Aligning to defective start codon in vpu

[Donaim]

In our HXB2 reference, vpu region is the following sequence:

TQPIPIVAIV ALVVAIIIAI VVWSIVIIEY RKILRQRKID RLIDRLIERA EDSGNESEGE ISALVEMGVE MGHHAPWDVD DL*

It does not start with M, and thus is defective [1].

It probably does not matter much, since it's a 1 base SNP, at a region boundary.
But it has some impact since most genomes do not have this mutation, and so they align worse.