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). |
| PROJECT_map_features.star | 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 _PROJECT_map_features.star 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. |
| PROJECT_seqmover.star | 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 Deleted_end_3prime Deleted_end Deleted_ends |
[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 |
Need more help with this?
Contact DNASTAR