Welcome to the Geography of Genetic Variants (GGV)
To begin, pick a dataset on the
dropdown menu. One can search variants within a dataset
by its rsID or position (Use the format
chromosome#:position, as in, 15:24608502 or
chr15:24608502) and clicking the search button or the
enter key. Click the "random" button to show a random
marker from the chosen dataset.
IGV browser at the bottom of the page can also also be
used to pick a variant for display.
display the population name, minor allele frequency,
minor allele count, and sample size, hover with the
mouse over a data point. Click on the plot title to open
up the UCSC genome browser at that variant.
Be sure to note we use a notion of a "frequency scale" to display rare variants and a "transparency scale" to indicate uncertain allele frequencies. These are explained in the legend.
If you use the maps in other works, include the source link: http://www.popgen.uchicago.edu/ggv
and/or make a formal reference to:
Marcus & Novembre (2016) Visualizing the Geography of Genetic Variants. Bioinformatics.
Keep in mind that this
is still an evolving project and many ideas/resources are in progress.
Questions/feedback/ideas/critiques are welcomed and appreciated!
Contact: josephhmarcus at gmail dot com or jnovembre at uchicago dot edu.