Per-base quality score system

The Ion Torrent™ technology per-base quality score system uses a Phred-like method to predict the probability of correct base calls. The prediction is based on the quality of the base incorporation signal that was used for generating the base calls. The quality score system used by the sequencers uses a set of six 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 a customer configuration. The lookup table is retrained for each software release and is shipped as part of the software package. Quality scores are published in the BAM file.