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$data{"HG00553"}[162][16287215] = "0 0"
$data{"HG00553"}[162][16287226] = "0 0"
...
$data{"HG00638"}[162][16287851] = "1 1"
...

while (<$in_file>) {
    print "$_";
...
        print "snp_bins: @snp_bins\n";
    }
}

$data{$individual}[162] = "something"

$data{$individual}[0..162]

$data{$individual}{162}{16287215} = "0 0"