Randomly vanishing / extremely small G and C Peaks in Sequence

[mikebravo]

Hi all,

I want to ask if anyone ever experienced randomly small G and C peaks in their sequence. We are using BDT1.1 on a AB3130 and AB310 sequencer. Since a while we observe every here and than very tiny G and C peaks in an otherwise normal and good sequence. This is reproducible on both sequencers. Sometimes the basecaller even regards it as a gap/deletion.
- Changing the LOT of the BDT1.1 did not help.
- Different PCR-Kits and conditions did not help
- Same observation on two sequencers.
- Changing the sequncing cycle programm did not help.

https://drive.google.com/file/d/0B1UuVdmRASJ0bHhobzhxSG9kRnM/view?usp=sharing

I am thankful for any idea.

-mike-

[Stephanie Nelson]

G/C shouldering in Sanger sequencing is a well-known phenomena. (Just Google it). Are you sure that you are not just seeing G/C shoulders which "disappeared" by resolving the second time?