Fig. 2.

Allele co-occurrence tables of correlated AMR genes. Co-occurrence of epistatic genes identified in a ethambutol and b isoniazid. For the rows on the bottom and on the far right, #R refers to the total number of strains that have the allele and are resistant to the specific drug. Total refers to the total number of strains that have that allele that were tested on that specific drug. Each cell is colored by the log odds ratio (LOR) with respect to the AMR phenotype. The numbers in the bottom right of each allele co-occurrence box describes the number of unique sublineages comprised by the strains with both alleles (Methods). The alleles enclosed by a purple box represent those chosen as features by the support vector machine (SVM). Note that in some cases the rows and columns do not sum up to the total strains due to rare cases when strains lack those alleles (Methods)