After running the Map Features step, the output consists of several files.
| File Name | Notes |
|---|---|
| PROJECT_map_features_console.txt | Copy of the text that appeared for this mapping in the Console side panel in the MegAlign Pro user interface. |
| PROJECT_map_features_report.tsv | See the text and table below this one for more 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. |
The report.tsv file is a tab-separated report file that can be opened in Notepad++ (freeware) or any spreadsheet utility. This report file contains a row for each feature that you directed MegAlign Pro 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 cannot be mapped with the current settings, or one/both align 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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