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Table 2 Genes with Variants in H37Ra Unique to our Assembly

From: SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis

Locus Tag Gene name Variant Notes
Rv0279ca, b PE_PGRS4 Two substitutions Both mutations are not specific to H37Ra
Rv0383ca, b Rv0383c A459399C - 84bp upstream of Rv0383c Potential sequencing error in H37Rv [8]
Rv1450ca, b PE_PGRS27 208bp inframe insertion  
Rv1764 Rv1764 insertion of IS6110  
Rv3303ca, b lpdA 174bp insertion 12bp upstream Tandem repeat CNV
Rv3343ca PPE54 1728bp insertion Tandem duplication with respect to H37Rv
Rv3508a PE_PGRS54 multiple variants  
Rv3514b PE_PGRS57 multiple variants Only two are H37Ra-specific
  1. The mutations in this table are with respect to the H37Rv reference (NC_000962.3), so variants with respect to the current H37Ra reference sequence (NC_009525.1) that cause agreement with the H37Rv sequence do not appear here.
  2. agene previously implicated as affected by H37Ra-specific mutations [5].
  3. bone or more mutations affecting this gene are also present in at least one of the sequences CDC1551 (NC_002755.2), H37RvBroad (NC_018143.2), H37RvSiena (NZ_CP007027.1), and H37RvTMC102 (NZ_CP009480.1)