I am new to sangar sequencing files. I am using the ABIF parser from biojava legacy package to load the raw data and process the data based on tag names. The ABIF format specification mentions that the PCON tag provides the quality values for each peak in AB1 file. I had printed out the PCON values of the sample from my lab and the compared them against the phd.1 file generated by the sequencer. They are mostly similar,but not the same. Why is that? when both are supposed to be quality scores for each base called by the sequencer,why is this difference?
I have searched net for different files generated by sangar sequencer,their format specifications and significance. but most of the links only talk about ab1 files. Should we use quality values from PCON offset data from raw ab1 file or phd.1 file for analysis?