Visualize variants in an analysis run with an Ion AmpliSeq™ HD analysis workflow

You can view a summary of data about the identified variants, and toggle to other views that provide more details about the same variants.

  1. In the Analyses tab, click Overview.

    The Analyses table lists all the available analyses results.

  2. Click the column headings to sort the results. Alternatively, use the available filters or the Search field to limit the list of analyses.
  3. Select the checkbox in the row of the analysis that you want to visualize or select two or more analyses if you want to visualize a side-by-side comparison of multiple results.
  4. Click Visualize.

    The Analysis Visualization screen opens to the Variant Matrix tab, displaying the Summary screen that shows all the identified SNVs/INDELs, CNVs, and Fusions.

    Note: A none detected result indicates that down to the displayed limit of detection (LOD), no variants were observed in the sample within or above the LOD range.

  5. Review detailed variant data.
    • In the Variant Matrix tab, in the Summary screen, click the gene name in the Gene column to access the HGNC report for that gene.

    • Click SNV/INDEL, CNV, or Fusion to view detailed analysis metrics. For a description of each metric, see Detailed analysis metrics.

    • In the SNV/INDEL, CNV, or Fusion screen, click the link in the Locus column to view specific variants in the Ion Reporter™ Genomic Viewer (IRGV) in a separate window.

      Note:

      • Ion AmpliSeq™ HD analyses group consensus reads into families. A family is a group of reads that are associated with the same DNA molecule before library amplification. Each family is identified using the molecular tags, and consensus reads with the same molecular tags are grouped into the same family. In IRGV data view, the color of the consensus reads is used to indicate a family. Side by side consensus reads with the same color belong to the same family.

      • Within each read track, each nucleotide variant is indicated by a different color. T, A, C, and G are red, green, blue, and orange, respectively. An "I" denotes insertion, and white color with a dash indicates deletion.

      Figure 1. Example SNV/Indel visualization in IRGV
      1. Variant density overview, illustrated as copy number (Y‑axis) at a specific position on the chromosome (X‑axis)

      2. Displayed chromosomal region; use the search field to view a different region

      3. Proband variant position on the displayed chromosomal region

      4. Proband read coverage tracks

      Figure 2. Example fusion visualization in IRGV
      1. Fusion target track

      2. 5′ (top) and 3′ (bottom) gene track

      3. Read coverage track

      4. Use the dropdown list or search for another fusion variant