KvarQ identified 62 drug resistance associated mutations in 33 of 388 patient isolates in a “blind” set of genome sequences from Walker et al.. Each circle represents one isolate (Patient number given as P-number, isolate given as ERR-number). Only isolates with drug resistance associated mutation identified by KvarQ are shown. The 62 individual drug resistance mutations are shown as colors of pies. Phylogenetic lineages were obtained with KvarQ and are shown as colored and dashed boxes. Group definitions were obtained from the original publication : cross-sectional isolates were paired pulmonary and extrapulmonary isolates from the same patient, longitudinal isolates were paired isolates from the same patient separated by at least 6 months, and genomic cluster 9 was a large MIRU-VNTR defined cluster of transmission in the community. Paired isolates (longitudinal and cross-sectional) as well as isolates of cluster 9 were found to harbour the same mutations, except for P000179, where three otherwise not detected mutations were found by KvarQ. For patient P000155, an additionally acquired mutation was found in two of three isolates. Two of the 390 whole genome sequences in the original publication were not found for download.