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
[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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