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Chapter 3
Graphical Analysis Display
Direction is selected for Automatically Adjust GenBank Direction, then the nucleotide
sequence is also displayed upside down.
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The nucleotide sequence for the forward reference trace.
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The nucleotide sequence for the forward sample trace.
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The nucleotide sequence for the reverse sample trace.
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The nucleotide sequence for the reverse reference trace.
An asterisk indicate inconsistencies in base calls between traces. A black asterisk (*)
indicates an inconsistency between a reference trace and a sample trace. A red asterisk (*)
indicates an inconsistency between a reference trace and the GenBank-derived trace.
Amino Acid frame
The Amino Acid frame displays the codon number and the IUPAC abbreviation for the
corresponding amino acid sequence for the called bases that fall within a coding region in the
GenBank sequence (the first line in the frame) and in the sample file (the second line in the
frame.) Any differences between the amino acid translations as the result of mutations in the
sample file are therefore visible in this frame. The frame also shows the coding DNA
reference sequence. Just like the Nucleotide Sequence frame, the location of the queried gene
(plus (+) or minus strand (-)) and the option that is selected for Automatically Adjust
GenBank Direction on the Others tab determines the order (ascending or descending) in
which the codon numbers and c.dna numbers are displayed.
Figure 3-3:
Amino Acid frame
Tracks frame
The Tracks frame is displayed only if information has been imported from an annotation
database for the project, and/or false positives and/or artifacts have been manually added to
the project. A reported single base variant at a specific chromosome position is indicated by
a green tick mark. A reported variant that spans multiple bases at a specific chromosome
position is indicated by a green horizontal line. You can place your cursor over a green tick
mark or horizontal line to open a popup that displays detailed information for the reported
variant.
Figure 3-4:
Tracks frame with mutation information displayed for a reported variant
Mutation Surveyor User’s Manual
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