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	rrs r.888g>a (1.00)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2

Family

Main Spoligotype

RDS

Gene	Chromosome Position	Mutation	Estimated fraction
rrs	1471896	r.51t>c	1.000
rrs	1471900	r.55c>t	1.000
rrs	1471911	r.66c>a	1.000
rrs	1472089	r.244c>t	0.846
rrs	1472094	r.249t>a	1.000
rrs	1472106	r.261g>a	0.995
rrs	1472112	r.267c>t	1.000
rrs	1472113	r.268t>c	1.000
rrs	1472127	r.282c>t	0.995
rrs	1472127	r.282cgg>c	0.981
rrs	1472128	r.283g>a	1.000
rrs	1472129	r.284g>c	1.000
rrs	1472130	r.285g>a	1.000
rrs	1472137	r.292g>a	1.000
rrs	1472150	r.305t>a	1.000
rrs	1472151	r.306c>t	1.000
rrs	1472172	r.327t>c	1.000
rrs	1472203	r.358g>a	1.000
rrs	1472344	r.499c>t	1.000
rrs	1472378	r.533g>t	0.995
rrs	1472379	r.534t>c	1.000
rrs	1472380	r.535g>c	1.000
rrs	1472396	r.551a>t	1.000
rrs	1472400	r.555c>t	1.000
rrs	1472507	r.662c>g	1.000
rrs	1472517	r.672t>a	1.000
rrs	1472518	r.673g>t	1.000
rrs	1472530	r.685g>a	1.000
rrs	1472537	r.692c>t	1.000
rrs	1472544	r.699c>a	1.000
rrs	1472545	r.700a>t	1.000
rrs	1472557	r.712g>a	0.988
rrs	1472566	r.721g>a	1.000
rrs	1472571	r.726g>c	1.000
rrs	1472579	r.734g>c	1.000
rrs	1472580	r.735c>t	1.000
rrs	1472581	r.736a>t	0.994
rrs	1472598	r.753a>c	1.000
rrs	1472599	r.754g>t	0.996
rrs	1472616	r.771g>a	1.000
rrs	1472647	r.802c>t	1.000
rrs	1472655	r.810g>a	1.000
rrs	1472658	r.813g>a	1.000
rrs	1472661	r.816a>g	1.000
rrs	1472680	r.835c>t	1.000
rrs	1472682	r.837t>c	1.000
rrs	1472683	r.838t>g	1.000
rrs	1472687	r.842a>t	1.000
rrs	1472689	r.844c>t	1.000
rrs	1472690	r.845c>a	1.000
rrs	1472713	r.868t>c	1.000
rrs	1472716	r.871c>t	1.000
rrs	1472742	r.897c>t	1.000
rrs	1472744	r.899a>g	1.000
rrs	1472781	r.936c>t	0.987
rrs	1472793	r.948a>t	1.000
rrs	1472803	r.958t>a	1.000
rrs	1472895	r.1050c>t	1.000
rrs	1473035	r.1190g>a	1.000
rrs	1473053	r.1208t>a	1.000
rrs	1473056	r.1211a>t	1.000
rrs	1473062	r.1217t>a	1.000
rrs	1473068	r.1223a>g	1.000
rrs	1473081	r.1236c>t	1.000
rrs	1473166	r.1321g>a	1.000
rrs	1473177	r.1332g>a	0.996
rrs	1473192	r.1347a>g	0.996
rrs	1473205	r.1360t>c	1.000
rrs	1473316	r.1471c>a	1.000
rrs	1473318	r.1473g>a	1.000
rrs	1473319	r.1474c>t	1.000
rrs	1473327	r.1482a>g	1.000
rrs	1473328	r.1483c>t	1.000
rrs	1473352	r.1507c>t	1.000
rrl	1473679	r.22t>c	1.000
rrl	1474218	r.561t>a	1.000
rrl	1474228	r.571t>c	1.000
rrl	1474249	r.592g>t	1.000
rrl	1474252	r.595t>a	1.000
rrl	1474753	r.1096ac>a	1.000
rrl	1474869	r.1212g>c	1.000
rrl	1474892	r.1235g>a	1.000
rrl	1474896	r.1239a>g	1.000
rrl	1474902	r.1245t>c	1.000
rrl	1474903	r.1246t>c	1.000
rrl	1474904	r.1247g>c	1.000
rrl	1474913	r.1256t>a	1.000
rrl	1474920	r.1263g>c	1.000
rrl	1475124	r.1467a>t	1.000
rrl	1475129	r.1472g>t	1.000
rrl	1475145	r.1488c>a	1.000
rrl	1475149	r.1492g>a	1.000
rrl	1475154	r.1497c>a	1.000
rrl	1475158	r.1501c>t	1.000
rrl	1475162	r.1505g>t	0.995
rrl	1475163	r.1506t>c	0.995
rrl	1475175	r.1518g>a	1.000
rrl	1475498	r.1841c>g	1.000
rrl	1475574	r.1917c>a	0.992
rrl	1475783	r.2126t>g	1.000
rrl	1475803	r.2146t>c	1.000
rrl	1475804	r.2147g>c	1.000
rrl	1475816	r.2159c>g	1.000
rrl	1475817	r.2160a>g	1.000
rrl	1475858	r.2201t>c	1.000
rrl	1475866	r.2209t>a	1.000
rrl	1475874	r.2217c>t	1.000
rrl	1476126	r.2469c>t	1.000
rrl	1476130	r.2473g>a	1.000
rrl	1476135	r.2478t>c	1.000
rrl	1476141	r.2484a>g	0.996
rrl	1476153	r.2496t>c	1.000
rrl	1476165	r.2508t>g	1.000
rrl	1476194	r.2537a>g	1.000
rrl	1476195	r.2538c>a	0.944
rrl	1476196	r.2539c>a	1.000
rrl	1476200	r.2543a>t	1.000
rrl	1476201	r.2544c>t	1.000
rrl	1476204	r.2547c>a	1.000
rrl	1476210	r.2553g>t	1.000
rrl	1476211	r.2554g>t	1.000
rrl	1476212	r.2555t>c	1.000
rrl	1476214	r.2557g>c	1.000
rrl	1476215	r.2558c>a	1.000
rrl	1476225	r.2568t>g	1.000
rrl	1476227	r.2570c>t	1.000
rrl	1476229	r.2572c>t	1.000
rrl	1476250	r.2593c>g	1.000
rrl	1476251	r.2594t>c	1.000
rrl	1476257	r.2600g>c	0.995
rrl	1476260	r.2603a>g	1.000
rrl	1476280	r.2623a>c	1.000
rrl	1476293	r.2636c>t	1.000
rrl	1476294	r.2637a>g	1.000
rrl	1476295	r.2638c>g	1.000
rrl	1476296	r.2639c>t	1.000
rrl	1476297	r.2640c>t	1.000
rrl	1476301	r.2644a>t	1.000
rrl	1476302	r.2645g>a	1.000
rrl	1476311	r.2654g>c	1.000
rrl	1476312	r.2655t>c	1.000
rrl	1476313	r.2656g>a	1.000
rrl	1476332	r.2675g>c	1.000
rrl	1476338	r.2681c>t	1.000
rrl	1476353	r.2696g>t	1.000
rrl	1476358	r.2701t>c	1.000
rrl	1476369	r.2712c>t	1.000
rrl	1476372	r.2715t>c	1.000
rrl	1476382	r.2725a>g	0.992
rrl	1476383	r.2726t>a	1.000
rrl	1476425	r.2768g>t	1.000
rrl	1476428	r.2771c>t	1.000
rrl	1476429	r.2772a>c	1.000
rrl	1476481	r.2824t>c	1.000
rrl	1476506	r.2849t>c	1.000
rrl	1476514	r.2857c>t	1.000
rrl	1476637	r.2980c>a	1.000