Extended Data Fig. 10: Reproducibility of single nucleotide (SNV) variant calls and the distribution of variable site among different coding positions used to assess the reliability of SNVs.

(a) The fraction of minority single nucleotide variant calls replicated in 95 samples which involve only a single pneumococcal lineage and were sequenced in replicate with separate reverse transcription, PCR amplification, and library preparation steps. The median and interquartile range is given by the horizontal lines with the whiskers indicating the largest and smallest values excluding those outside 1.5 times the interquartile range (b). The distribution of the number of variable sites among different coding positions. Variable sites are dominated by those seen at the third codon position similar to that observed in Dyrdak et al., 2019. The stability of the fractions at lower frequencies suggests that the variant calling pipeline has successfully filtered out erroneous variant calls. At higher frequencies, the reduction in the total number of variants leads to increased variability.