After running the Map Features step, the output consists of approximately seven files of several file types.
|Results file containing the mapped features. Can optionally be generated outside the project directory. Default is Genbank (.gb).
|SeqNinja script that adds the annotations in the .starff table to the target sequence.
|Table of mapped features which are added to the target sequence when the Run button is pressed in the Map Features dialog, or when the SeqNinja script _PROJECT_map_features.star is loaded and run.
|Copy of the text that appeared for this mapping in the Console panel in the SeqNinja user interface.
|See the text and table below this one for additional information.
|Report of intervals in the target sequence to which no features were mapped. Generated only if requested in the Map Features Options screen under Unmapped Interval Report.
|SeqNinja script that describes the target sequence in terms of segments common with the source, and segments unique to the target.
The report file is a tab-separated report file that can be opened in a spreadsheet (recommended) or a text editor. This report file contains a row for each feature that you directed SeqNinja to map. The “Variation” column summarizes the most significant variation of the mapped feature against the source feature:
|Label in report
|Can occur when the feature doesn’t map at all, or when the feature maps, but not well enough to pass the mapping thresholds.
|[Non-protein sequences] First residue and/or last residue does not map or aligns with a target gap.
|Both insertions and deletions have occurred
|An insertion has occurred
|A deletion has occurred.
|[CDS only] The initial codon in the mapped feature is not a start codon.
|[CDS only] A substitution has resulted in an interior stop codon.
|[CDS only] The last codon in the mapped feature is not a stop codon.
|[CDS only] Non-synonymous substitution occurred.
|[CDS only] Synonymous substitution occurred.
|[Non-CDS] A substitution has occurred.
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