#### TB618_S_hana_miseq results ####

#### Drug resistance associated small variants ####
AMIKACIN	R	rrs (514A>C, 0.992857142857)
AMINOGLYCOSIDES	R	rrs (514A>C, 0.992857142857)
BEDAQUILINE		
CAPREOMYCIN		
CLOFAZIMINE		
ETHAMBUTOL		
ETHIONAMIDE		
FLUOROQUINOLONES		
ISONIAZID		
KANAMYCIN		
LINEZOLID		
PARA-AMINOSALISYLIC_ACID		
PYRAZINAMIDE		
RIFAMPICIN		
STREPTOMYCIN	R	rrs (514A>C, 0.992857142857)
MDR	
XDR	


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


#### Lineage ####
lineage4	0.991097922849	Euro-American	LAM;T;S;X;H	None
lineage4.8	0.992424242424	Euro-American (mainly T)	T1;T2;T3;T5	RD219

#### Other small variants in candidate genes ####
Chromosome	7362	gyrA	Rv0006	21E>21Q	missense	1.0
Chromosome	1416222	embR	Rv1267c	376F>376L	missense	0.278048780488
Chromosome	1416234	embR	Rv1267c	372C>372G	missense	0.288461538462
Chromosome	1474001	rrl	rrl	344C>T	non_coding	1.0
Chromosome	1917972	tlyA	Rv1694	11L	synonymous	0.992857142857
Chromosome	4043901	panD	Rv3601c	381GT>G	frameshift	0.0283687943262
Chromosome	4242643	embC	Rv3793	927R	synonymous	1.0
