~~~~~~code~~~~~~~~~
# Program in Perl
use Data::Dumper;
use POSIX;
my @sumY, @numY;
open my $fh, '<', "output.txt" or
     die "could not open file: $!";
$line = <$fh>;
while (my $line = <$fh>) {
    my($Chr, $Pos, $Y) =  split /\s+/, $line;
    $cPos = floor($Pos / 100000) ;
    $sumY[$Chr][$cPos]+=$Y;
    $numY[$Chr][$cPos]++;
}
for (my $j= 1; $j <= 2; $j++)
{
    for (my $i= 0; $i <= 5; $i++)
    {
        $range = ($i+1)*100000;
        if ( !defined $numY[$j][$i] )
           { $avg = 0; }
        else
           { $avg = $sumY[$j][$i] / $numY[$j][$i]; }
        print "$j $range $avg\n";
    }
}
close $fh;

~~~~Output~~~~~~
1 100000 -1.43249333333333
1 200000 -0.392446
1 300000 -0.1234
1 400000 2.2456
1 500000 0
1 600000 0
2 100000 -0.3122582
2 200000 -0.366919
2 300000 0
2 400000 0
2 500000 0
2 600000 -1.00859

#!/usr/bin/perl
use warnings;
use strict;

my $sum = 0;
my $n = 0;
while (<>) {
    $sum += $_;
    $n++;
}
print $sum/$n, "\n";