You can view a summary of data about the identified variants, and toggle to other views that provide more details about the same variants.
- In the Analyses tab, click Overview.
- Click the column headings to sort the results. Alternatively, use the available filters or the Search field to limit the list of analyses.
- 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.
- Click Visualize.
Review detailed variant data.
Click SNV/INDEL, CNV, or Fusion to view detailed analysis metrics. For a description of each metric, see Detailed analysis metrics.
Figure 1. Example SNV/Indel visualization in IRGV
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.
Sort read coverage tracks by variant
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.