#### TBS153__hana_miseq results ####

#### Drug resistance associated small variants ####
AMIKACIN		
AMINOGLYCOSIDES		
BEDAQUILINE		
CAPREOMYCIN		
CLOFAZIMINE		
ETHAMBUTOL		
ETHIONAMIDE	R	Rv1482c-fabG1 (-15C>T, 1.0)
FLUOROQUINOLONES		
ISONIAZID	R	Rv1482c-fabG1 (-15C>T, 1.0), kasA (312G>312S, 1.0)
KANAMYCIN		
LINEZOLID		
PARA-AMINOSALISYLIC_ACID		
PYRAZINAMIDE		
RIFAMPICIN	R	rpoB (432Q>432K, 0.928571428571)
STREPTOMYCIN		
MDR	R
XDR	


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


#### Lineage ####
lineage1	0.987878787879	Indo-Oceanic	EAI	RD239
lineage1.2.1	1.0	Indo-Oceanic	EAI2	RD239

#### Other small variants in candidate genes ####
Chromosome	6112	gyrB	Rv0005	291M>291I	missense	1.0
Chromosome	7362	gyrA	Rv0006	21E>21Q	missense	1.0
Chromosome	7585	gyrA	Rv0006	95S>95T	missense	1.0
Chromosome	8452	gyrA	Rv0006	384A>384V	missense	1.0
Chromosome	9143	gyrA	Rv0006	614I	synonymous	0.979591836735
Chromosome	9260	gyrA	Rv0006	653L	synonymous	1.0
Chromosome	9304	gyrA	Rv0006	668G>668D	missense	1.0
Chromosome	760439	rpoB	Rv0667	211D	synonymous	0.975609756098
Chromosome	760476	rpoB	Rv0667	224R>224C	missense	1.0
Chromosome	763031	rpoB	Rv0667	1075A	synonymous	1.0
Chromosome	763531	rpoC	Rv0668	54P	synonymous	1.0
Chromosome	763884	rpoC	Rv0668	172A>172V	missense	0.978723404255
Chromosome	763886	rpoC	Rv0668	173R	synonymous	0.978260869565
Chromosome	764809	rpoC	Rv0668	480R	synonymous	1.0
Chromosome	765049	rpoC	Rv0668	560L>560F	missense	1.0
Chromosome	1417019	embR	Rv1267c	110C>110Y	missense	0.982142857143
Chromosome	1917972	tlyA	Rv1694	11L	synonymous	1.0
Chromosome	2154724	katG	Rv1908c	463R>463L	missense	0.975
Chromosome	2518132	kasA	Rv2245	6T	synonymous	1.0
Chromosome	2715455	eis-Rv2417c	Rv2416c-Rv2417c	-123C>A	intergenic	1.0
Chromosome	4240671	embC	Rv3793	270T>270I	missense	0.977777777778
Chromosome	4241042	embC	Rv3793	394N>394D	missense	1.0
Chromosome	4242643	embC	Rv3793	927R	synonymous	0.971428571429
Chromosome	4243580	embA	Rv3794	116V	synonymous	0.951219512195
Chromosome	4244420	embA	Rv3794	396V	synonymous	1.0
Chromosome	4245969	embA	Rv3794	913P>913S	missense	1.0
Chromosome	4247578	embB	Rv3795	355L	synonymous	1.0
Chromosome	4247646	embB	Rv3795	378E>378A	missense	1.0
Chromosome	4407588	gid	Rv3919c	205A	synonymous	1.0
Chromosome	4407873	gid	Rv3919c	110V	synonymous	0.972222222222
