Figure 3
ConcatSeq correctly identifies single-nucleotide variants (SNVs) in an oncology amplicon panel. (a) Schematic depicting the bioinformatics analysis pipeline describing all steps and tools used, starting with PacBio raw reads (subreads) to determining allele frequencies (AFs) of known SNVs in HD701. (b) Scatterplot showing comparison of AFs identified in replicates of concatenation samples plotted against the expected frequencies. Average values from three independent experiments are shown. Error bars indicate standard deviation from the three measurements. (c) Scatterplot showing a comparison of AFs identified in replicates of concatenation samples plotted against frequencies found in the non-concatenation control sample. Average values from three independent experiments are shown. Error bars indicate standard deviation from the three measurements. (d) Barplot comparing amplicon coverage in non-concatenated and three replicates of concatenation samples. Frequencies were calculated by dividing the number of fragments that aligned to each of the 20 amplicons by the total number of aligned fragments. Pearson’s r was calculated for every replicate independently, and the lowest of the three correlation coefficients is indicated in the plot.
