Searching for a specific Marker

From the VCMap start page, clicking on VCMap Query will allow the user to search for specific information from the VCMap build. There are two options:

4.1 Query by Marker

‘Querying by marker (Option 1)’ allows the user to search the anchor file to generate reports for an individual marker.

Enter the marker or cR details and click the display button.

For example, For Rn.14443 , the result will look like:

Click to see result.

This will generate individual marker report. To obtain data not shown in the report the search query can be expanded to have map positions flanking the marker:
Since Rn.14443 is mapped, choosing a region between 0 and 60 will result in:

Click to see result.

This tabulated report displays hyperlinked marker list, bin and stream predictions in the given chromosomal region where the query marker is mapped.

4.2 Query by Chromosomal regions

‘Querying by chromosomal region (option 2)’ displays the Chromosomal Region Report plus Bin and Stream Prediction Reports based on a specified backbone species for the entire chromosome or a selected region. Either distances or marker names can be entered to define the displayed region. Entering a single marker name will display the region +/- 50cR from the marker.

For rat chromosome 1, between 0 and 60 cR, the Query Result would look like:

Click to see result.

 

Question: What do I see if I query for specific region from the map?

Querying for a chromosomal region generates a Chromosomal Region Report consisting of table with hyperlinked marker symbols and corresponding genes if any. In this report, mapped markers for human, mouse and rat are listed in 3 columns.

Click to see result.

Bin predictions and Stream predictions, unique to VCMap are also listed on the same page.

 

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