#### TB0207__hana_miseq results ####

#### Drug resistance associated small variants ####
AMIKACIN		
AMINOGLYCOSIDES		
BEDAQUILINE		
CAPREOMYCIN		
CLOFAZIMINE		
ETHAMBUTOL		
ETHIONAMIDE	R	inhA (21I>21V, 1.0)
FLUOROQUINOLONES		
ISONIAZID	R	inhA (21I>21V, 1.0)
KANAMYCIN		
LINEZOLID		
PARA-AMINOSALISYLIC_ACID		
PYRAZINAMIDE		
RIFAMPICIN	R	rpoB (435D>435Y, 1.0)
STREPTOMYCIN		
MDR	R
XDR	


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


#### Lineage ####
lineage1	0.994828700711	Indo-Oceanic	EAI	RD239
lineage1.2.1	0.989361702128	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	0.989247311828
Chromosome	7585	gyrA	Rv0006	95S>95T	missense	0.975903614458
Chromosome	8452	gyrA	Rv0006	384A>384V	missense	1.0
Chromosome	9143	gyrA	Rv0006	614I	synonymous	1.0
Chromosome	9260	gyrA	Rv0006	653L	synonymous	0.991869918699
Chromosome	9304	gyrA	Rv0006	668G>668D	missense	0.984496124031
Chromosome	763031	rpoB	Rv0667	1075A	synonymous	1.0
Chromosome	763884	rpoC	Rv0668	172A>172V	missense	1.0
Chromosome	763886	rpoC	Rv0668	173R	synonymous	0.988505747126
Chromosome	1417019	embR	Rv1267c	110C>110Y	missense	1.0
Chromosome	1472151	rrs	rrs	306C>T	non_coding	0.0763888888889
Chromosome	1472172	rrs	rrs	327T>C	non_coding	0.0933333333333
Chromosome	1472235	rrs	rrs	390G>C	non_coding	0.059880239521
Chromosome	1473198	rrs	rrs	1353GC>G	non_coding	0.0229885057471
Chromosome	1475526	rrl	rrl	1869C>A	non_coding	0.0632183908046
Chromosome	1917972	tlyA	Rv1694	11L	synonymous	1.0
Chromosome	1918525	tlyA	Rv1694	196G>196R	missense	0.985611510791
Chromosome	2154724	katG	Rv1908c	463R>463L	missense	0.988505747126
Chromosome	2518132	kasA	Rv2245	6T	synonymous	0.987341772152
Chromosome	4240005	embC	Rv3793	48P>48L	missense	0.981981981982
Chromosome	4240671	embC	Rv3793	270T>270I	missense	1.0
Chromosome	4241042	embC	Rv3793	394N>394D	missense	0.989473684211
Chromosome	4242643	embC	Rv3793	927R	synonymous	1.0
Chromosome	4244420	embA	Rv3794	396V	synonymous	0.977777777778
Chromosome	4244631	embA	Rv3794	467T>467A	missense	1.0
Chromosome	4245969	embA	Rv3794	913P>913S	missense	0.987012987013
Chromosome	4247646	embB	Rv3795	378E>378A	missense	1.0
Chromosome	4408087	gid	Rv3919c	116CG>C	frameshift	0.961165048544
