Resolution of viral haplotype estimation.

Displayed are the resolution of error correction (binomial test only) and of haplotype reconstruction as a function of the number of reads. The resolution of the error correction is defined as the smallest frequency of a mutation that will be visible over the background error rates; it is calculated with error rate �� = 0.0025 and significance level �� = 0.001. The resolution of the haplotype reconstruction (derived from the Lander�CWaterman model) is the smallest haplotype frequency expected to be entirely covered by reads. For small read sizes, haplotype reconstruction is the limiting factor (underlined in the table) but for over approximately 35,000 reads, error correction is the limiting factor.