The Quality Calculation

The Quality Calculation described here (which is available from the gap4 File menu) applies either of the two simple consensus calculations (see section Consensus Calculation Using Base Frequencies) and (see section Consensus Calculation Using Weighted Base Frequencies) to the data for each strand of the DNA separately. It produces, not a consensus sequence, but an encoding of the "quality" of the data which defines whether it has been determined on both strands, and whether the strands agree. This quality is used as the basis for problem searches, such as find next problem, and the Quality Display within the Template Display (see section Quality Plot).

The categories of data and the codes produced are shown in the table. For example 'c' means bad data on one strand is aligned with good data on the other.

+Strand -Strand

a

Good Good (in agreement)

b

Good Bad

c

Bad Good

d

Good None

e

None Good

f

Bad Bad

g

Bad None

h

None Bad

i

Good Good (disagree)

j

None None

the "Configure cutoffs" command in the

In the "Consensus algorithm" dialogue in the main gap4 Options menu (see section Consensus Algorithm), setting the configuration to treat readings flagged using the "Special Chemistry" Experiment File line (CH field) (see section Experiment File) affects this calculation. When set, the reading counts for both strands in the Consensus and Quality Calculations, and hence is equivalent to having data on both strands.