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Relationship between hash-cgMLST gene differences and SNPS in C. difficile genomes from consecutive infections in six English hospitals. (A) Distribution of hash-cgMLST gene differences between pairs of genomes within ≤2 SNPs. (B) Distribution of SNPs within pairs of genomes within ≤2 gene differences. Panels A and B were generated using SPAdes assemblies with the “-careful -only-assembler” flags. (C and D) The same analysis using the SKESA assembler.
