I just posted a new version of SnpMap that adds a few little features. Here is the link:
Now would be a good time to give an introduction into SnpMap. The purpose of SnpMap is to help you explore your autosomal genome data from 23andMe or FamilyTreeDNA. In particular, it's meant to help identify segments of your chromosomes that show ancestry, either recent or ancient, that show similarities with different regions of the world, and the populations within those regions. One thing you'll discover, is that genetically, people all over the globe are quite similar. At some positions on the chromosome, people can have alternate alleles for that position. Some of these are the SNP locations that the DNA services test. Although any allele can occur in people from any part of the globe, studies have shown that the frequencies of the alleles are often different among people from different parts of the world. For most SNPs the frequency differences are small - too small to be very useful for identifying the region or population from which a person might have ancestry. But there are some SNPs that have sizable frequency differences. These difference usually vary over distance, so that the difference is small between adjacent populations, or even adjacent regions, but significant between distant regions. Finding these SNPs and displaying information about them is what SnpMap helps you do.
SnpMap will add display markers to point out notable situations. The '≠' symbol is the negative marker. It indicates that your allele occurs in very low frequency within that region or population, and there is at least one other region or population that shows frequencies several times higher. The '●' symbol is the positive marker. It indicates that your allele occurs several times more frequently than any of the other regions/populations. This marker is not that common to get, especially when comparing many regions/populations, because there are not very many SNPs where a single region/population has a uniquely higher frequency for an allele. The '◦' symbol is the shared positive marker. This is new to this version, and is described in more detail below. In version 1.0.2 and earlier, I used a happy face for the positive marker, and an empty circle for shared positive, but changed them to support Windows XP. Some of the screenshots still have the older symbols.
To help you learn more about populations data and SNPs, you can right click on the populations list, or an SNP row and a menu will display with links to the Alfred and NIH website pages containing detailed information.
You can control which SNP rows SnpMap displays by using the check boxes above the SNP grid.
Double Negative Markers
Single Negative Markers
Shared Positive Markers
In my next post, I will show some examples of real segments, and pointers on identifying them.