1. GS Amplicon Variant Analyzer Application
:
1.8 The Flowgrams Tab
: 1.8.1 Populating the Flowgrams Tab
1.8.1
Populating the Flowgrams Tab
When you open an Amplicon Project in the AVA software, the Flowgrams tab has no content and is grayed-out. To populate it, you must use the “Open Flowgrams <Name of the Read>” action from the contextual menu that appears when you right-click one of the following two sources:
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A single read on the Global Align tab (make sure that its Read Type control is set to “Individual”)
•
A single read on the Consensus Align tab (which always displays individual reads)
Once the Flowgrams tab is populated, a small green arrow points to the flow corresponding to the nucleotide upon which you right-clicked. To load the Flowgrams tab with another read, you can use again the right-click method above and replace the displayed tri-flowgram by another one. But when in the Flowgrams tab, you have another, more powerful option: this tab has two “Read” controls in its upper-left corner that allow you to browse through and navigate all the reads that are present in the source tab that generated the one currently displayed (the Global Align or the Consensus Align tab). These controls are described in detail in section
1.8.3
. As you navigate to other reads with these controls, the AVA software attempts to maintain the focus of the green arrow on the same corresponding nucleotide in the source tab. By observing the distribution of signals for a particular nucleotide over many reads, one may obtain increased (or diminished) confidence for a given variation.