All bases identified by the SeqMan Pro variant discovery method as variants are initially evaluated as putative. Any base in a contig can be evaluated or re-evaluated as a putative variant, a confirmed variant, or a rejected variant, using either of the methods described below.
Note: SeqMan Pro will automatically reject variants that occur within features of the type unsure. Please see Editing Features for information on how to change a feature type.
In the SNP column found in the All Found Variants (disabled for BAM-based projects) and Variants Summary reports, a symbol indicates how a variant base is currently evaluated:
|
Symbol |
Meaning |
Description |
|
? |
Putative variant |
The base may or may not be an actual variant. |
|
P |
Confirmed variant |
The base is an actual variant. |
|
x |
Rejected variant |
The base is not a variant. |
|
- |
Combination |
Found in the Variants Summary report only, a dash is displayed if the column contains some combination of putative, confirmed, and rejected variants. |
Click on a mark to change the evaluation. In the All Found Variants report, this will change the evaluation for the base in the designated row. In the Variants Summary report, this will change the evaluation for all of the variants in the aligned column.
You can also evaluate variants while viewing them in the Alignment View. To do this, select the base(s) you wish to change, and then select one of the following options:
•Select Variant > Putative Variant to change the evaluation to putative.
•Select Variant > Confirm Variant to change the evaluation to confirmed.
•Select Variant > Reject Variant to change the evaluation to rejected.
Note: SeqMan Pro will only consider bases marked as confirmed variants when annotating your consensus sequence. Only positions on the consensus that contain a confirmed variant in any of the constituent sequences at that position are annotated as “variation” features during export (See Opening a Sequence in Another Lasergene Application or Exporting Consensus Sequences.) Variants must be displayed in order to be included in the export.