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

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Appendix B Advanced Topic: Data Analysis Overview
Color-space and base space as applied in the SOLiD 4 System
Color-space formats
Figure 4 Relationship between color-space, base position, and
sequencing chemistry
Color-space data are presented in three slightly different formats. In
two of the formats, a base (A, C, G, or T) is appended to the colorspace
calls.
Note: Color-space data are self-complementary: In some situations,
when you might expect to see complemented data (for example,
reverse), the data appear the same. For example, AC = 1, TG = 1.
The different types of color-space data are:
Processed color-space data: Consists of a numeric string
prefixed (suffixed if reversed) by a single base. The base that
precedes the numeric (color code) data is the first base of the
actual sequence (in base space, not color-space).
Unprocessed color-space data: Consists of a numeric string
prefixed by a single base. This base is the final base of the
sequencing adapter and is not part of the target sequence. It is
included to disambiguate the first color call.
146 Applied Biosystems SOLiD 4 System SETS Software User Guide