#### TB674_S_hana_miseq results ####

#### Drug resistance associated small variants ####
AMIKACIN		
AMINOGLYCOSIDES		
BEDAQUILINE		
CAPREOMYCIN		
CLOFAZIMINE		
ETHAMBUTOL		
ETHIONAMIDE		
FLUOROQUINOLONES		
ISONIAZID	R	kasA (312G>312S, 0.987341772152)
KANAMYCIN		
LINEZOLID		
PARA-AMINOSALISYLIC_ACID		
PYRAZINAMIDE		
RIFAMPICIN	R	rpoB (430L>430P, 1.0)
STREPTOMYCIN		
MDR	R
XDR	


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


#### Lineage ####
lineage1	0.988363072149	Indo-Oceanic	EAI	RD239
lineage1.2.1	0.992592592593	Indo-Oceanic	EAI2	RD239

#### Other small variants in candidate genes ####
Chromosome	6112	gyrB	Rv0005	291M>291I	missense	0.991228070175
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	0.989361702128
Chromosome	9143	gyrA	Rv0006	614I	synonymous	1.0
Chromosome	9260	gyrA	Rv0006	653L	synonymous	1.0
Chromosome	9304	gyrA	Rv0006	668G>668D	missense	0.980392156863
Chromosome	9695	gyrA	Rv0006	798T	synonymous	1.0
Chromosome	760439	rpoB	Rv0667	211D	synonymous	1.0
Chromosome	763031	rpoB	Rv0667	1075A	synonymous	1.0
Chromosome	763531	rpoC	Rv0668	54P	synonymous	0.991071428571
Chromosome	763884	rpoC	Rv0668	172A>172V	missense	1.0
Chromosome	763886	rpoC	Rv0668	173R	synonymous	0.988888888889
Chromosome	764809	rpoC	Rv0668	480R	synonymous	1.0
Chromosome	1417019	embR	Rv1267c	110C>110Y	missense	0.979166666667
Chromosome	1917972	tlyA	Rv1694	11L	synonymous	1.0
Chromosome	2154724	katG	Rv1908c	463R>463L	missense	0.9875
Chromosome	2518132	kasA	Rv2245	6T	synonymous	1.0
Chromosome	4240671	embC	Rv3793	270T>270I	missense	1.0
Chromosome	4241042	embC	Rv3793	394N>394D	missense	1.0
Chromosome	4242643	embC	Rv3793	927R	synonymous	1.0
Chromosome	4243580	embA	Rv3794	116V	synonymous	0.982456140351
Chromosome	4244420	embA	Rv3794	396V	synonymous	1.0
Chromosome	4245969	embA	Rv3794	913P>913S	missense	1.0
Chromosome	4247578	embB	Rv3795	355L	synonymous	0.970149253731
Chromosome	4247646	embB	Rv3795	378E>378A	missense	1.0
Chromosome	4407588	gid	Rv3919c	205A	synonymous	1.0
Chromosome	4407873	gid	Rv3919c	110V	synonymous	1.0
