Restating...
I want it to compare each element ($currentMutation) in the @numberMutation array to each element in the @organism array and set the @organism[$i] = $currentMutation if (@organism[$i] < $currentMutation)

The @organism array is preset to all 1's.
Given this logic, ALL the elements of @organism will always be set to the highest value of $currentMutation.

I don't think that's what you want!?

use strict;
## Simplified for testing

my @numberMutation = ();
while (<DATA>) {
    chomp;
    @numberMutation = split(//,$_);
}

my @organism = (1,1,1,1,1,1,1,1,1);
foreach (@numberMutation) {
    my $currentMutation = $_;
    my $i = 0;

    foreach (@organism) {
        if ($_ < $currentMutation) {
            $organism[$i] = $currentMutation;
            $i++;
        }
    }
}

print "ORG: @organism\n";  ## prints ORG: 9 9 9 9 9 9 9 9 9 
print "MUT: @numberMutation\n";

__DATA__
31415926535897932384626433832
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