Panzea Allele Frequency Display Tutorial

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Panzea Allele Frequency Display Tutorial

• 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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Panzea Allele Frequency Display Tutorial

• Tasks demonstrated

• Choose the marker of interest and display initial
  map
• Change to hybrid (combined map satellite)
  view
• Choose a single species or subspecies to display
• Change the zoom level
• Obtain underlying information for a pie graph
• Simplify pie graphs by pooling low frequency
  alleles
• Display pie graphs for a single allele
• Reposition the map

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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
Then click the Filter button (hidden under this
drop down list in this view)
spp. mays will display maize landraces only
(since inbred lines do not have geographical
coordinates)
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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