#### TB240_S_hana_miseq results ####

#### Drug resistance associated small variants ####
AMIKACIN		
AMINOGLYCOSIDES		
BEDAQUILINE		
CAPREOMYCIN		
CLOFAZIMINE		
ETHAMBUTOL		
ETHIONAMIDE		
FLUOROQUINOLONES		
ISONIAZID		
KANAMYCIN		
LINEZOLID		
PARA-AMINOSALISYLIC_ACID		
PYRAZINAMIDE		
RIFAMPICIN	R	rpoB (450S>450L, 0.960526315789)
STREPTOMYCIN		
MDR	
XDR	


#### Big Deletions in candidate genes ####


#### Lineage ####
lineage4	0.990867579909	Euro-American	LAM;T;S;X;H	None
lineage4.3	1.0	Euro-American (LAM)	mainly-LAM	None
lineage4.3.3	0.981412639405	Euro-American (LAM)	LAM;T	RD115

#### Other small variants in candidate genes ####
Chromosome	7362	gyrA	Rv0006	21E>21Q	missense	1.0
Chromosome	7585	gyrA	Rv0006	95S>95T	missense	1.0
Chromosome	8040	gyrA	Rv0006	247G>247S	missense	0.988636363636
Chromosome	9304	gyrA	Rv0006	668G>668D	missense	0.985074626866
Chromosome	764995	rpoC	Rv0668	542A	synonymous	1.0
Chromosome	765847	rpoC	Rv0668	826N>826K	missense	1.0
Chromosome	1416222	embR	Rv1267c	376F>376L	missense	0.254901960784
Chromosome	1416234	embR	Rv1267c	372C>372G	missense	0.252336448598
Chromosome	1834513	rpsA	Rv1630	324S	synonymous	1.0
Chromosome	1917972	tlyA	Rv1694	11L	synonymous	1.0
Chromosome	2518919	kasA	Rv2245	269G>269S	missense	0.984615384615
Chromosome	3073868	thyA	Rv2764c	202T>202A	missense	0.987654320988
Chromosome	4242643	embC	Rv3793	927R	synonymous	1.0
Chromosome	4408156	gid	Rv3919c	16L>16R	missense	1.0
