To specify the variant call settings for an mtDNA project
1. On the Mito Alignment viewer main menu, click Filter Settings.
The Filter Settings dialog box opens. The Mito Alignment tab is the open tab.
2. Open the Mito Variant tab
3. Do one of the following three options:
• Review the default settings, and if you are satisfied that the Mito Variant filter settings are correct as-is for your project, then go to Step 4.
• Edit any of the default values for the Mito Variant filter settings. See the table below.
 | If you edit any of the default values for the Mito Variant filter settings, you can click Default, and then click Yes in the Default values message that opens and all values are immediately reset to their default values. |
• Click Load to open the Load Filter Settings dialog box, and then browse to and select a Filter Settings (.settings) file.
Both Mito tabs are populated with the values in the settings file. You can leave the values as-is on the Mito Variant tab, or you can edit any of the values before you apply the settings. See the table below.
Option | Description |
|---|---|
Variant Percentage | The percent of reads that must contain the variant for the variant to be called at the indicated position. |
Variant Allele Coverage | The total number of reads that must contain the variant at the indicated position for the variant to be called. |
Total Coverage | The total number of reads that must occur at the indicated position for the variant to be called. |
Allele Score Difference | A value that is calculated for each minor allele to determine if the allele is a true variant and therefore, is to be included in the analysis results, or if the allele is a false positive and therefore, is to be filtered from the results. See Allele Score Difference. |
Allele Balance Ratio | A value that is calculated for each allele to determine if the allele is a true variant and therefore, is to be included in the analysis results, or if the allele is a false positive and therefore, is to be filtered from the results. See Allele Balance Ratio. |
SNP. Default value is < 2.5. | |
Indel. Default value is < 5.0. |
4. If you must change the reference region for the analysis, then go to To set the reference region settings for an mtDNA project; otherwise, do one of the following:
• Click OK to close the Filter Settings dialog box and immediately update the Mito Alignment viewer display based on the settings.
• If you edited any of the filter settings and want to save these edits before applying them, then click Save to open the Save Filter Settings dialog box and save the filter settings to a Filter Settings (.settings) file.
Note the following about saving a Filter Settings file:
• You must enter a name for the file.
• The file type is Filter Settings File (.settings) and you cannot change this.
• The default location for saving the Filter Settings file is the project folder, but you can always select a different location.
• You cannot save individual filter settings files for the Mito Variant Tab and the Mito Alignment tab. All settings on both Mito tabs are saved when you save a filter settings file for an mtDNA project.
After you save the filter settings file, you can click OK to close the Filter Settings dialog box and immediately update the Mito Alignment viewer display based on the applied settings.