The software evaluates peaks in the data for each capillary. To be identified as a
possible allele, peaks must be within the following ranges (nominal allele size, or
reference bin size, is hard-coded):
Fragment analysis
HID analysis
All markers between ±0.4 bp and ±0.5 bp of
nominal size for the allele
• All markers except TH01: ±0.7 bp of
nominal size for the allele
• TH01:
– Seven markers are ±0.7 bp of
nominal size for the allele
– Three markers are ±0.5 bp of
nominal size for the allele
For all peaks that are within the nominal size range, the software calculates the
Average Peak Height and the Sizing Precision. Peaks that meet the following
thresholds pass.
Result
Description
Threshold
Min Peak Height Minimum of peak heights for
observed allele peaks of the
included capillaries.
• Fragment: >175 RFU
• HID: >400 RFU
Sizing Precision Standard deviation of the observed
allele fragment sizes
<0.15 for expected alleles
Pass/Fail
Alleles with a sizing precision and minimum peak height that do not
meet thresholds fail.
For information only
Nominal Size
Expected allele fragment peak size (bp).
Mean
Average fragment size for the observed allele peaks.
Peak Height % >
Min
Percentage of observed allele peaks with a peak height above the
minimum threshold.
Sizing Accuracy Difference between the expected allele size and the mean allele size.
1.
Examine the number of size standard and allele peaks found for each capillary.
2.
If all capillaries pass, click Accept Results.
If any capillaries fail, the Accept Results button is dimmed. Evaluate the raw
data for failed capillaries to determine if the install check can be accepted with
the failed capillaries. If the run is acceptable, the software allows you to deselect
capillaries and recalculate results.
Pass/fail criteria
for the
fragment/HID
install check
Evaluate fragment
install standard
data
Chapter 6
Run calibrations and install checks
Run a fragment/HID install check
6
3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1
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