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

Glossary
Stringency Stringency is one criterion used to filter out junk reads in
ReadBuilder stage. For filtered reads, csfasta and QV.qual are stored
in the reject folder instead. The valid range of stringency is from 0 to
80. Any stringency less than 0 is treated as 0, where all reads will
pass the stringency threshold. If stringency is set larger than 80,
maximal possible stringency of 80 is used to avoid over filtering
good beads.
TAG-ID A unique identifier for every tag, which consists of four components:
panel_xpixel_ypixel_tagtype. Each tag has a TAG-ID. For example,
1_567_321_F3 describes a bead in panel 1 at coordinates 56, 321
(X,Y) with the R3 tag (second tag in a mate-pair).
Note: A Tag ID describes the bead and its data within files.
Values A dot (.) is used in color space to show that there is no call for this
position. Although low values may have been measured, during
clustering it was determined that no call could be made.
A minus one (−1) in a set of calculated values (for example, N2S)
indicates that there is no data for this point; that is, a dot (.) is in the
color space for this position.
A zero (0) in a set of calculated values (for example, N2S) means zero
(0). The calculated result after rounding is zero (0).
204 Applied Biosystems SOLiD 4 System SETS Software User Guide