After running the Map Features step, the output consists of approximately seven files of several file types.

File Name Notes
PROJECT.EXT 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.
PROJECT_map_features.starff 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 is loaded and run.
PROJECT_map_features_console.txt Copy of the text that appeared for this mapping in the Console panel in the SeqNinja user interface.
PROJECT_map_features_report.tsv See the text and table below this one for additional information.
PROJECT_map_features_unmapped.tsv 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:

Category Label in report Comments
Not mapped Not_mapped Can occur when the feature doesn’t map at all, or when the feature maps, but not well enough to pass the mapping thresholds.
Indels Deleted_end_5prime
[Non-protein sequences] First residue and/or last residue does not map or aligns with a target gap.
Indel Both insertions and deletions have occurred
Insertion An insertion has occurred
Deletion A deletion has occurred.
Substitutions No_start [CDS only] The initial codon in the mapped feature is not a start codon.
Nonsense [CDS only] A substitution has resulted in an interior stop codon.
No_stop [CDS only] The last codon in the mapped feature is not a stop codon.
Non-synonymous [CDS only] Non-synonymous substitution occurred.
Synonymous [CDS only] Synonymous substitution occurred.
Substitution [Non-CDS] A substitution has occurred.
No change Identical

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