Beckman Coulter CEQ 8000, User Manual

Page: 227 / 382

Creating a Reference File
User’s Guide 213
Quality Values
If you are using a single sequence, the quality value assigned to each base in the
consensus will match each base in the sequence. If you are using two sequences and
the bases agree, one of two calculations will occur: If the orientation of the two
sequences is opposing, the two quality values will be added. If the orientation is the
same, the higher quality value will be used. If the bases disagree, a calculation will be
performed to determine the probability of error for that position, providing a quality
value that will be the difference between the higher and lower value.
To set the value at which bases in the consensus will be considered low quality, select
Edit | Quality Threshold
. Low quality bases will be identified in the Differences line,
the Navigator toolbar and the Discrepancy Map.
Viewing CEQuence Investigator Differences
The system uses codes to denote the type of discrepancy encountered when the
comparison was performed. These codes are shown in the Differences section of the
Alignment pane. You may turn the Differences line on or off by clicking the
View
menu, and checking or unchecking
Differences
. The highest level code will appear in
the Differences line in the location where the discrepancy occurred.
Any consensus position may have multiple Difference codes associated with
it. The codes have been assigned a hierarchy; the code with the highest pre-
cedence will be shown. To view all difference codes associated with any posi-
tion, ensure the Navigator toolbar is displayed by clicking on the
View |
Toolbars | Navigator
. The Differences text box in the Navigator toolbar will
display the difference code(s) in order of precedence.