Fig. 4: SNP calling accuracy for a set of clonal mock samples.
a Genotyping results from Clair3 for seven clonal mock samples and across 41 antimalarial resistance-associated mutations. Samples were sequenced with a R10.4.1 Flow Cell on a MinION Mk1b device. b Mean F1-Score (harmonic mean of precision and recall) of SNP calling compared to PacBio data from for Dd2 and HB3 mock samples randomly downsampled to different read depths. Each square gives the mean F1-Score across twenty in silico replicates (ten replicates for each of Dd2 and HB3) at the indicated read depth (columns) and across the indicated region (rows). In total, there are 200 in silico replicates across all depths. Top panel is limited to coding sequence ("CDS") and bottom panel the entire span of the amplicons ("Amplicon"). c Visualisation of true positive and false positive rate of sites spanning the crt amplicon in chromosome 7. From top to bottom, panels show an exon diagram of crt; the true positive rate (green) and false positive rate (red) of each site across twenty replicates at a given read depth (indicated by circle size); A+T% in 20bp sliding windows (blue shade) and homopolymer length (red line); and heatmap of nucleotide composition. d Same as (c) but for dhps amplicon. e Heatmaps showing measures of sequence complexity in 20 bp windows surrounding sites where errors were observed. Rows indicate A+T% of the 20 bp window, columns indicate length of the longest hompolymer within the 20 bp window and colour gives number of errors. Top panel shows errors which were corrected with additional read depth (i.e., exist at depth < 100); bottom panel shows errors that persist at a depth of 100 reads. Selected sequences are shown; asterisk (*) marks sequences that are an example from a bin with greater than one sequence.
