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Detecting deletions via a sequencing trace? - (Aug/14/2005 )

Can you do this? The sequence came through reporting a deletion, but when I look at the trace I see a double peak.

the sequence should read TTC TCA ACGT A

The trace says TTC TC- ACGT A

take a peek boys and girls. Any help would be appreciated.



There is no question -- there are two A's in that sequence, as you expected. The base caller
got it wrong.


not knowing what template you have seqeunced but could it be a C/A polymorphism?



It's unlikely that it is a c/a polymorphism. Look at the two C's. Both have "echos" one base position to the right. There could be a frame shift between the region shown and the primer for a small portion of the sample, but I don't even think that is likely, since we don't see anything like an echo on the G. It's just noise, and the base caller mis-called it. If you are worried (which I would not be) then you could sequence in the reverse direction.