Presumably you are calling your sub like this:

versatility( %hash1, %hash2 );
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That doesn't work. All the keys and values will be assigned to %genome1 inside the subroutine and %genome2 will get nothing.

You need to re-write your subroutine to take hash references:

sub versatility {
    my( $genome1, $genome2 ) = @_;
    
    for my $key ( keys %{ $genome1 } ) {
        my @genome1 = $genome1->{ $key } =~ /(\d+)/g;
        my @genome2 = $genome2->{ $key } =~ /(\d+)/g;
        my $m = ( $genome1[1] - $genome2[1] ); 
        my $n = ( $genome1[0] - $genome2[0] );
        if( $n == 0 ){
            print "number of occurance for $key in two genome are same
+\n";
        } 
        else{
            my $slope = $m / $n;
            print "domain versatility= $slope\n";
        } 
    }
}
[download]

And then call it like this:

versatility( \%hash1, \%hash2 );
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(BTW: Do start adding some horizontal whitespace into your code. It makes it so much more readable. Maybe then people would recognise your subroutine as a subroutine :)