GeneMarkerHTS Online Help : GeneMarkerHTS Viewers and Reports : STR Analysis Viewer Overview and Layout : STR Results Table pane
STR Results Table pane
The STR Results Table pane (also referred to as the STR Results table) displays all the alleles that were identified for each marker along with critical analysis information. The marker order follows the order of the markers in the panel that was used for the analysis, with the background color alternating by marker between gray and white. Default colors are used for specific table cells to indicate critical information about the analysis results, such as the Filter Status or the User Call for a marker allele. (You can edit any or all of these default table cell colors. See To edit the STR Analysis viewer highlighting colors.)
When you are navigating the STR Results Table, note the following:
• If you double-click any cell in the table, then the focus is reset in both the Histogram Viewer pane and the STR Results Table pane and all the rows for the corresponding marker are automatically highlighted in light blue.
• A selected cell is highlighted in dark blue. To clear all selected cells in a single step, including all automatically highlighted marker rows, click either the Histogram Viewer pane or the STR Results Table pane, and then press Esc on the client keyboard.
The table below lists all the data columns that can be shown for each marker allele in the STR Results Table pane and whether the column is shown (visible) by default. Up to 24 data columns are available for display in the STR Results Table pane. To edit the table layout, including configuring the shown (visible) and hidden table data columns, the order in which the columns are displayed, or both, see To work with the STR Results Table pane configuration.
 
Table Field
Default
Description
Category
 
One of three categories for the marker: Amelogenin, Autosomal STR, or ChrY STR.
Marker
X
The autosomal STR or Y-STR locus (marker) name.
Allele Name
X
The capillary electrophoresis (CE) name for a marker.
Report
X
Selected by default. If selected, the allele sequence is included in the NGS and CE reports. See STR Analysis viewer reports.
Filter Status
X
One of two statuses is possible based on the STR Filter settings and STR Stutter Filter settings that are specified for the project.
• Passed: A read passed all specified STR settings.
• Flagged: A read failed one or more specified STR settings.
Filter Reason
X
The STR filter settings and the STR Stutter filter settings that were triggered if a read was flagged.; otherwise, if a read passed, then the Filter Reason is set to > IT, which indicates that the allele counts were above the interpretative threshold.
SW Call
X
The software call based on the analysis parameters., where:
• Called means all analysis parameters were met.
• -1 Stutter (and any other stutter positions) are based on the following calculation:
Sequence Total Count of potential stutter peak/Allele Total Count of true peak = Peak height ratio of potential stutter peak to True allele
If the value of this calculation falls below the STR Stutter filter settings, then the call is Stutter; otherwise, if the value falls above the STR Stutter filter settings, then the call is a True Peak.
Note: If multiple stutter calls are available for an allele, then the SW call differentiates between them.
User Call
X
You can double-click the User Call for a flagged Filter Status to open the Edit User Call dialog box and enter a custom user call. See To work with user calls and comments in the STR Results Table pane.
User Comment
X
Displays any optional user comments that were made in support of/explanation of the User Call. See To work with user calls and comments in the STR Results Table pane.
Bracket Sequence
X
The STR repeat sequence for the allele. The specified Bracket Sequence settings determine the format for the sequence display. See To edit the bracket sequence settings.
Sequence Group
 
A grouping method that was used prior to Bracket Sequences. Maintained only for backwards compatibility.
Sequence Forward Count
X
The total number of forward reads that contain the bracket sequence.
Sequence Reverse Count
X
The total number of reverse reads that contain the bracket sequence.
Sequence Total Count
X
The total number of reads (F+R) that contain the bracket sequence.
Sequence Allele Percent
X
The percentage of the reads that contain the bracket sequence for the allele, calculated as Sequence Total Count/Allele Total Count.
Sequence Marker Percent
X
The percentage of the reads that contain the bracket sequence for the marker, calculated as:
Sequence Total Count/Marker Total Count.
Sequence Balance Ratio
X
The greatest value from all the following calculations:
• Sequence Forward %/Marker Forward %
• Marker Forward %/ Sequence Forward %
• Sequence Reverse %/Marker Reverse %
• Marker Reverse %/Sequence Reverse %
Allele Forward Count
X
The total number of reads for the allele in the forward direction, which includes filtered reads and sequence variants that have the same CE allele name.
Allele Reverse Count
X
The total number of reads for the allele in the reverse direction, which includes filtered reads and sequence variants that have the same CE allele name.
Allele Total Count
X
The total number of reads for the allele, which includes filtered reads and sequence variants that have the same CE allele name.
Allele Total Count Filtered
X
The number of reads for the allele that were filtered.
Allele Marker Percent
X
The ratio of the allele to all alleles for the marker.
Marker Forward Count
 
The total number of reads for the marker in the forward direction, including filtered reads.
Marker Reverse Count
 
The total number of reads for the marker in the reverse direction, including filtered reads.
Marker Total Count
X
The total number of reads (F+R) for the marker, including filtered reads.
Marker Total Count Filtered
X
The total number of reads for the marker that were filtered.
Sequence
X
The complete sequence for the read, with flanking sequences shown in lower case and repeat sequences shown in upper case.
Left Flank
X
The sequence for the left flank of the sequence read.
Repeat
X
The sequence for the repeat portion of the reads, but it is not shown in brackets.
Right Flank
X
The sequence for the right flank of the sequence read.