ab1 file nucleotide confidence score

Question

[kapil.joshi036]

I have an ab1 file in which i want to know the confidence score of each nucleotide at each position .

if its showing heteroplasmy then i also need to know the confidence score of them also

thank you advance

[Benn]

I think you might wanna meet "Phred"

http://www.phrap.com/phred/#qualityscores

[kapil.joshi036]

Sir, i tried phred but basically it useful for the trimming and it dnt give you the individual confidence score

[Benn]

Did you produce ".qual" files? They contain phred scores of each base call.

Or what do you exactly mean with "confidence score"?

[kapil.joshi036]

yes i know it produces phd qual and seq files but if I plot a heterozygous chromatogram i want the score of both nuclotide at that position induvidually

[st.ph.n]

You will need a GUI program that can read in the Sanger data to produce the chromatogram for you. .ab1 files are binary files containing the sequence, and information of how each base was called given the chromatogram, which will tell you if you have a mixture. Biopython can extract the sequence in fasta/gb format, but I'm unaware of any CLI programs that will generate a chromatogram.