Information relating to the base interpretation of the trace is stored
at byte offset from the start of the file. Stored for each base are: its
character representation and a number (an index into the Samples data
structure) indicating its position within the trace. The relative
probabilities of each of the 4 bases occurring at the point where the
base is called can be stored in **prob_A** , **prob_C** ,
**prob_G** and **prob_T** . The Amersham FilmReader uses
**Bases.spare[0]** to store the confidence level of the base. The
value ranges from 0 (low confidence) to 8 (high), and 9 indicating the
base has been manually edited.

From version 3.00 these items are stored in the following order: all "peak indexes", i.e. the positions in the sample points to which the bases corresponds; all the accuracy estimates for base type A, all for C,G and T; the called bases; this is followed by 3 sets of empty int1 data items. These values are read into the following data structure by the routines in the io library.

/* * Type definition for the sequence data */ typedef struct { uint_4 peak_index; /* Index into Samples matrix for base posn */ uint_1 prob_A; /* Probability of it being an A */ uint_1 prob_C; /* Probability of it being an C */ uint_1 prob_G; /* Probability of it being an G */ uint_1 prob_T; /* Probability of it being an T */ char base; /* Called base character */ uint_1 spare[3]; /* Spare */ } Base;

URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/formats_5.html