This tool processes raw sequence data to infer strain type and identify known drug resistance markers.

A stand alone version of this tool is now available and can now be run on linux or mac. Installation instructions can be found on GitHub and on the bioconda page.

This tool is for Research Use Only. Data and information provided through use of this tool are not intended for medical purpose or objective and should not be used for clinical diagnosis, patient management, or human clinical trials.

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Single nucleotide polymorphisms (SNPs) in coding regions are annotated using the reference amino acid, codon number and alternative amino acid (e.g. Ser315Thr in katG). SNPs in non-coding regions (i.e. RNA genes and intergenic regions) are annotated using the reference nucleotide, gene coordinate and alternative nucleotide (e.g. A1401G in rrs or C-37A in eis promoter). Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG).

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Drug1	Resistance	Supporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin	R	rpsL p.Lys43Arg (1.00), rrs r.799c>t (0.11)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2	Family	Main Spoligotype	RDS
lineage2	East-Asian	Beijing	RD105
lineage2.2	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
lineage2.2.1	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181

Gene	Chromosome Position	Mutation	Estimated fraction
gyrA	7362	p.Glu21Gln	1.000
gyrA	7585	p.Ser95Thr	1.000
gyrA	9304	p.Gly668Asp	1.000
rpoB	762863	c.3057T>C	0.167
rpoB	762872	p.Met1022Ile	0.162
rpoB	762878	p.Ile1024Met	0.167
rpoB	762879	p.Met1025Leu	0.167
rpoB	762896	c.3090G>C	0.194
rpoB	762925	p.Thr1040Ile	0.179
rpoB	762938	c.3132G>C	0.158
rpoB	762939	p.Met1045Leu	0.162
rpoB	762942	p.Ile1046Val	0.162
rpoB	762953	c.3147G>A	0.167
rpoB	762965	c.3159T>C	0.162
rpoB	763031	c.3225T>C	1.000
rpsL	781395	c.-165T>C	1.000
rrs	1472102	r.257g>a	0.118
rrs	1472106	r.261g>a	0.143
rrs	1472112	r.267c>t	0.143
rrs	1472113	r.268t>c	0.143
rrs	1472150	r.305t>a	0.205
rrs	1472160	r.315c>t	0.139
rrs	1472172	r.327t>c	0.588
rrs	1472181	r.336g>a	0.136
rrs	1472210	r.365a>t	0.492
rrs	1472214	r.369c>g	0.429
rrs	1472215	r.370a>g	0.159
rrs	1472225	r.380c>a	0.515
rrs	1472234	r.389t>c	0.154
rrs	1472235	r.390g>c	0.333
rrs	1472240	r.395g>c	0.492
rrs	1472242	r.397c>t	0.483
rrs	1472251	r.406g>c	0.375
rrs	1472252	r.407g>a	0.367
rrs	1472259	r.414c>a	0.396
rrs	1472344	r.499c>t	0.310
rrs	1472389	r.544g>a	0.210
rrs	1472390	r.545t>a	0.210
rrs	1472391	r.546c>t	0.210
rrs	1472494	r.649a>g	0.171
rrs	1472496	r.651t>a	0.167
rrs	1472498	r.653c>t	0.167
rrs	1472558	r.713g>a	0.128
rrs	1472569	r.724g>a	0.140
rrs	1472581	r.736a>t	0.170
rrs	1472597	r.752g>a	0.167
rrs	1472598	r.753a>c	0.130
rrs	1472599	r.754g>t	0.132
rrs	1472607	r.762g>a	0.164
rrs	1472616	r.771g>a	0.213
rrs	1472655	r.810g>t	0.105
rrs	1472713	r.868t>c	0.288
rrs	1472716	r.871c>t	0.340
rrs	1472734	r.889c>t	0.194
rrs	1472741	r.896g>a	0.203
rrs	1472742	r.897c>t	0.493
rrs	1472744	r.899a>g	0.297
rrs	1472767	r.922g>a	0.174
rrs	1472781	r.936c>t	0.506
rrs	1472785	r.940g>t	0.177
rrs	1472786	r.941c>g	0.177
rrs	1472793	r.948a>t	0.500
rrs	1472803	r.958t>a	0.286
rrs	1472812	r.967a>c	0.186
rrs	1472814	r.969g>a	0.145
rrs	1472887	r.1042g>c	0.411
rrs	1472895	r.1050c>t	0.110
rrs	1473121	r.1276t>c	0.111
rrs	1473145	r.1300c>t	0.114
rrs	1473163	r.1318c>t	0.209
rrs	1473164	r.1319c>g	0.195
rrs	1473166	r.1321g>a	0.143
rrs	1473177	r.1332g>a	0.367
rrs	1473192	r.1347a>g	0.351
rrs	1473199	r.1354ca>c	0.370
rrs	1473202	r.1357c>t	0.148
rrs	1473204	r.1359c>t	0.145
rrs	1473205	r.1360t>c	0.364
rrs	1473226	r.1381c>t	0.145
rrs	1473252	r.1407t>c	0.158
rrs	1473259	r.1414c>t	0.132
rrs	1473270	r.1425g>a	0.122
rrs	1473352	r.1507c>t	0.105
rrl	1474151	r.494c>t	0.176
rrl	1474155	r.498g>a	0.143
rrl	1474164	r.507c>t	0.128
rrl	1474171	r.514c>t	0.125
rrl	1474181	r.524c>t	0.133
rrl	1474184	r.527c>t	0.133
rrl	1474185	r.528g>a	0.133
rrl	1474197	r.540c>t	0.146
rrl	1474199	r.542g>a	0.146
rrl	1474202	r.545t>c	0.146
rrl	1474218	r.561t>a	0.123
rrl	1474228	r.571t>c	0.135
rrl	1474249	r.592g>t	0.320
rrl	1474252	r.595t>a	0.140
rrl	1474269	r.612c>t	0.133
rrl	1474584	r.927c>t	0.111
rrl	1474864	r.1207c>t	0.139
rrl	1474883	r.1226t>c	0.122
rrl	1474904	r.1247g>c	0.128
rrl	1475699	r.2042c>t	0.103
rrl	1475783	r.2126t>g	0.293
rrl	1475791	r.2134a>g	0.145
rrl	1475803	r.2146t>c	0.491
rrl	1475804	r.2147g>c	0.491
rrl	1475816	r.2159c>g	0.492
rrl	1475817	r.2160a>g	0.492
rrl	1475881	r.2224t>c	0.293
rrl	1475883	r.2226a>c	0.189
rrl	1475892	r.2235a>c	0.163
rrl	1475894	r.2237c>g	0.167
rrl	1475898	r.2241a>g	0.143
rrl	1475899	r.2242g>a	0.125
rrl	1475900	r.2243a>g	0.154
rrl	1475904	r.2247g>a	0.136
rrl	1475916	r.2259c>g	0.128
rrl	1475937	r.2280a>t	0.154
rrl	1475943	r.2286g>a	0.158
rrl	1475952	r.2295a>g	0.167
rrl	1475963	r.2306g>t	0.121
rrl	1475970	r.2313c>t	0.121
rrl	1475975	r.2318c>t	0.114
rrl	1475977	r.2320a>g	0.114
rrl	1475978	r.2321c>t	0.114
rrl	1476164	r.2507a>g	0.115
rrl	1476194	r.2537a>g	0.217
rrl	1476200	r.2543a>t	0.227
rrl	1476201	r.2544c>t	0.227
rrl	1476214	r.2557g>t	0.200
rrl	1476215	r.2558c>t	0.200
rrl	1476224	r.2567a>g	0.174
rrl	1476245	r.2588c>t	0.160
rrl	1476252	r.2595t>g	0.154
rrl	1476253	r.2596a>g	0.154
rrl	1476256	r.2599a>g	0.154
rrl	1476260	r.2603a>g	0.160
rrl	1476281	r.2624t>c	0.130
rrl	1476336	r.2679c>t	0.211
rrl	1476337	r.2680c>t	0.171
rrl	1476338	r.2681c>t	0.250
rrl	1476356	r.2699c>a	0.154
rrl	1476357	r.2700t>c	0.133
rrl	1476358	r.2701t>c	0.196
rrl	1476359	r.2702c>g	0.386
rrl	1476369	r.2712c>t	0.222
rrl	1476381	r.2724g>c	0.298
rrl	1476382	r.2725a>g	0.211
rrl	1476383	r.2726t>a	0.220
rrl	1476384	r.2727g>t	0.137
rrl	1476408	r.2751g>a	0.386
rrl	1476411	r.2754g>t	0.263
rrl	1476425	r.2768g>t	0.290
rrl	1476428	r.2771c>t	0.147
rrl	1476429	r.2772a>c	0.328
rrl	1476442	r.2785t>a	0.254
rrl	1476443	r.2786g>t	0.380
rrl	1476455	r.2798c>a	0.359
rrl	1476456	r.2799a>t	0.215
rrl	1476463	r.2806c>a	0.235
rrl	1476466	r.2809c>t	0.453
rrl	1476470	r.2813c>t	0.250
rrl	1476481	r.2824t>c	0.281
rrl	1476483	r.2826g>a	0.175
rrl	1476501	r.2844c>t	0.245
rrl	1476506	r.2849t>c	0.409
rrl	1476515	r.2858c>t	0.207
rrl	1476524	r.2867c>t	0.185
rrl	1476525	r.2868a>g	0.185
rrl	1476530	r.2873c>t	0.185
rrl	1476536	r.2879g>a	0.167
rrl	1476539	r.2882a>g	0.167
rrl	1476540	r.2883c>g	0.167
rrl	1476547	r.2890c>t	0.179
rpsA	1834177	c.636A>C	1.000
tlyA	1917972	c.33A>G	1.000
katG	2154724	p.Arg463Leu	1.000
ald	3086788	c.-32T>C	1.000
fbiA	3640377	c.-166G>A	0.963
alr	3841662	c.-242A>G	0.239
alr	3841663	c.-243G>A	0.265
embC	4242643	c.2781C>T	1.000
embA	4243460	c.228C>T	1.000
gid	4407588	c.615T>C	1.000
gid	4407927	p.Glu92Asp	1.000