9.11 Viewing GST hits in GGV
Now we can navigate to the GGV browser and look up the distribution of allele frequencies for this variant.
Note that the “position” has changed due to the new coordinate system, but we are looking at the same SNP. This variant has huge allele frequency differences across populations, consistent with the high GST value that we computed.
Also note that two populations in the Americas also carry this variant at high frequency. These are both African American populations – African Caribbean in Barbados (ACB) and African Ancestry in SW USA (ASW).
Fig. 5. Allele frequencies of our top GST hit.