The Variation Frequency Plot

1.6.2

The Variation Frequency Plot (Figure 1‑58) located in the top panel of the Global Align tab shows graphically all the variations (relative to the Reference Sequence) observed in the reads included in the last computation and associated with the Sample-Reference Sequence combination and the Amplicon(s) selected, and the depth of coverage at each position of the multi-alignment.

•	The horizontal axis represents the Reference Sequence, gapped as needed to accommodate any insertions in the reads.

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The left vertical axis shows the percentage frequency of the variations, whereby individual variants are represented as colored bars keyed to the legend at the bottom-left of the tab for each position of the Reference Sequence; if more than one variation occurs at any given position, the bars are stacked vertically.

•	The right vertical axis shows the depth of coverage for each Reference Sequence position, in number of reads, shown on the plot by a light blue line.

Figure 1‑58: The Variation Frequency Plot. In this example, the plot was zoomed in to show the Reference Sequence along the horizontal axis.

The plot has all the standard navigation features (scrollbars, zoom buttons, mouse tracker, etc.) described in section 1.1.3.3. In addition, the Variation Frequency Plot and the multiple alignment of the bottom panel are reciprocally linked, in the following ways:

•	Three small triangles (two black and one green) located at the bottom of the plot panel have the following meanings:

◦	The black triangles indicate the boundaries of the subset of the plot that is visible in the multi-alignment panel.

◦	The green triangle shows the position in the plot that corresponds to the highlighted nucleotide in the alignment.

•	Clicking in either the plot or the multi-alignment panel centers the other panel on the position clicked.

◦	If you clicked on the plot, the nucleotide column in the multi-alignment is also highlighted.

◦	If you clicked in the multi-alignment, the position of the tracking triangles on the Variation Frequency Plot is also adjusted accordingly.