Please fix your formatting to make your code readable. Put one opening <code> at the beginning of the code, one closing </code> tag at the end of your code, and no <code> tag in the middle of your comments.

Otherwise, your splitting is very inefficient. You could get your 3 variables in just one operation:

while (my $line=<$fh>){ 
     chomp $line;
     my ($low, $high, $id) = split /\t/, $line;
     # ...
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