use strict;
use warnings;

my @chrnums = (
    [qw(chr1 10)],
    [qw(chr3 20)],
    [qw(chr1 30)],
    [qw(chr3 5)],  
    [qw(chr5 5)],
    );

@chrnums = map {
    #Extract sorted rows
    $_->[1]
    } sort {$a->[0] cmp $b->[0]} map {
    #Transform to keys and refs
    [(sprintf "%5d%5d", $_->[0] =~ /(\d+)/, $_->[1]), $_]
    } @chrnums;

print "$_->[0] $_->[1]\n" for @chrnums;

##</code><code>##

chr1 10
chr1 30
chr3 5
chr3 20
chr5 5