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;

##</code><code>##

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

##</code><code>##

use strict;
use warnings;

use Acme::Tools;

my (%count, %organisms, %med, %number);
my ($contig, $accession, $organism, $eval, $con_length, $map_length);

#my $ref_filelist = $ARGV[0];
#open(FILELIST, $ref_filelist )
#   or die "Could not open Reference filelist...($!)";
 
print "Organism\tFrequency\tMedian_Eval\tMedian_Contig_Length\tMedian_Mapped_Length\n"; 

#while (<FILELIST>){
while (<DATA>){
    ( $contig, $accession, $organism, $eval, $con_length, $map_length ) = split ( '\t',);

    #my $median = $eval[($#eval / 2)];
    my $med_calculated = median(@{$organisms{$organism}});  
    $med{$organism} = $med_calculated;

    #$organisms{$organism} = $eval;
    my $number_calculated = ++$count{$organism};    
    $number{$organism} = $number_calculated;
}

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


__DATA__
contig1	AC344	organism1	1e-1	122	45
contig1	AC344	organism1	1e-2	122	45
contig1	AC346	organism2	1e-102	122	46
contig1	Ac346	organism2	1e-100	122	46
contig1	Ac346	organism2	1e-114	122	46
contig1	Ac346	organism2	1e-111	122	46
contig2	NC333	organism3	1e-2	155	90
contig3	NC444	organism4	1	188	50
contig3	NC444	organism4	12	188	50