Set Analysis Parameters

Set Analysis Parameters

1 In the App Session Name field, enter the analysis name.

By default, the analysis name includes the app name, followed by the date and time that the analysis session starts.

2 From the Project field, select the project that stores the app results.
3 From the Samples field, browse to the sample you want to analyze, and select the checkbox.
4 From the Minimum Base Call Quality Score for a Call (Q) field, enter the quality score.

The default value is 30. At each coordinate, reads at or above the Q value can contribute to the variant call.

5 From the Analysis Threshold % field, enter the percentage.

The default value is 10. If a nucleotide call is at less than the value of the Analysis Threshold (%), then the nucleotide call is not visible or reported as part of the call.

6 From the Interpretation Threshold % field, enter the percentage.

The default is 25. A nucleotide with a total number of reads greater than the interpretation threshold percentage contributes to the call for the coordinate. When more than one base exceeds this percentage for a coordinate, the app reports the base call code for the bases. See Base Call Codes.

7 From the Minimum Read Count field, enter the number of reads required at the coordinate to produce a base call.

The default value 10.

8 From the Genome field, select the genome to be analyzed.
9 From the PCR Primer Description field, select from the following options:
▶ Whole Mito Genome Amplicon Manifest
▶ DLoop Amplicon Manifest
▶ Custom Manifest.
10 [Optional] If you select Custom Manifest, complete the following steps:
    a Enter the start coordinate (5', 0-based) for the forward PCR primer.
    b Enter the start coordinate (5', 0-based) for the reverse PCR primer.
    c Enter the base length of the forward PCR primer.
    d Enter the base length of the reverse PCR primer.

Click the plus (+) sign to add additional rows.

11 Click Continue.

The mtDNA Variant Processor App begins analysis.

When analysis is complete, the app updates the status of the session and sends an email to notify you.