Allozyme genetics exercise

[Data_Source]: Allozyme_genotypes.txt; The data file consists of diploid genotypes for 20 fruit flies at 5 allozyme loci (EST1 to EST5) sampled from many populations. Please find the population assigned to you (Data_Assignment.txt). Each distinct allele at a locus is given a unique number (e.g. 12 = heterozygous individual with allele 1 and allele 2). There is a maximum of 3 alleles per locus.

Analyse the data to estimate the parameters below

1. Allele frequencies (p1,p2,p3)

2. Number of Alleles/Locus, a

3. Observed Heterozygosity / locus Hobs

4. Expected Heterozygosity / locus Hexp

5. Proportionate reduction in heterozygosity due to inbreeding, Fis

6. x2 for HWE test

7. df for HWE test

8. p value for HWE test

Provide me with a completed table like below; report 2 decimal places for all estimates, but keep 3 decimal places while doing the calculations

Is your population inbreeding: Yes / No

Back up you answer with evidence (2 to 3 lines):

Sequence analysis exercise:

You’ve sequenced 1000 bp of your favourite gene from 5 haploid individuals. The dataset specifies all polymorphic positions in the sequences (their location does not matter here). Estimate the following parameters;

1. Proportion of Segregating Sites, S [3 decimal places]

2. Number of mismatches at each segregating site, presented in the same order as in the dataset and separated by commons [eg: 3,4,4,3,…]

3. Nucleotide diversity, π [4 decimal places]

dataset