Thermo Scientific appliedbiosystems SeqStudio Flex Series User Manual page 293

Chapter 11 Manage library resources on the instrument
11
Analysis settings library
Setting Description
Mixed base threshold When selected (default), determines the secondary peak height ratio, where
the secondary peak is considered a potential mixed base. Reaching the
threshold is a necessary but not sufficient condition for the basecalling
algorithm to call a mixed basecall.
For example, with the default setting of 25%, a secondary peak that is 10%
of the main peak is not identified as a mixed basecall.
Note: The default sequencing analysis settings are optimized for PCR
amplicon sequencing. For sequencing of plasmid templates, create analysis
settings with the following selections: for the End base setting, deselect At
PCR stop; for the Mixed base threshold setting, deselect Use Mixed base
identification.
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SeqStudio ™ Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide