You've been given complete answers to your question, but I would comment that:

• You don't need to chomp your line, since you are not using its end
• You're not using $chrpos anywhere, so don't need to process it
• In the code below, there is also in principle no use for $chromosome, but I left it because maybe you actually want to use it
• It is better to discard useless lines at the beginning of the loop, rather than splitting them, etc., and then not use the result of this work;

So the code could be made significantly shorter (and probably slightly faster) as follows, without losing any clarity:

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");
}
[download]

I'm not saying that your code was bad, it wasn't, but I'm just trying to show some opportunities for improvement.

Update: Fixed a typo (s/loosing/losing/), thanks to 1nickt for letting me know.