Sequencher 4.8 User Manual--PC - Bioinformatics and Biological ...

Note: This can produce a very long report.
Variance Detail Report
As its name indicates, the Variance Detail Report contains comprehensive information
on the variants in a Variance Table. Below the Common Header, you will see detailed
information for each of the described variants.
The information for each variant consists of the sample name and comparison range for
the parent sequence. The Detail Table is divided into two parts. The first part contains
the sequence name, orientation, confidence score (where available), base call, primary
peak base call, secondary peak base call and the height of the secondary peak as a
percentage of the primary peak. The second part of the table contains a tracelet, which
is an extract of the sequence trace of the variant combined with some flanking bases
(see Figure 13-21). The tracelet only appears in the report if the sequence has associated
chromatogram data.
Figure 13-21 Extract from a Variance Detail Report
Note: If the Detail Table displays a gap for a specific base position, this will still be given
a confidence value. The confidence value will be equal to the average confidence ratings
of the bases flanking the gap. Sequencher will append an asterisk to the confidence value
and a footnote will explain how the value was derived.
Population Report
The Population Report is a special report which groups together all sequences sharing
the same set of variants. This report contains the Common Header and a report-specific
header. The report-specific header lists the number of population groups and the how
many samples this consists of. This header also indicates whether any samples have
been dropped from the report. This will only happen if a sample does not have complete
Comparison Range coverage. This report consists of two types of tables, a Population
Table and individual Detail Tables.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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