Effect of RNase H activity on (a) recombination and (b) mutation. RNA was extracted from an equal mix of WT and MK virus. SSIII was used to reverse transcribe 160 ng and 1600 ng as input template and AMV was used to reverse transcribe 2000 ng. All conditions complied with the manufacturers recommendations. Resulting cDNA was diluted and amplified using an optimised 2-step PCR and 27 cycles to minimise PCR-induced recombination . Recombination and mutation rates are expressed as rate per 1000 nucleotides and the confidence intervals, as estimated via bootstrapping, are shown. Significant differences (at 95% CI) are indicated.