If you put use warnings; at the top of your code you would get some hints that you have a problem.

Your 2 regexes work for two different lines. The first line matches the left regex, and the first 5 special vaiables are set ($1 - $5). But, since $6 is not set from the 1st input line, you get a warning "Use of uninitialized string...".

The 2nd line matches the right regex, but it only sets $1. Maybe you're looking for something more like this:

use strict;
use warnings;

while (<DATA>) {
    chomp;
    s/^\s+//;
    s/\s+$//;
    my @tokens = split /\t/;
    if ((scalar @tokens) == 5) {
        print $_;
    }
    elsif ((scalar @tokens) == 3) {
        if (/number=(.*)/) { print "\t$1\n" }
    }
}

# not sure how many tabs you have in your 2nd line
__DATA__
Chr21    NT_113958    STS    76092    76265                
Chr21    NT_113958    number=1
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