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.

      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


  6. Review proband read coverage tracks.

    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.

    You can sort, adjust, and view details about variants and base calls that are visualized in each read coverage track.

    Option

    Description

    Sort read coverage tracks by variant

    In the coverage track, place the cursor at the position of the variant, then right-click and select Sort by Base.

    Adjust (IRGV) BAM tracks

    Click (Actions) next to the read coverage track, then select an option to adjust the view of the track. For more information, see Adjust (IRGV) BAM tracks.

    Review detailed data about a BAM read

    Single-click on the read track to get information such as the mapping quality, the strand and the read base.

    Review distribution of base calls at a selected position

    Click the density plot (the gray bar at the top of the read coverage tracks) to view information about the total count, total reads, and total number of molecules, the distribution of single nucleotides at that position, and the number of insertions and deletions.

    Note: The number of molecules in the (IRGV) coverage track can be slightly different from what is reported in the VCF output. The values seen in IRGV are based on initial estimates made by the variant caller, whereas read or molecular counts in VCF output are based on calculations that can include additional processing by the variant detection pipeline.