mitochondria reference HG19 or Cambridge

[foxyg]

I am trying to decide which reference to use for mito seqencing. I noticed there are some difference comparing HG19 chrM and Cambridge Reference sequence. I am not sure which to pick here.

Anyone with experience please let me know.

Thanks

[bpetersen]

As far as I know, the Cambridge sequence is the one now being used by the majority. It's also supposed to be implemented in hg20. We've also just switched to the Cambridge reference .
So that's what I heard, but no guarantees...:-)