I'm interested in searching for mutations associated with an altered phenotype in a bacteria via resequencing (probably Illumina). This particular bacterial genome is ~7Mb and there is a reference available. I figure I should aim for single nucleotide resolution to be able to detect nearly 100% of SNPs. My question is, how can I determine the amount of coverage necessary to be able to detect 100% of SNPs? I found a reference from Holt et al. 2009 in Bioinformatics where they state they can detect 80% of SNPs at 45X coverage (http://bioinformatics.oxfordjournals.org/content/25/16/2074.full).
A paper that spells it out would be best, but if that isn't available do you think I could use Lander-Waterman and the error rate associated with Illumina to estimate the necessary coverage?
I welcome opinions and other considerations.