#### TB1007__hana_miseq results ####

#### Drug resistance associated small variants ####
AMIKACIN		
AMINOGLYCOSIDES		
BEDAQUILINE		
CAPREOMYCIN		
CLOFAZIMINE		
ETHAMBUTOL		
ETHIONAMIDE		
FLUOROQUINOLONES		
ISONIAZID	R	kasA (312G>312S, 1.0)
KANAMYCIN		
LINEZOLID		
PARA-AMINOSALISYLIC_ACID		
PYRAZINAMIDE		
RIFAMPICIN	R	rpoB (445H>445Y, 1.0)
STREPTOMYCIN		
MDR	R
XDR	


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


#### Lineage ####
lineage1	0.991922455574	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	1.0
Chromosome	9260	gyrA	Rv0006	653L	synonymous	1.0
Chromosome	9304	gyrA	Rv0006	668G>668D	missense	1.0
Chromosome	763031	rpoB	Rv0667	1075A	synonymous	1.0
Chromosome	763531	rpoC	Rv0668	54P	synonymous	0.981818181818
Chromosome	763884	rpoC	Rv0668	172A>172V	missense	1.0
Chromosome	763886	rpoC	Rv0668	173R	synonymous	1.0
Chromosome	1416222	embR	Rv1267c	376F>376L	missense	0.38
Chromosome	1416234	embR	Rv1267c	372C>372G	missense	0.380530973451
Chromosome	1417019	embR	Rv1267c	110C>110Y	missense	1.0
Chromosome	1417055	embR	Rv1267c	98P>98L	missense	1.0
Chromosome	1917972	tlyA	Rv1694	11L	synonymous	1.0
Chromosome	2154724	katG	Rv1908c	463R>463L	missense	0.986301369863
Chromosome	2518132	kasA	Rv2245	6T	synonymous	1.0
Chromosome	4240671	embC	Rv3793	270T>270I	missense	0.973684210526
Chromosome	4241042	embC	Rv3793	394N>394D	missense	1.0
Chromosome	4242643	embC	Rv3793	927R	synonymous	1.0
Chromosome	4243580	embA	Rv3794	116V	synonymous	1.0
Chromosome	4244420	embA	Rv3794	396V	synonymous	0.981481481481
Chromosome	4245969	embA	Rv3794	913P>913S	missense	1.0
Chromosome	4247578	embB	Rv3795	355L	synonymous	0.959183673469
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
