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    my $med = median(@{$organisms{$organism}});  #bad form, masks %med
+ declared in outer scope. Use a different name for this variable, eg.
+ $med_calculated.
    $med{$organism} = $med;

foreach $organism (sort {$number{$a} <=> $number{$b}} keys %organisms)
+{
    print "$organism:\t$number{$organism}\t$organisms{$organism}\t$med
+{$organism}\n" ;
}

use strict;
use warnings;
...
contig2    NC333    organism3    1e-2    155    90
contig3    NC444    organism4    1    188    50
contig3    NC444    organism4    12    188    50