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Panzea Allele Frequency Display Tutorial
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• With the Panzea Allele Frequency Geographic Display tool, you can display pie graphs that show the geographic distribution of allele frequencies for a SNP, SSR or isozyme marker
• The display is based upon Google Maps. Hence, you can use their standard controls to change between map, satellite or hybrid view or to move or resize the map
• Upon moving or resizing the map, the grid upon which the allele frequencies are based is redrawn, and new pie graphs are calculated and displayed
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Tasks demonstrated:
1) Choose the marker of interest and display initial map2) Change to “hybrid” (combined map & satellite) view3) Choose a single species or subspecies to display4) Change the zoom level5) Obtain underlying information for a pie graph6) Simplify pie graphs by pooling low frequency alleles7) Display pie graphs for a single allele8) Reposition the map
Panzea Allele Frequency Display Tutorial
www.panzea.org
1) Choose marker of interest and display initial map
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1) Choose marker of interest and display initial map
We will use an SSR marker as an example, so here we will only change the Marker Type, and leave the other options in their default settings
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1) Choose marker of interest and display initial map
For example
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2) Change to ‘hybrid’ (combined map & satellite) view
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3) Choose a single species or subspecies to display
spp. mays will display maize landraces only (since inbred lines do not have geographical coordinates)
Then click the “Filter” button (hidden under this drop down list in this view)
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4) Change the zoom level
Click here to zoom out
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5) Obtain underlying information for a pie graph
Click on a pie chart for details
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5) Obtain underlying information for a pie graph
Details for that pie chart then appear here. Use the scroll bar at the right to see them all
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6) Simplify pie graphs by pooling low freq. alleles
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6) Simplify pie graphs by pooling low freq. alleles
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7) Display pie graphs for a single allele
Choose allele 92 (for example), and then click the “Filter” button (hidden under this drop down list in this view)
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7) Display pie graphs for a single allele
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8) Reposition the map
Use these arrow buttons to move the map, or click on the map and drag (hand tool)
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8) Reposition the map
