You're a victim of typos. When I ran your code through perl -c, I got a log of messages like:
Global symbol "$conig" requires explicit package name at 349376.pl line 555.
You spell that variable as "$contig" in some places and "$conig" in others. However, that's not the entire scope of your problem. You declare $contig as my in different scopes, so I'd expect that your code wouldn't run as you expect. A short demonstration of what I'm talking about: 
my $contig = 3;
my $foo = 6;
if ($foo < 8) {
   my $contig = 5;
}
print "contig = $contig\n";
__END__
contig = 3

[download]

As a matter of style, you should probably avoid the whole "if..elsif..elsif..elsif..." routine for this. As I'm sure you found out, it's very tedious to type. A more visually appealing (and easier to maintain) to do something like the following: 

my %master = (
   167280 => (chromosome => 1, contig => 'NT_077402.1'),
   217280 => (chromosome => 1, contig => 'gap'),
   257582 => (chromosome => 1, contig => 'NT_077911.1'),
   # etc
);
NUMBER: foreach my $number (@numbers) {
   foreach my $key (sort { $a <=> $b } keys %master) {
      if ($number < $key) {
         my $chromosome = $master{$key}{chromosome};
         my $contig     = $master{$key}{contig};
         #do whatever processing here; I'll just print

         print "chromosome = $chromosome, contig = $contig\n";
         next NUMBER;
      }
   }
}

[download]
This style has the advantage of maintainability. Should you find an error in your processing logic (for example, if I found that I had misspelled 'chromosome' in my print statement'), you have exactly one place to fix it.

Hope this helps,
thor

Update: I just thought of another reason to avoid the "if..elsif..." paradigm. Once, someone came to me for help in trying to run a tool that had such a thing in it. perl core dumped because the script was too large. I converted the solution to a hash, and it ran in no time at all.

In reply to Re: Selecting a random number, and back calculating to chromosome and contig! by thor
in thread Selecting a random number, and back calculating to chromosome and contig! by Sameet

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