This aspect of the Consensus Align tab differs from the Global Align tab in that it lacks the ‘Alignment Data’ and Read Type’ controls, as these would not apply in this context. The other display controls, for ‘Reported Frequency’ and ‘Read Orientation’, are the same as in the Global Align tab (see section 1.6.4 for a full description of these display options features).

Note that consensi (in the Global Align tab) are always constructed from reads of the same orientation and from the same Amplicon; forward and reverse reads, and reads from two Amplicons, even if they overlap, will not be commingled in a single Consensus read. The system can thus automatically select the appropriate ‘Read Orientation’ option for the Individual reads of the Consensus at the time the Consensus Align tab is populated. This is important so that the estimated frequency of variation be correctly calculated when the Global Reported Frequency is selected, i.e. without including the depth of both read orientations in the denominator of the calculated frequency (see section 1.6.4.4 for more details on this).