Perhaps the following will be helpful:

use strict;
use warnings;

my ( %hash, $lowPos, $highPos );

while (<>) {
    my ( $position, $frequency ) = (split)[ 1, 2 ];
    $hash{$position} = $frequency;
}

for my $pos ( sort { $a <=> $b } keys %hash ) {
    if ( !defined $lowPos ) {
        $lowPos = $pos;
        next;
    }

    if ( $hash{$pos} > $hash{$lowPos} ) {
        $lowPos = $pos;
        last;
    }
}

for my $pos ( sort { $b <=> $a } keys %hash ) {
    if ( !defined $highPos ) {
        $highPos = $pos;
        next;
    }

    if ( $hash{$pos} > $hash{$highPos} ) {
        $highPos = $pos;
        last;
    }
}

print "Lowest, most frequent position : $lowPos\n";
print "Highest, most frequent position: $highPos\n";

Usage: perl script.pl inFile [>outFIle]

The last, optional parameter directs output to a file.

Output on your dataset:

Lowest, most frequent position : 8848
Highest, most frequent position: 11761

This uses a hash to store position/frequency info as key/value pairs. To obtain the lowest, high-frequency position, it numerically sorts the keys in ascending order, then 'looks' for the first frequency value higher than the first position's value. It then does a similar procedure for the highest, high-frequency position.

Hope this helps!

If you will look at some basic unix commands you should be able to do it yourself. If your file is a tab delimited file, then try

cut -f2 yourfile.txt | sort -n will print the second column in increasing order

cut -f2 yourfile.txt | sort -n | head -1 will print the smallest value

cut -f2 yourfile.txt | sort -n | tail -1 will print the highest value

To get min and max in a specific column using awk:

cat table.txt | awk 'min=="" || $2 < min {min=$2} END{ print min}'
cat table.txt | awk 'max=="" || $2 > min {max=$2} END{ print max}'