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

Table 2 Genes with Variants in H37Ra Unique to our Assembly

Locus Tag	Gene name	Variant	Notes
Rv0279c^{a, b}	PE_PGRS4	Two substitutions	Both mutations are not specific to H37Ra
Rv0383c^{a, b}	Rv0383c	A459399C - 84bp upstream of Rv0383c	Potential sequencing error in H37Rv [8]
Rv1450c^{a, b}	PE_PGRS27	208bp inframe insertion
Rv1764	Rv1764	insertion of IS6110
Rv3303c^{a, b}	lpdA	174bp insertion 12bp upstream	Tandem repeat CNV
Rv3343c^a	PPE54	1728bp insertion	Tandem duplication with respect to H37Rv
Rv3508^a	PE_PGRS54	multiple variants
Rv3514^b	PE_PGRS57	multiple variants	Only two are H37Ra-specific

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.
^agene previously implicated as affected by H37Ra-specific mutations [5].
^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)

ISSN: 1471-2164