Histogram Viewer pane
The Histogram Viewer pane displays a histogram for every STR marker that was analyzed, with each bar on the histogram corresponding to a marker allele. From top to bottom, the histograms follow the order of the markers in the panel that was used for the analysis. A marker histogram has the following characteristics:
• The X-axis variable is the allele name, with the histogram bars arranged in increasing order, from the smallest number of tandem repeats to the largest number of tandem repeats for all the marker alleles.
• The Y-axis variable is the total number of read counts (forward + reverse) for the allele.
• The colored part of a histogram bar contains the non-filtered allele counts with allele counts displayed blue and the iso-allele counts displayed in different colors. The number of different colors that are displayed is based on how many iso-alleles are called for a given allele.
• The gray part of a histogram bar contains the filtered out allele counts for both true allele positions and allele positions that do not have data.
• The “U” allele on the X-axis represents “unknown,” which are the reads that have the correct primers for the marker but GeneMarkerHTS cannot detect the number of repeats and therefore, cannot assign the read to a specific allele.
If you double-click a histogram in the Histogram Viewer pane, then the corresponding marker results are automatically highlighted in the STR Results Table pane.
 | For detailed information about the types of non-filtered allele counts that are contained in the colored portion of a histogram bar, see To specify the STR filter settings for an STR analysis project. |
By default, when the Histogram Viewer pane first opens, the Zoom in level is set to 100%, where each histogram is displayed by itself in the pane. The following options are available for adjusting the zoom level of all the histograms at the same in the Histogram Viewer pane, where a zoom out level of 100% is the fully zoomed out view and all histograms for the project sample are displayed in the Histogram Viewer pane at the same time:
• You can use the Zoom slider bar that is displayed on the Viewer Options menu.
• You can use the View menu options of Zoom in and Zoom out:
• You also right-click any histogram that is displayed in the pane to open a context menu that has a Zoom in and a Zoom out option.
Options for working with and adjusting the default display of the histograms in the Histogram Viewer pane are available from a histogram context menu and the Histogram Settings dialog box. See: