Effect of coverage and frequency on variant concordance with custom panels on FFPE samples.

<p><b>A:</b> Variant frequency (VF) was highly preserved in replicate measurements from the same samples. <b>B and C:</b> Concordant variants had statistically significant higher coverage and frequency as compared to discordant ones (red lines: mean values). However, both high and low coverage and frequency were observed for discordant variants and followed the same bimodal pattern in these categories. <b>D.</b> Out of the 181 different positions accounting for the 1267 variants under study, calls were constantly concordant in 83 (45.8%), partially concordant in 26.0%, and constantly discordant in 28.2%. <b>E.</b> Distribution of VF and amplicon GC% according to high and low coverage for the categories indicated on the bottom of the graphs. Red and lilac dots: high coverage in discordant and concordant variants, respectively; turquoise and green dots: low coverage, respectively. Among discordant only variants, those of high coverage were almost exclusively of low VF (boxed).