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while($line=<INPUTR>){
    chomp $line;
...
    next if (exists $hashfreq{$gene} and $hashfreq{$gene} >= $freq);
    $hashfreq{$gene} = $freq;
}

20   SEMA4G     20
80   CTBP2      80
...
20   OR4C3      40
40   OR4C45     60
60   OR4C45     60