For 2 different SNP positions, the following associations were observed in a pop

Question

For 2 different SNP positions, the following associations were observed in a population:
SNP1 SNP2 Observed number
C T 29
C C 3
A T 1
A C 15
It has been already determined that the genotypic frequencies are not at random.
a. Calculate the allele frequencies.
b. Calculate the genotypic frequencies.
c. Estimate the absolute and the relative linkage disequilibrium between both SNPs.
d. If the frequency of recombination between both SNPs is 3.5 x 10-5,, calculate the time needed to reduce the LD from its maximum value (calculated in c) to its current value (also calculated in c).

Explanation / Answer

Genotypic freque allele frequencies of C T 29 29/48=60.41 f(C)=(29+2*3+15)/144=.34 C C 3 3/48=6.25 f(T)=(29+1)/96=.31 A T 1 1/48=2.08 f(A)=(15+1)/96=.166 A C 15 15/48=31.25 total=48

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