Summary statistics of sequencing experiments, read mapping, and error rates.

For all four experiments, the total number of reads obtained and those overlapping amino acids 10 to 93 of the protease are reported. All 454/Roche reads mapping to this region were used in the haplotype reconstruction. For the Illumina Genome Analyzer, only those mapping to the region of highest entropy were considered. The last column reports mean and standard deviation of the sequencing error rate (1 – θ, where the parameter θ is estimated during haplotype reconstruction).