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

SNPs and errors
High accuracy for SNP detection
Applied Biosystems SOLiD 4 System SETS Software User Guide
Appendix B Advanced Topic: Data Analysis Overview
Data analysis considerations B
Because a SNP generates two adjacent and valid color-space
mismatches to the reference sequence, the software allows a
minimum of two color-space mismatches during alignment to the
reference sequence. Depending on the complexity of the alignment,
the optimum number of mismatches in alignment is at least three. If
only two errors are allowed, then whenever there is a SNP (two
mismatches) and a measurement error, the third error causes
omission of that read. You can override the omission by using an
alignment program setting that counts two adjacent mismatches as a
single mismatch. Therefore, two adjacent mismatches and a
measurement error are classified as two errors, whereas three nonadjacent
errors are classified as three errors.
2-base encoding provides high system accuracy and built-in error
checking because it enables discrimination between measurement
errors and true sequence polymorphisms. The SOLiD software
interrogates each base twice in two independent reactions.
Information about each base is included in two adjacent pieces of
color-space data. Because the system uses four fluorescent dyes,
there are 16 possible two-color combinations (Figure 7).
Figure 7 Color-space transitions
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