Analysis of Positive Selection in 10,000 Mtb Genomes

Note: ignore gaps '---', which could indicate gaps of variable size (not necessarily 3), or even uncertain nucleotides (e.g. due to sequencing ambiguity).
These are not really gaps; they are just a mask to indicate to genomegaMap not to include these codons in the analysis.

About the collection of Mtb clinical isolates:

• 10,626 total Mtb genomes (fastq files downloaded from SRA/ENA and assembled using Pilon)
• the set was selected to be diverse with respect to lineage and geographic region
• lineages: (determined using TB-profiler)
  • L1: 632 (5.8%)
  • L2: 2751 (25.9%)
  • L3: 2912 (27.4%)
  • L4: 4310 (40.6%)
• countries:

  Moldova	India	UK	Canada	Spain	Peru
  2065	1671	827	486	481	480
  Russia	Italy	Netherlands	China	SouthAfrica	Ukraine
  474	454	452	451	431	414
  Germany	VietNam	Pakistan	Bangladesh	Tanzania	Other
  409	361	354	310	304	250

• drug-resistance: Sensitive=6037, any genotypic Resistance: 4619 (43%) (includes 1764 MDR-TB)