[Turn] Fst Index
Reprinted from http://blog.csdn.net/zhu_si_tao/article/details/71513099
And http://blog.sina.com.cn/s/blog_4ab0b3390102viol.html
Population genetics --Fst index, i.e., the differentiation between the population index analysis for differentiation among groups.
Population genetics indicators to measure the degree of differentiation among populations, there are many, the most common is Fst index. Fst index, from the evolution of the F statistic. F statistic (FIS, FIT, FST) there are three. Fst is for a pair of alleles, the presence of multiple alleles if the locus, it is necessary to measure with Gst, Differentially factor gene (gene differentiation coefficient, Gst).
Assuming s local group, the k-th local communities relative size (proportion) of wk. In one locus, the k-th local population allele frequency of the i-th QK (i), heterozygote frequency obsd hk. Then the entire population observed in heterozygote frequency average HI, where the desired population is a population of hybrid frequency over the average HS, over the entire population of the desired hybrid population frequencies HT, respectively:
The FIS, HI with respect to the HS is the ratio of the amount of reduction, i.e., the average coefficient of inbreeding of the local communities.
The FST, HS is reduced relative to the amount of HT ratio, i.e., having an average coefficient of inbreeding of genetic relationship between local communities.
Wherein, HS: ideal population groups where a desired average frequency hybrid HT: groups over the entire population of a desired frequency hybrid
FIT, HI with respect to HT is the ratio of the amount of reduction, i.e., the average coefficient of inbreeding of the entire group.
Visible, the relationship between the three in number is:
From the genetic point of view the relationship between gametes analysis, FIT and FST are equivalent to the entire population and local communities to carry a pair of alleles is the probability of homologous, and FST from two local groups of two gametes is a random selection of the same probability sources. From two local groups in a random selection of two gametes is a high probability homologous, indicated that the genetic composition of two local groups similar to the low level of differentiation; antisense high degree of differentiation.
FST in the range [0,1], the maximum value of 1 indicates that the allele is fixed to the local population, fully differentiated;
The minimum value is 0, meaning that different genetic structure of local populations exactly the same, there is no differentiation among populations.
Fst (Fixation index) is generally used to measure the genetic distance between the population. 1 illustrates two population is completely independent. 0 Description free interbreeding between the two population. Fst value is larger, described farther genetic distance. The lower the value, indicating that the majority of genetic variation occurred in the same population.
Wright suggested that the actual study, the FST is 0 to 0.05: genetic differentiation between small, may not be considered;
FST 0.05 to 0.15, a moderate level of genetic differentiation between populations;
FST 0.15 to 0.25, a large genetic differentiation between;
FST is 0.25 or more, there is a lot of genetic differentiation among populations.
Pi is mainly used to measure nucleotide divergency of each site.
These parameters may be calculated by the same vcftools:
vcftools：
vcftools --vcf test.vcf --window-pi 3000 --out Tenera
vcftools --vcf test.vcf --TajimaD 3000 --out Tenera
vcftools --vcf test.vcf --weir-fst-pop A2.txt --weir-fst-pop A134567.txt --fst-window-size 3000 --out A2.all.Fst