STR Report Settings dialog box
On the report toolbar, click the STR Report Settings icon 
to open the STR Report Settings dialog box and indicate the information that is to be displayed in the STR report. By default, all columns for the Locus report and the Allele report are selected for display. Also by default, the Allele Sequence report is displayed.
to open the STR Report Settings dialog box and indicate the information that is to be displayed in the STR report. By default, all columns for the Locus report and the Allele report are selected for display. Also by default, the Allele Sequence report is displayed. Setting | Description |
|---|---|
Locus report display settings | |
Locus | The name of the locus that was analyzed. |
Locus Coverage | The total number of reads that were aligned to the locus. |
Locus Percentage | Locus coverage/Total number of aligned reads. |
Allele Number | The total number of alleles that were identified for the locus. |
Allele Name | The names of the individual alleles that were identified for the locus. If the locus is Unknown, then N/A is displayed in this column. |
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 locus. (Shown as a percentage.) The information is relative to the order of the alleles listed in the Allele Name column. |
Allele Total Coverage | The total number of reads that are assigned to each allele. The information is relative to the order of the alleles listed in the Allele Name column. |
Allele Percent Matched | The percentage of the sequence for the sample allele that matches the sequence for the reference allele. The information is relative to the order of the alleles listed in the Allele Name column. • If the match is 100%, then the allele is considered to be a Matched allele. • If the match is less than 100%, then the allele is considered to be a Possible allele. |
Allele sequence report display settings | |
Sequence/Length | The default value is Sequence, which shows the sequence for the sample allele. If you select Allele length report for the report type, then report display is changed to show the length, which is the length of the sample allele in base pairs based on the consensus length of all the reads that were assigned to the allele. See Report type. Note: You can also click the Show Allele Sequence/Show Allele Length Report icon to toggle the display of the Allele report. See STR project report toolbar. |
Matched Allele Name | The name of the sample allele that was matched to the reference allele. Based on the allele name that was defined in the custom FASTA reference file. |
Status | The status for the allele—Matched, Possible, or Unknown. |
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 locus. (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 | |
Allow possible allele matches | If selected, report both matched and possible alleles, which contain one or more mismatches. If not selected (the default value), then report only matched alleles. Note: You can also click the Allow Possible Alleles/Check Matched Alleles Only icon on the report toolbar to toggle between reporting both Matched alleles and Possible alleles in the STR report, or reporting only Matched alleles. See STR project report toolbar. |
Maximum differences | Available only if Allow possible allele matches is selected. 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 Unknown. |
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 Unknown. 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 Unknown. |
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 Unknown. |
Report type | |
Allele sequence report | Selected by default. Display the allele sequence (Sequence column) in the Allele report. |
Allele length report | Display the allele length (Length column) in the Allele report. |
Note: You can also click the Show Allele Sequence Report icon on the report toolbar to toggle the display of the Allele report. | |
 | Optionally, you can also do either or both of the following: • Click Load Settings and browse to and select a Settings file (.ini file) to generate the STR 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 STR report for another project based on the settings in the file. |