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Chromosome  has X genes
Chromosome KLHL13 has X genes
Chromosome UTY has Y genes
Chromosome SPIN2B has X genes
Chromosome PIR has X genes

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foreach my $geneid (
    sort { $geneids{$a} <=> $geneids{$b} } keys %geneids
...
        print OUT "Chromosome $geneid has $geneids{$geneid} genes\n"; 
    }
}