while (my $line = <FILE>) {
    next if $. == 1;
    next if $line =~ /^\s*chrM/;
    my ($chromosome, $nmreads, $mutants) = (split "\t", $line)[0, 8, 9];  # note: $chromosome is not used, this could be simplified further
    my $totalreads = $nmreads + $mutants;
    print ("$nmreads $mutants $totalreads\n");
}