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#!/usr/bin/perl -w
use strict;
use warnings;
...
} ## end foreach my $filename (qw/one.txt two.txt three.txt/)

print dump( \%data );

{
  chromosome1 => { 50000 => { value1 => 64, value2 => 73 } },
  chromosome2 => { 20000 => { value1 => 4,  value2 => 63 } },
...
  chromosome4 => { 21414 => { value1 => 4,  value2 => 1  } },
  chromosome6 => { 12141 => { value1 => 12, value2 => 22 } },
}