As best I can figure out the negative position adjustments are probably:
- -43 through -1258 increment 1
- -175 maybe no adjustment?
- -1259 through -1770 decrement 4
Positions from -1237 through -1258 are a 22bp A repeat in the CYP2D6 reference and a 27bp A repeat in the GRCh37 reference sequence (minus orientation). This repeat has several known lengths and various systems of notation, so great care should be used when dealing with changes in this range. In addition there is a SNP at -1235 which is sometimes described as a 2bp to 6bp indel (e.g. rs1080988).
This has been verified only for the following positions: 19, -629, -740, -1011, -1584.
Alignment seems to work right for all other positions except for -175, so there is still some uncertainty.
--Jlick 00:58, 6 August 2010 (UTC)