You can use read alignment to evaluate the quality of the sequencing reaction and the quality of the corresponding library when an accurate reference is available. Reads are aligned to a reference genome sequence. Any discrepancy in alignment to a reference, whether biological (actual variant) or technical (sequencing error) is listed as a mismatch. Alignment performance metrics are reported using the alignment quality (AQ) score, which defines the accuracy of sequencing reads when compared to a reference genome sequence. Torrent Suite™ Software reports alignment quality using three parameters:
AQ17—the greatest length at which the error rate is 2% or less.
AQ20—the greatest length at which the error rate is 1% or less.
