Applied Biosystems 3500 - Understand Quality Values (QVs)

2.
Sort as needed.
3.
To compare signal across all samples on a plate, select Uniform Y Scaling.
4.
Click the View Tables buon to close the thumbnail pane.
Understand Quality Values (QVs)
We recommend the following ranges for QVs (set in Preferences, see “Overview“ on
page 36):
• Pure bases: Low QV < 15, Medium QV = 15 to 19, High QV = 20+ (default).
• Mixed bases: Low QV < 5, Medium QV = 5 to 10, High QV > 10 (investigate to
determine the best range for your application).
Pure bases and mixed bases have the same probability of error for the associated
basecall (10
–q/10
). Note the following:
• High-quality pure bases typically have QVs of 20 or higher.
• The distribution of quality values for mixed bases diers dramatically from that
of pure bases.
• Mixed bases have a maximum QV of 20.
• Review all mixed base calls.
QV
Pe QV Pe
1 79.0% 30 0.10%
5 32.0% 35 0.032%
10 10.0% 40 0.010%
15 3.2% 45 0.0032%
20 1.0% 50 0.0010%
25 0.32% 60 0.00010%
Quality value
r
anges
Pure base versus
mixed base QVs
Quality values (QV)
and probability of
error (Pe)
Chapter 4 Re
view sequencing results
Understand Quality Values (QVs)
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3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1