The Ion Torrent™ per-base quality score system uses a Phred-like method to predict the probability of correct base call. The prediction is based on the quality of the base incorporation signal that was used for generating the base calls. The sequencers' quality score system uses a set of 6 predictors whose values are correlated with the probability of a base miscall.

A Phred lookup table is used for converting the values of predictors to error probabilities. The lookup table is generated by training on a representative data set in customer configuration. The lookup table is re-trained for each software release and is shipped as part of the software package. Quality scores are published in the BAM file.