View single sample aneuploidy details

You can view an interactive view of details from a single sample aneuploidy analysis in the Ion Reporter™ Genomic Viewer (IRGV). This visualization provides a view of the genomic data that you can zoom in on to view individual chromosomal data, and a table of events that were called. You can adjust the list of events to show only events that were filtered in for the analysis by the applied filter chain.

You must have IRGV set as the default viewer for this procedure. For more information, see Set IRGV or IGV as the default viewer.

  1. In the Analyses tab, click Overview.
  2. Select the Workflow filter and enter ReproSeq to find analyses that used a ReproSeq analysis workflow, or select a specific analysis workflow filter, such as ReproSeq No Gender PGS w.1.1.
  3. Select one or more analyses then click Visualize.

    The Analysis Visualization screen opens in the IRGV & Generate Report tab.

  4. Click in a row of the Gains/Losses table. The IRGV Details screen opens in a new browser tab.
    Figure 1. IRGV Details screen
    1. Analysis Whole Genome View. Provides a genome-wide perspective of the data. Metrics above the view are:
      1. Productive Read Count— The sum of mapped reads from a sample that align to the autosomes and chrX in females or to the autosomes and chrX + chrY in males. If the CNV finding parameter Remove Duplicates is set to True, then the Productive Read Count metric excludes duplicates. Productive reads are the specific reads that are used to establish the relative coverage of tiles across the sample.
      2. Confidence
      3. Filter Chain — The filter chain that was applied to the analysis.
    2. Click in a row of the Gains/Losses table to open a visualization with the data charts and a table of the events in a separate tab. Select an option in the table to see all events, or only events that passed the applied filter chain.
    3. Enter a chromosome coordinate in the Search field to zoom into chromosome data, or click on a chromosome in the Karyogram to view its chromosome coordinate. Zoom in and out of the Karyogram, and click Reset to return to the default chromosome view.
    4. Select a chromosome on the Karyogram to the chromosome coordinate, narrow the focus of the whole genome view, and update the IRGV tracks to reflect the selection.
    5. IRGV tracks. Each track updates dynamically as you select data in the whole genome view or the Karyogram view.
    6. Adjustable ploidy scale for selected chromosomes or chromosome regions. Change the track name or track height for the histogram, or hide the track. See Adjust IRGV BAM tracks for more information.
    7. Adjustable reference and preferred transcript tracks. Change the BAM track name, track height, and track color, or collapse, squish or expand the track. See Adjust IRGV BAM tracks for more information.
    8. Export the visualization, or change the IRGV preferences. See Set IRGV preferences for more information.
Related Topics
Parent topic: Visualize aneuploidy analysis results