Performance of Illumina and 454 sequencing for the detection of nucleotide minority variants within the control library.

The control library was created by mixing 6 HIV-1 integrase clones at concentrations of 60%, 33.4%, 5%, 1%, 0.5%, and 0.1%. Expected variant percentages include positions where a MV is present on more than one clone. Median variant % reflects only the minority variants detected by each platform and does not include the undetected variants. N represents the number of nucleotide positions in the control library where the variant frequency is expected. Illumina detected 1 false positive minority variant present at 0.2% of the viral population (0.3% false positive rate) and 454 detected 5 false positive minority variants ranging from 0.09% to 0.6% (1.4% false positive rate). FN, false negative.