I have identified frequency of SNPs, heterozygotes and homozygotes per 100kb for my eukaryotic species (which is maintained for 100 generations by inbreeding) by read-mapping illumina paired-reads to reference genome. From Drake et al. Genetics, 1998, it is inferred that fixed mutations for eukaryotes (mutation rate are measured in substitutions) is 0.003 mutations per genome per generation. Can I use this for mutation rate calculation for of my eukaryotic species?. How can I correlate my mutation rate to zygosity?
I also came across this tool: http://guanine.evolbio.mpg.de/cgi-bin/mlRho/mlRho.cgi.pl for estimating population mutation.