Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data
Figure 3
Error rates were not uniformly distributed.
Error rates varied by (A) read position, (B) base transition, and (C) base quality score. We counted as errors any mismatches to the consensus assembly for each of the two runs in the control read set under the assumption that the NL-43 infectious clone had no diversity. We defined the read position relative to the beginning or end of the read, whichever was closer. We defined a base transition as a dinucleotide representing the transition from the preceding base to the current base, and we scored a transition as an error if the current base was a mismatch. Base quality scores came from the sequencing process.