STR analysis project report

NextGENe Online Help : NextGENe Viewer : STR (Short Tandem Repeats) Analysis Project : STR analysis project report

After you open an STR analysis project in the NextGENe viewer, the Show STR Report option is displayed on the Report Selection icon. Select this option to open the STR report in addition to the Alignment view. The report has two sections. The top section is the Locus report, which shows the different loci that were analyzed along with associated information for each locus. The bottom section is the Allele report, which displays a row for each allele, by name, that was identified in the sample for a selected locus. The information is relative to the order of the alleles listed in the Allele Name column in the Locus report. Double-click any entry in the Locus report to update the display in the NextGENe viewer and the Allele report accordingly. You can also double-click any allele in the Allele report to change the focus of the display to the selected allele.

Column	Description
Locus report
Locus	The name of the locus that was analyzed. Any loci that failed any of the Filter settings for the report are grouped into a row with Unknown displayed in this column. See STR Report Settings dialog box.
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. Note: Depending on the Filter settings that were specified for the report, these values might not be the same as the Frequency values in the Allele report. See STR Report Settings dialog box.
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 report
Sequence/Length	The default value is sequence, which shows the sequence for the sample allele. You can change the report settings 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 STR Report Settings dialog box.
Matched Allele Name	The reference allele name for the allele to which the sample data is matched. Based on the allele name that was defined in the custom FASTA reference file.
Status	• If the sample allele sequence matched 100% to the reference allele sequence, then Matched is displayed for the status. • If the sample allele sequence matched less than 100% to the reference allele sequence, then Possible is displayed for the status. • If the allele’s locus is Unknown, then N/A is displayed for the status.
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.) Note: Depending on the Filter settings that were specified for the report, these values might not be the same as the Allele Frequency values in the Locus report. See STR Report Settings dialog box.
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. • For matched alleles, the difference = 0. • For possible alleles, the difference > 0.

By default, when the STR report first opens in the NextGENe viewer, it is displayed on the right side of the opened viewer, and the focus in the Alignment viewer is set to the first locus in the list of analyzed loci. A blue cross centered in the Alignment viewer indicates the position of the locus. The Allele report details the alleles that were identified for this first locus. You can click the Switch Report Layout icon on the NextGENe Viewer toolbar to select the location for showing the report (to the right or at the bottom of the NextGENe Viewer), or to elect to show only the report (the Alignment viewer is hidden), or to hide the report.

The STR report is interactive.

Option	Description
Change the sort order of the Locus report	By default, when the STR report is first generated, the Locus report is sorted alphabetically by Locus reference (Sort by Reference). At the top of the report, select a different sort option (Sort by Decrease of Locus Coverage or Sort by Increase of Locus Coverage)
Change the focus in the Alignment view to that of a specific locus	Double-click the locus. The Allele report display is dynamically updated.
Change the focus in the Alignment viewer to that of a specific allele	Double-click the allele. A blue cross is displayed in the Alignment viewer to indicate the position of the selected allele on the locus.
Copy selected text or text in a range of cells in the report to your clipboard	1. Press and hold the left mouse button, and then drag your cursor over the continuous report cells that you are copying. The selected cells are highlighted in light blue. 2. Right-click anywhere in the selected cells. and on the context menu that opens, select Copy to copy the selected cells to your clipboard. 3. Use standard keyboard commands or menu commands to paste the copied cells into a third-party application.

Other options are available on the report toolbar. See STR project report toolbar.