Beckman Coulter CEQ 8000, User Manual

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User’s Guide 249
Figure 140:Locus Tag Editor window - Allele ID Criteria tab
Stutter Definition
Stutter are usually small peaks, generally DNA amplification artifacts that form as a
result of halted polymerase activity. When this happens, allele fragments are formed
that differ in length from the true allele by an integral number of repeats (i.e., n-1, n-2,
etc.). The absolute size of a fragment is a function of the variety of repeats (i.e.,
dinucleotides, trinucleotides, etc.).
The
Stutter Definition
area of the window allows you to set the parameters for
which the system will identify these peaks as stutter and not as true alleles.
1. Select this check box if you want the system to search for stutter . When
selected, you must also choose at least one of the options in steps 4 and 5 below.
2. Select the number of repeats to specify the
width of the window
around each
allele in which stutter will be detected.
3. Specify the maximum height percent of the stutter relative to the true
allele below which detected peaks are considered stutters. Peaks above this
threshold will be considered unknown alleles.
4. Selecting this check box enables the system to
detect stutters shorter than
(occurring prior to) the allele
.