Figure 5.

Advantages of amplicon-based variant calling. (A) Example of deamination artifact (G>A/C>T) in mapped sequencing reads which was captured in early rounds of PCR by only one of two overlapping amplicons. True variants (including low abundance alleles near assay VAF thresholds) do not demonstrate this finding. (B) Example of allele drop out due to a clinically relevant indel affecting primer binding in one of two overlapping amplicons. Amplicon-based variant calling more accurately estimates variant allele fraction by computing the AO/RO ratio only for reads from amplicon 9_1 (most 5’ amplicon displayed).