Use The Electropherogram Screen - Thermo Scientific appliedbiosystems SeqStudio Flex Series User Manual

Table 2 QC thresholds and quality alerts that are used to determine Sample QC (these tests and alerts are
not shown in the software) (continued)
QC tests
Fragment analysis QC tests
SQ (size quality)
Broad peak in size
standard peaks
Number of size standard
peaks
Manual spectral calibration QC test
Borrowed capillary
Install run QC test
CRL value (sequencing)
Alleles within bins
(fragment analysis)

Use the electropherogram screen

This section describes using the electropherogram screen on the instrument.
For more information on accessing the electropherogram screen and the parts of the screen, see:
• "View real-time results in the Run Queue screen"
• "View real-time results in the home screen"
• "View results for a completed run (Run history)"
• "Parts of the sequencing electropherogram screen"
• "Sequence analysis results"
• "Parts of the fragment analysis electropherogram screen"
• "Fragment analysis results"
SeqStudio ™ Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide
(green, good)—≤0.75
(yellow, caution)—0.25–0.74
(red, error)—<0.25
How Size Quality is determined
The Size Quality algorithm evaluates the similarity between the fragment pattern
for the size standard dye specified in the size standard definition and the actual
distribution of size standard peaks in the sample, then calculates an interim SQ (a
value between 0 and 1).
For more information, see the following sections:
• "QC error and alert troubleshooting"
• "Sample and data troubleshooting"
(yellow, caution)—Broad peaks are detected in the size standard.
(red, error)—Fewer than the expected number of standard peaks are detected.
(yellow, caution)—Spectral data was borrowed for the capillary.
(red, error)—CRL value is below the internally specified limit.
(red, error)—At least one allele is not within an internally specified bin.
on page 175
on page 179
Chapter 7 View results on the instrument

Use the electropherogram screen

Quality alert
on page 489
on page 512
on page 162
on page 153
on page 170
on page 175
on page 179
7
173