aligned read length

The aligned length of a read at a given accuracy threshold is defined as the greatest position in the read at which the accuracy in the bases up to and including the position meets the accuracy threshold. For example, the AQ17 length of a read is the greatest length at which the read error rate is 2% or less. The "perfect" length is the longest perfectly aligned segment. For all of these calculations, the alignment is constrained to start from position 1 in the read—that is, no 5′ clipping is allowed.