Figure 3

Overall accuracy of SRST2 allele calling and gene detection. (a) MLST analysis of public data from five species (N = 543 genomes, 3,801 loci, details Additional file 1: Table S1). Tests were grouped by read depth and accuracy rates (left y-axis, correct allele calls as a proportion of tests), calculated at each depth (x-axis, red slashes indicate scale change). Grey bars, number of tests at each depth (right y-axis); Lines, accuracy of allele calling. (b) MLST analysis of Listeria monocytogenes data (N = 231 genomes, 1,671 loci) conducted in a public health laboratory; colours and axes as in (a). (c) Accuracy of vanB resistance gene detection for E. faecium read sets subsampled to low depth; y-axis shows proportion of correct (presence vs. absence) calls as a proportion of 100 tests at each depth; colours and axes as in (a). A call of `present implies detection of ?90% of the length of the gene at ?90% nucleotide identity.