The 1000 Genomes Selection Browser is a database of Signatures of Selection in the Human Genome, based on the 1000 Genomes Phase I data. It is freely accessible at http://hsb.upf.edu/
The browser, based on a custom UCSC Genome Browser installment, allows to easily navigate the genome and visualize regions that are candidate for having been involved in an event of selection in any of the African, European, or Asian populations. The data can also be easily downloaded for further analysis here.
Our browser includes a total of 17 tests for selection. For each test of selection, we provide a raw score, plus a ranked score which compares each position to the rest of the genome.
- Tajima’s D (Tajima, 1989): Comparison of estimates of the number of segregating sites and the mean pairwise difference between sequences.
- CLR (Nielsen et al., 2005). Multilocus Composite Likelihood Ratio Test. Read more about the CLR
- Fay and Wu’s H (Fay & Wu, 2000): Comparison of the number of derived segregating sites at low and high frequencies and the number of variants at intermediate frequencies.
- Fu and Li’s F* (Fu, 1997): Comparison of the number of singleton mutations and the mean pairwise difference between sequences.
- Fu and Li’s D* (Fu, 1997): Comparison of the number of singleton mutations and the total number of nucleotide variants.
- R2 (Ramos-Onsins and Rozas. 2002) Comparison of the difference between the number of singletons per sequence and the average number of nucleotide differences.
- XP-EHH (Sabeti et al., 2007): Cross-population extended haplotype homozygosity.
- Delta iHH (Voight et al., 2006, Grossman et al., 2010): difference between two integrated haplotype homozygosity scores.
- iHS (Voight et al., 2006): log ratio between two integrated haplotype homozygosity scores.
- EHH average (Sabeti et al., 2002): Extended halotype homozygosity; weighted average for all core haplotypes of the position at which the haplotype homozygosity decays to <=0.5.
- Wall’s B (Wall, 2000): Counts the number of pairs of adjacent segregating sites that are congruent (if the subset of the data consisting of the two sites contains only two different haplotypes)
- Wall’s Q (Wall, 2000): Adds the number of partitions (two disjoint subsets whose union is the set of individuals in the sample) induced by congruent pairs to Wall’s B.
- Fu’s Fs (Fu, 1997): Based on Ewens’ sampling distribution, taking into account the number of different haplotypes in the sample.
- Dh (Nei, 1987): Summary statistic based on the number of different haplotypes in the sample
- Fst (Weir and Cockerham, 1984) : global and pairwise
- delta DAF: difference of Derived allele frequencies between 2 populations.
- XP-CLR (Chen et al., 2010): Multilocus allele frequency differentiation between two populations.
The database has been published in the NAR Database issue 2014:
Pybus M, Dall'olio GM, Luisi P, Uzkudun M, Carreño-Torres A, Pavlidis P, Laayouni H, Bertranpetit J, Engelken J. 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans. Nucleic Acids Res. 2014 Jan 1;42(1):D903-9. doi: 10.1093/nar/gkt1188. Epub 2013 Nov 25. PubMed PMID: 24275494. Available at http://nar.oxfordjournals.org/content/42/D1/D903.short
For completeness we also also link dbPSHP, a database of curated publications about positive selection in different human populations, which also presents the results of 15 tests for positive selection.
Cool resource and nice post describing it!