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

Glossary
Mate-Pair Fragments from the genome paired during sequencing and separated
by the same number of bases. For a known reference sequence of size
5 Mbp and a read length of 25 bp per tag, the system allows a total of
six mismatches when placing the F3 and R3 tags. These mismatches
can be distributed in any allocation across the F3 and R3 tags as long
as the total number of mismatches does not exceed six. Any beads
with F3 and R3 tags, which map under this mismatch allowance and
which satisfy the mate-pair constraints, are considered to be a
successfully placed mate-paired read. The mate-pair constraints are as
follows:
The distance between the F3 and R3 tags must be within a prescribed
range of distances determined by the insert size and library
preparation.
Multiplex
sequencing
The tags must map such that R3 comes before F3 reading
5′ > 3′ .
The tags must map such that F3 and R3 map to the same strand on
the reference sequence.
Sequencing of multiple barcoded fragment libraries on a single spot
on a slide.
Panel The region of the array that the camera can image at one time.
Successive cycles result in four images for each panel (one per color).
Beads are identified by position within a panel, that is, x,y coordinates
are not unique values across panels. The combination of panel and x,y
coordinates uniquely identifies a bead.
202 Applied Biosystems SOLiD 4 System SETS Software User Guide