Mitochondrial Amplicon Report settings dialog box
On the report toolbar, click the Mitochondrial Amplicon Report Settings icon 
to open the Mitochondrial Amplicon Report Settings dialog box and indicate the information that is to be displayed in the report. By default, all columns for the Mitochondrial Amplicon report and the Allele report are selected for display. Options that are unavailable (grayed-out) are applicable only for the STR analysis report.
to open the Mitochondrial Amplicon Report Settings dialog box and indicate the information that is to be displayed in the report. By default, all columns for the Mitochondrial Amplicon report and the Allele report are selected for display. Options that are unavailable (grayed-out) are applicable only for the STR analysis report. Setting | Description |
|---|---|
Amplicon report display settings | |
Amplicon | The name of the amplicon that was analyzed. |
Amplicon Coverage | The total number of reads that were aligned to the amplicon. |
Amplicon Percentage | Amplicon coverage/Total number of aligned reads. |
Allele Number | The total number of alleles that were identified for the amplicon. |
Allele Frequency | The number of reads that were assigned to each allele out of the number of reads that were assigned to all accepted alleles for the amplicon. (Shown as a percentage.) |
Allele Total Coverage | The total number of reads that are assigned to each allele. |
Allele report display settings | |
Sequence/Length | The sequence for the sample allele. |
Start | The start position of the allele within the reference. |
End | The end position of the allele within the reference. |
Frequency | The number of reads that were assigned to the allele out of the total number of reads that were aligned to the amplicon. (Shown as a percentage.) |
Total Reads | The total number of reads that aligned to the allele. |
Forward Reads | The number of reads that were assigned to the allele that were forward reads. |
Reverse Reads | The number of reads that were assigned to the allele that were reverse reads. |
Differences | The number of bases in the sample allele sequence that do not match the reference allele sequence. |
Filter settings | |
Maximum differences | If the number of differences between the sample allele sequence and the reference allele sequence exceeds the indicated value, then the allele is classified as Incomplete. |
Minimum forward/reverse balance | Indicates the balance for the #F/#R reads for the allele and vise-versa. For example, if set to 5%, then if there were 100 reverse reads for the allele, there must at least 5 forward reads for the allele, otherwise, the allele would be classified as Incomplete. The default value is zero, which means that there is no requirement for the Forward/Reverse balance. Note: Adjusting this setting can help reduce the rate of false positives. |
Minimum count | The minimum number of reads that are required for an allele, otherwise, the allele is classified as Incomplete. |
Minimum frequency | The minimum value (expressed as a percentage) for the ratio of the number of reads for the allele to the total number of reads for the locus. If the frequency for the allele is does not meet or exceed this threshold, then the allele is classified as Incomplete. |
 | Optionally, you can also do either one or both of the following: • Click Load Settings and browse to and select a Settings file (.ini file) to generate the Mitochondrial Amplicon report based on the saved settings in the file. • Click Save Settings to save your settings for the report in a Settings file (.ini file). You can use this saved Settings file to generate the Mitochondrial Amplicon report for another project based on the settings in the file. |