Quality following alignment

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.

• Perfect—the longest perfectly aligned segment.