i am getting sm compilation errors...

It's always a very good idea to say just what errors you are getting, but I can make a few guesses.

while (<FILE>)
{
    push (@line, $_);
    my $count++;
}
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The
    my $count++;
statement in the  while loop above creates and then increments a lexical variable each time through the loop. The value of this variable will never be other than 1 because it goes out of existence at the end of the loop. That's why Perl complains (I'm guessing) about accessing the  $count variable in the subsequent  forloop: the variable has never been defined in any current scope.

In the  for loop, the  if statement
    if (($st [4] eq /chr1/) && ($st [10] eq /chr1/)) { ... }
is wrong because the // match operator binds to (ie., matches against) a variable via the  =~ binding operator, not the  eq operator. Without explicit binding, it binds to the  $_ default scalar.

Not errors, but...

The whole  while loop can be replaced by
    my @line = <FILE>;
and then the number of elements in the array (i.e., the number of lines) will be
    my $count = @line;
but this variable is not really needed since the  for loop can be better expressed as
    for my $l (@line) { do_something_with_line($l); }

Update: As Kenosis has pointed out, it is better practice to use the three-argument form of open:
    open my $fh, '<', $filename1 or die "opening '$filename1': $!";