The bases were called by the software using the relative intensity of each putative basepair signal and the local spacing of the signals.
Multiple applications require single-base pair accuracy across populations of closely related sequences.
An example is amplicon sequencing to assess the relative contribution of DNA from diverse organisms to a sample.
The requirement for single basepair accuracy led to the development of methods which drew on frequency data distributed across several samples to identify variant sequences which shared the same frequency profile and were thus likely errors from the same original sequence.
[1][2] The ability to use higher-order statistics to correct sequences is an important element in decreasing the burden of error in DNA sequence datasets.