Post date: May 16, 2014 7:18:47 PM
grep theta *afs
#It looks like h and theta converged after 30 runs for all subpopulations
#h in this case is the proportion of nucleotides in which an individual is heterozygous
#to get traditional expected h, will turn genotypes into allele frequencies, get 2pq and average across the loci
grep theta *30.afs
C-ELsites.30.afs:[bcf_p1_read_prior] heterozygosity=0.006339, theta=0.004367
C-F1sites.30.afs:[bcf_p1_read_prior] heterozygosity=0.006651, theta=0.004522
C-F2sites.30.afs:[bcf_p1_read_prior] heterozygosity=0.006166, theta=0.004269
C-F3sites.30.afs:[bcf_p1_read_prior] heterozygosity=0.006880, theta=0.004659
W-CSsites.30.afs:[bcf_p1_read_prior] heterozygosity=0.010179, theta=0.006127
W-ELsites.30.afs:[bcf_p1_read_prior] heterozygosity=0.008345, theta=0.005312
W-POsites.30.afs:[bcf_p1_read_prior] heterozygosity=0.010684, theta=0.006389
W-SGsites.30.afs:[bcf_p1_read_prior] heterozygosity=0.008288, theta=0.005014
W-UPsites.30.afs:[bcf_p1_read_prior] heterozygosity=0.007698, theta=0.004576
#Wild population Ne's using = (theta)/(4)(mutation rate 1.1 x 10^-8 from human genome (wikipedia))
W-CS: 139250
W-EL: 120727
W-PO: 145204
W-SG: 113954
W-UP: 104000