I read in https://jodyphelan.github.io/TBProfiler/en/lineages/ that the lineages are assigned according to the papers from Coll et al., and further refined with the results from Napier et al. and Zwyer et al.
However, I noticed that in Napier et al.
1.2.2 528781 G->A 58E groEL2 Rv0440 VDA
So I get 1.2.2 when I analyze using Napier's lineage-specific SNPs but I get 1.2.1 when using TB Profiler.
Also, may I know if there were any other data that went into the TB Profiler database for the lineage-specific SNPs? Because I noticed that Coll's and Napier's papers didn't have a number of the sub-lineages like 1.2.1.2 etc
Hi Jody,
I read in https://jodyphelan.github.io/TBProfiler/en/lineages/ that the lineages are assigned according to the papers from Coll et al., and further refined with the results from Napier et al. and Zwyer et al.
However, I noticed that in Napier et al. 1.2.2 528781 G->A 58E groEL2 Rv0440 VDA
But in TB profiler, https://github.com/jodyphelan/tbdb/blob/master/barcode.bed Chromosome 528780 528781 lineage1.2.1.2 A Indo-Oceanic NA RD239
So I get 1.2.2 when I analyze using Napier's lineage-specific SNPs but I get 1.2.1 when using TB Profiler.
Also, may I know if there were any other data that went into the TB Profiler database for the lineage-specific SNPs? Because I noticed that Coll's and Napier's papers didn't have a number of the sub-lineages like 1.2.1.2 etc
Thank you for your help!