Hello. I have just received the gene sequencing result but the result does nott make sense. In the result, the peak of G (black) is significantly higher than the peak of A (green). However, the final result reads the nucleotide as A. So which nucleotide should I inteprete?
Thank you
Dear Anh Pham:
I did not think the company was wrong in your case. Probably the company use an algorhytm to resolve the sequence. However, you as user may dissagree to what the company give you. That is why the also send you the original file_name.abi file along with the suggested file_name.txt one.
In our lab, before deciding the concensus sequences - we will always evaluate both the .txt and the .abi files together, especially if the sequencing quality is questionable.
Base on the picture you sent, in my opinion you actually have an SNP at the particular base position (nt 188). Base on that, your pcr product may actually at least contain two different dna sequences, one fragment having an "A" in the nt 188 and the other a "G." Therefore, there is an A/G SNP at the 188 position of you sequences.
Best of luck.
I agree with S. Sudarsono that this is a snp that just fails in intensity to be called both A and G but it would be interesting to see the original sequence .abi file in case this is a systematic error like very weak signal and high background or a pull up of A bases under Gbases or that there were many As earlier in the sequence so A is lower intensity and just fails to reach the intensity where the software can call a SNP
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