Extended Data Fig. 1: Verification of lineage and serotype calling pipelines.
From: Pneumococcal within-host diversity during colonization, transmission and treatment
(a) The number of true positive and false negative GPSC lineage calls in 44 artificial laboratory mixtures from Knight et al., 2021. (b) Recall of GPSC lineage calls in 1158 samples which also had WGS performed on single colony pick in Chewapreecha et al., 2014. (c) The recall of resistance calls in the same 1158 samples. (d) The number of mismatches between latex sweeps and either mGEMS/seroba or the serocall algorithms at the subgroup serotype level. As mGEMs/seroba was found to better agree with latex sweeps in cases of conflict between the two algorithms, the mGEMs/seroba result was chosen. (e) Intersection between the serotype calls of latex sweeps and the combined mGEMs/seroba and serocall pipeline for all typable isolates and (f) same as in e. but for non-typable.
