One of the new features of PeakTrace 6.96 is the ability to generate PHRED .poly files.
The .poly file has the name [filename].poly where [filename] is the name of the input .ab1 file. The first line of
the .poly file consists of a header line containing the file name, the smallest amplitude normalization factor, and the amplitude normalization factors for the A, C, G, and T channels.
On each line after the header line is the basecall, the position of the basecall (in scans), the area of the basecalled peak, the relative area of the basecalled peak, the uncalled base, the position of the uncalled base, the area of the uncalled base, the relative area of the uncalled base, and the amplitudes of the four
channel (A, C, G, T) at the position of the basecall. An example of a .poly file output is shown below.
The .poly file provides information on the relative height of each peak in the trace and can be useful for detecting polymorphisms or secondary peaks in traces.
To generate .poly files choose one of the two alternatives under .phd.1 file output option, poly or poly+phd.