895 Aligned= 148 Unaligned= 0
chr22 length= 51304566 Aligned= 100 Unaligned= 0
chr2 length= 243199373 Aligned= 897 Unaligned= 0
chr3 length= 198022430 Aligned= 763 Unaligned= 0
chr4 length= 191154276 Aligned= 841 Unaligned= 0
chr5 length= 180915260 Aligned= 755 Unaligned= 0
chr6 length= 171115067 Aligned= 730 Unaligned= 0
chr7 length= 159138663 Aligned= 646 Unaligned= 0
chr8 length= 146364022 Aligned= 642 Unaligned= 0
chr9 length= 141213431 Aligned= 466 Unaligned= 0
chrM length= 16571 Aligned= 2650 Unaligned= 0
chrX length= 155270560 Aligned= 1068 Unaligned= 0
chrY length= 59373566 Aligned= 11 Unaligned= 0
NoCoordinateCount= 0

Data_Set_108: BAM Index Statistics_on_data 107.html
chr10 length= 135534747 Aligned= 45 Unaligned= 0
chr11 length= 135006516 Aligned= 49 Unaligned= 0
chr12 length= 133851895 Aligned= 31 Unaligned= 0
chr13 length= 115169878 Aligned= 47 Unaligned= 0
chr14 length= 107349540 Aligned= 24 Unaligned= 0
chr15 length= 102531392 Aligned= 26 Unaligned= 0
chr16 length= 90354753 Aligned= 22 Unaligned= 0
chr17 length= 81195210 Aligned= 23 Unaligned= 0
chr18 length= 78077248 Aligned= 20 Unaligned= 0
chr19 length= 59128983 Aligned= 9 Unaligned= 0
chr1 length= 249250621 Aligned= 89 Unaligned= 0
chr20 length= 63025520 Aligned= 19 Unaligned= 0
chr21 length= 48129895 Aligned= 5 Unaligned= 0
chr22 length= 51304566 Aligned= 13 Unaligned= 0
chr2 length= 243199373 Aligned= 81 Unaligned= 0
chr3 length= 198022430 Aligned= 53 Unaligned= 0
chr4 length= 191154276 Aligned= 55 Unaligned= 0
chr5 length= 180915260 Aligned= 56 Unaligned= 0
chr6 length= 171115067 Aligned= 55 Unaligned= 0
chr7 length= 159138663 Aligned= 44 Unaligned= 0
chr8 length= 146364022 Aligned= 52 Unaligned= 0
chr9 length= 141213431 Aligned= 32 Unaligned= 0
chrM length= 16571 Aligned= 1 Unaligned= 0
chrX length= 155270560 Aligned= 52 Unaligned= 0
chrY length= 59373566 Aligned= 3 Unaligned= 0
NoCoordinateCount= 0

Data_Set_100: BAM Index Statistics_on_data 99.html
chr10 length= 135534747 Aligned= 25340 Unaligned= 0
chr11 length= 135006516 Aligned= 24577 Unaligned= 0
chr12 length= 133851895 Aligned= 24335 Unaligned= 0
chr13 length= 115169878 Aligned= 17653 Unaligned= 0
chr14 length= 107349540 Aligned= 16826 Unaligned= 0
chr15 length= 102531392 Aligned= 15506 Unaligned= 0
chr16 length= 90354753 Aligned= 17098 Unaligned= 0
chr17 length= 81195210 Aligned= 14604 Unaligned= 0
chr18 length= 78077248 Aligned= 14139 Unaligned= 0
chr19 length= 59128983 Aligned= 10155 Unaligned= 0
chr1 length= 249250621 Aligned= 43427 Unaligned= 0
chr20 length= 63025520 Aligned= 11568 Unaligned= 0
chr21 length= 48129895 Aligned= 6897 Unaligned= 0
chr22 length= 51304566 Aligned= 6766 Unaligned= 0
chr2 length= 243199373 Aligned= 45536 Unaligned= 0
chr3 length= 198022430 Aligned= 36213 Unaligned= 0
chr4 length= 191154276 Aligned= 34693 Unaligned= 0
chr5 length= 180915260 Aligned= 33941 Unaligned= 0
chr6 length= 171115067 Aligned= 31529 Unaligned= 0
chr7 length= 159138663 Aligned= 29473 Unaligned= 0
chr8 length= 146364022 Aligned= 27419 Unaligned= 0
chr9 length= 141213431 Aligned= 22254 Unaligned= 0
chrM length= 16571 Aligned= 169 Unaligned= 0
chrX length= 155270560 Aligned= 28121 Unaligned= 0
chrY length= 59373566 Aligned= 534 Unaligned= 0
NoCoordinateCount= 0
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