Applied Biosystems SOLiD™ 4 System SETS Software User Guide ...

D
Appendix D Advanced Topic: Primary Analysis
Understanding quality values in the SOLiD System
together can estimate whether there is a localized problem over the
whole sample (larger deviation with no outliers), a regional problem
(outlier population that spans channels), or a transient problem
(outliers in a single channel).
A difference with the blur metric, however, is that whereas the blur
metric is constant over the number of beads present in a panel, the
exposure is more sensitive to the number of beads. A baseline
exposure value per channel is determined based on a sampling
strategy, but panels with either significantly more or fewer beads can
be affected differently. As with the blur value, the reported value is
the largest mean exposure value of the four channels over all panels
in the sample.
Understanding quality values in the SOLiD System
The SOLiD primary analysis software analyzes the raw image data
collected by the system and generates a color-space read for each tag.
The software generates a quality value (QV) for each color call,
which is an estimate of confidence for that color call.
The SOLiD 4 System QVs are similar to those generated by Phred
and the KB Basecaller software for capillary electrophoresis
sequencing. The quality value q for a particular call is
mathematically related to its probability of error p.
The algorithm used to predict QVs for the SOLiD 4 System is
similar to Phred and the KB Basecaller software. (Refer to the
paper, Ewing B., Green P., 1998, Base-calling of automated
sequencer traces using Phred. II. Error probabilities. Genome
Research 8:186-194.)
The algorithm relies on training or calibration to a large set of control
data and color calls for which the correct call is known. In the
SOLiD 4 System, the correct call is determined by mapping the
read to a known reference sequence.
180 Applied Biosystems SOLiD 4 System SETS Software User Guide