#### TB487_S_hana_miseq results ####

#### Drug resistance associated small variants ####
AMIKACIN		
AMINOGLYCOSIDES		
BEDAQUILINE		
CAPREOMYCIN		
CLOFAZIMINE		
ETHAMBUTOL		
ETHIONAMIDE		
FLUOROQUINOLONES		
ISONIAZID	R	katG (315S>315T, 0.984126984127)
KANAMYCIN		
LINEZOLID		
PARA-AMINOSALISYLIC_ACID		
PYRAZINAMIDE		
RIFAMPICIN	R	rpoB (450S>450L, 0.992907801418)
STREPTOMYCIN		
MDR	R
XDR	


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


#### Lineage ####
lineage2	0.985372340426	East-Asian	Beijing	RD105
lineage2.2	0.991978609626	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
lineage2.2.1	0.970588235294	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
lineage2.2.1.1	0.986301369863	East-Asian (Beijing)	Beijing-RD150	RD105;RD207;RD181;RD150

#### 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	9304	gyrA	Rv0006	668G>668D	missense	1.0
Chromosome	763031	rpoB	Rv0667	1075A	synonymous	1.0
Chromosome	1416222	embR	Rv1267c	376F>376L	missense	0.229885057471
Chromosome	1416234	embR	Rv1267c	372C>372G	missense	0.242774566474
Chromosome	1416672	embR	Rv1267c	226G>226S	missense	0.98773006135
Chromosome	1834177	rpsA	Rv1630	212R	synonymous	0.986928104575
Chromosome	1917972	tlyA	Rv1694	11L	synonymous	1.0
Chromosome	2154724	katG	Rv1908c	463R>463L	missense	1.0
Chromosome	4242643	embC	Rv3793	927R	synonymous	1.0
Chromosome	4243460	embA	Rv3794	76C	synonymous	1.0
Chromosome	4247361	embB	Rv3795	848T>TGA	frameshift	0.0333333333333
Chromosome	4407588	gid	Rv3919c	205A	synonymous	1.0
Chromosome	4407927	gid	Rv3919c	92E>92D	missense	0.984
