Detected insertions and deletions (indels).

Indel positions were annotated by sequencing selected clones of PCR products. Indel positions are accounted relative to the beginning of the RefSeq genome sequence or to the beginning of the Mycobacterium tuberculosis pncA gene. The number of reads supporting indel and their orientation (F/R) is shown. Error in indel location is the difference between a predicted indel position and the position of indel shown by clone sequences; “n/a” shows that the cloning experiment was not done for a sample.*type: (major strain vs. wild-type, minor strain vs. wild-type). E.g.,(0,+1) means major ≡ wild-type, minor has a 1 bp insertion.