Table 2.

Comparisons of Indels calls by UVP and validated variants previously shown to be present in given isolates.

Sample ID	PubMed ID	Affected gene	H37Rv reference genomic position	Indel	UVP inferred Indel	Lineage information	tap gene(Rv1258c) frameshift mutation
ERR502929	27021327	dfrA, thyA	3073130–3074471	complete deletion	complete deletion	2.2.1	present
ERR751361	27021327	Wt	3073130–3074471	no deletion	no deletion	2.2.1	present
ERR751453	27021327	dfrA, thyA	3073130–3074471	complete deletion	complete deletion	2.2.1	present
ERR751483	27021327	Wt	3073130–3074471	no deletion	no deletion	2.2.1	present
ERR775373	27021327	dfrA, thyA	3073130–3074471	complete deletion	complete deletion	2.2.1	present
ERR779910	27021327	dfrA, thyA	3073130–3074471	complete deletion	complete deletion	2.2.1	present
SRR2333215	27021327	dfrA, thyA	3073130–3074471	complete deletion	complete deletion	2.2.2	absent
SRR1952721	25977398	pncA	2288681–2289241	complete deletion	complete deletion	2.2.1	present
SRR1948177	25977398	pncA	2288681–2289241	complete deletion	complete deletion	2.2.1	present
R721_C13	26496891	atsD	756970	C > CG	C > CG	2.2.1.1	present
R721_C13	26496891	regX3	581317	G > GCG	G > GCG	2.2.1.1	present
R966_C5	26496891	Rv3861	4338065	AC > A	AC > A	2.2.1	present
R160_C13	26496891	adhD	3452173	CG > CGCCAT	CG > CGCCATG	4.1.1.3	absent
R376_C11	26496891	Rv3256c	3636924	ACC > AC	ACC > AC	4.1.2.1	absent
R912_C11	26496891	yrbE4A	3920814	GA > G	GAA > GA	1.2.2	absent
R965_C1	26496891	adhA	2110232	A > AG	AG > AGG	2.2.1	present
R458_C3	26496891	espR	4323810	GC > G	GC > G	4.1.2	absent
R641_C1	26496891	Rv2375	2655550	A > AT	AT > ATT	2.2.1.1	present