Fig. 1

GenoMycAnalyzer pipelines. A The GenoMycAnalyzer platform includes five modules: pre-processing, identification, variant calling, genotypic DST, and visualization and report. (B-D) Example of WGS analyzed by GenoMycAnalyzer. B Partial result of the 'Analysis Summary' is displayed. The strain is identified as M. tuberculosis, with lineage (2.2.1) and spoligotype (000000000003771). Genotypic DST for 15 types of antimicrobial drugs is color-coded (resistant: red, susceptible: green). A Circos plot represents the sequencing coverage depth and detected variants for 17 genes harboring group 1 or 2 mutations. C Among the detected variants, overlapped variants with the WHO mutational catalogue are shown in ‘RAV (resistance-associated variants)’. D The reads mapping status of gyrA p.D94G, which confers resistance to fluoroquinolone, is shown in IGV implemented in GenoMycAnalyzer