About mutation rate

mutation rate should be across all loci: so we have the following

mutation rate: assume 1x10-8
Lenght: all sites considered by ANGSD after filtering:
SNPS_1: all SNPS initally dsicovered by ANGSD (Filtered but not thinned)
SNPS_2: number of snps after thinning to one SNP per rad tag

So for site strict NS_BS

L=2660910
SNPS_1= 19192

Unlinked SNPS = 17197
SNPS2= SNPs kep using projection 36 x 162,  16270 SNPs


L = 2660910 x (16270 / 19192) = 2255784
u=0.225578 # for unlinked data (need this when using theta from optimization and FIM)
u=0.0266091 # for all data  (need this when using using theta from GIM, i.e. bootstraps based on all data)