Skip to main content
Fig. 4 | BMC Bioinformatics

Fig. 4

From: Predicting bacterial resistance from whole-genome sequences using k-mers and stability selection

Fig. 4

Examples of genomic variation patterns captured by k-mers in the ofloxacin, isoniazid, and rifampicin signatures. For each signature, mutliple alignments of haplotypes found in the training dataset are shown. Unitigs are surrounded by colored boxes and coordinates refer to nucleic positions on the H37Rv chromosome (NC_000962.3). a Ofloxacin - DNA gyrase subunit A - gene gyrA: a single SNP in gyrA predicts oxfloxacin resistance. At the SNP position, the 4 bases can be observed in the training dataset, the haplotype with the “G” being wild-type sensitive phenotype. b Isoniazid - catalase peroxidase - gene katG: 2 SNPs in katG predict isoniazid resistance, and these 2 SNPs are captured by a single unitig. c Rifampicin - DNA directed RNA polymerase beta subunit - gene rpoB: 8 SNPs in rpoB predict rifampicin resistance, and these 8 SNPs are captured by 3 unitigs

Back to article page