#!/usr/bin/perl -w
use strict;
my @Fields;
my @Array;
open (FILE,"file") or die "Can't open file\n";
while (<FILE>) {
  next if (/^#/);
  @fields = split "\t" , $_;
  next unless (@Fields == 7);
  push @Array , [ @Fields[0,3,6] ];
}
foreach my $foo (@fields) {
  print "$foo->[2]\n" if ($foo->[2] != 3);
}