use warnings;
use strict;
use 5.010;

my @pos;

while(<DATA>){
    my( $chr, $start, $end ) = split;
    $pos[ $_ ]++ for $start .. $end;
}

for my $pos ( 0 .. $#pos ) ){
    next unless defined $pos[ $pos ];
    say $pos,"\t", $pos[ $pos ];
}