Fig. 2

a Posterior mean deviance for different strain numbers, G, for the synthetic strain mock Escherichia coli SCSG positions. We ran five replicates of the Gibbs sampler at each value of G on 1,000 random positions from the 6,044 variants identified. b SNV accuracy as a function of sample number. The number of incorrectly inferred SNVs averaged across all five strains and 20 replicates of a random subset of the 64 samples. c Comparison of true E. coli strain frequency vs. DESMAN predictions. We compare the known E. coli strain frequencies as relative coverage against the frequencies in each sample of the DESMAN-predicted haplotype it mapped onto (R ²=0.9998, p-value <2.2×10⁻¹⁶). d Comparison of gene presence inferred for the haplotypes and the known assignment of genes to strain genomes. Gene presence/absence was inferred for the haplotypes using Eq. 8 and compared to known references. Overall accuracy was 95.7%. These results were for the run with G=5, which had the lowest posterior mean deviance. E. coli Escherichia coli, SNP single-nucleotide polymorphism, SNV single-nucleotide variant