Population Mutation Rate And Snp

Question

[jackuser1979]

In our lab we have species which inbreeded over 100 generations. We have identified SNP, zygosity (heterozygous & homozyous) using illumina paired-end reads of same species mapping to reference genome of same speicies.How population mutation rate (theta) estimation will helpful in knowing fixed mutation and genetic diversity for my species?. How we can correlate population mutation rate to zygosity?

Answer 1

[Zev.Kronenberg]

Check out "Gene Genealogies and Variation and Evolution" from your library. You can also look at select sections on google books.

Chapter six really addresses the questions you have been asking.

Just to give you an idea of what the book has to offer:

Watterson's theta estimator = the observed number of variable sites in the genomic window / harmonic mean (p.g. 170)

harmonic mean = sum(1/number of chromosomes). Sum from 1 to number of chromosomes.

edit: number of mutations => number of segregating / variable sites