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

Alignment Matrix The alignment matrix is displayed as:
AA is encoded as 0
CG is encoded as 3
AACG is encoded as 0 1 3
Color Codes Four dye colors, encoded as follows:
6-FAM = 0
CY3 ® = 1
Texas Red ® = 2
CY5 ® = 3
Cycle Order The order in which the data are generated.
Applied Biosystems SOLiD 4 System SETS Software User Guide
Glossary
Location For processed files, describes the location of the prepended base on
the base-space reference sequence.
201