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
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2	Family	Main Spoligotype	RDS
lineage2	East-Asian	Beijing	RD105
lineage4	Euro-American	LAM;T;S;X;H	None

Gene	Chromosome Position	Mutation	Estimated fraction
gyrB	6100	c.861G>A	0.895
gyrB	6115	c.876A>G	0.947
gyrB	6121	c.882C>T	0.950
gyrB	6127	c.888G>C	0.950
gyrB	6133	c.894G>C	0.950
gyrB	6136	c.897G>A	0.950
gyrB	6151	c.912C>T	0.905
gyrB	6172	c.933C>T	0.950
gyrB	6184	c.945C>T	0.950
gyrB	6193	c.954G>A	0.923
gyrB	6196	c.957C>T	0.917
gyrB	6202	c.963C>T	0.900
gyrB	6203	p.Ser322Ala	0.900
gyrB	6214	c.975G>C	0.900
gyrB	6223	c.984G>C	0.900
gyrB	6655	c.1416T>C	1.000
gyrB	6664	c.1425C>T	1.000
gyrB	6673	c.1434A>C	1.000
gyrB	6676	c.1437T>G	1.000
gyrB	6700	c.1461T>C	1.000
gyrB	6703	c.1464G>C	1.000
gyrB	6706	c.1467G>A	1.000
gyrB	6709	c.1470A>G	1.000
gyrB	6712	c.1473G>C	1.000
gyrB	6727	c.1488G>T	1.000
gyrB	6728	c.1489C>T	1.000
gyrB	6739	c.1500C>T	1.000
gyrB	6745	c.1506T>C	1.000
gyrB	6754	c.1515C>T	1.000
gyrB	6763	c.1524G>C	1.000
gyrB	6775	c.1536G>C	1.000
gyrB	6793	c.1554T>C	1.000
gyrB	6798	p.Gly520Ala	1.000
gyrB	6808	c.1569C>G	1.000
gyrB	6824	c.1585C>T	1.000
gyrB	6838	c.1599C>T	1.000
gyrB	6841	c.1602T>C	1.000
gyrB	6862	c.1623C>G	1.000
gyrB	6869	c.1630T>C	1.000
gyrB	6872	c.1633T>C	1.000
gyrB	6878	c.1639T>C	1.000
gyrB	6889	c.1650G>A	1.000
gyrB	6898	c.1659G>C	1.000
gyrB	7006	c.1767T>G	1.000
gyrB	7010	p.Leu591Met	1.000
gyrB	7015	c.1776G>A	1.000
gyrB	7018	c.1779G>C	1.000
gyrB	7024	c.1785G>A	1.000
gyrB	7033	c.1794G>C	1.000
gyrB	7051	p.Glu604Asp	1.000
gyrB	7060	c.1821T>C	1.000
gyrB	7066	c.1827G>T	1.000
gyrB	7081	c.1842T>C	1.000
gyrB	7084	c.1845A>G	1.000
gyrB	7090	c.1851C>T	1.000
gyrB	7093	c.1854T>C	1.000
gyrB	7100	c.1861T>C	1.000
gyrA	7343	c.42G>C	0.935
gyrA	7355	c.54T>A	0.935
gyrA	7362	p.Glu21Gln	1.000
gyrA	7391	c.90C>T	0.967
gyrA	7394	c.93T>C	0.967
gyrA	7397	c.96G>C	0.967
gyrA	7412	c.111C>G	0.967
gyrA	7421	c.120G>C	0.900
gyrA	7424	c.123G>C	0.900
gyrA	7427	c.126G>C	0.900
gyrA	7433	c.132G>C	0.900
gyrA	7439	c.138C>T	0.889
gyrA	7442	c.141G>C	0.889
gyrA	7451	c.150C>A	0.824
gyrA	7457	c.156T>C	0.824
gyrA	7499	c.198G>C	0.983
gyrA	7511	c.210C>T	0.986
gyrA	7523	c.222C>G	0.987
gyrA	7526	c.225G>C	0.987
gyrA	7547	c.246C>T	0.966
gyrA	7559	c.258G>C	0.990
gyrA	7565	c.264C>T	0.990
gyrA	7574	c.273G>C	0.990
gyrA	7585	p.Ser95Thr	1.000
gyrA	7589	c.288G>C	0.990
gyrA	7595	c.294C>T	0.989
gyrA	7607	c.306C>T	0.989
gyrA	7637	c.336C>A	0.943
gyrA	8121	c.820T>C	1.000
gyrA	8129	c.828T>C	1.000
gyrA	8156	c.855T>C	1.000
gyrA	8168	c.867A>G	1.000
gyrA	8174	c.873C>G	1.000
gyrA	8177	c.876A>C	1.000
gyrA	8187	p.Leu296Ile	1.000
gyrA	8192	c.891C>G	1.000
gyrA	8198	c.897T>C	1.000
gyrA	8207	c.906T>C	1.000
gyrA	8267	c.966G>C	1.000
gyrA	8283	p.Ile328Leu	1.000
gyrA	8288	c.987T>C	1.000
gyrA	8294	c.993T>C	0.976
gyrA	8327	c.1026C>T	0.953
gyrA	8330	c.1029C>G	0.953
gyrA	8339	c.1038A>G	0.944
gyrA	8340	p.Ala347Ser	0.944
gyrA	8354	c.1053G>C	0.929
gyrA	8366	c.1065G>A	0.929
gyrA	8372	c.1071G>T	0.926
gyrA	8382	c.1081C>T	0.905
gyrA	8571	c.1270C>T	1.000
gyrA	8576	c.1275C>G	1.000
gyrA	8580	p.Ile427Val	1.000
gyrA	8603	c.1302A>C	1.000
gyrA	8609	c.1308G>C	1.000
gyrA	8619	c.1318T>C	1.000
gyrA	8624	c.1323G>T	0.952
gyrA	8633	c.1332C>G	0.952
gyrA	8636	c.1335A>T	0.952
gyrA	8642	c.1341A>G	0.952
gyrA	8645	c.1344C>G	0.952
gyrA	8649	p.Arg450Lys	0.952
gyrA	8666	c.1365G>C	0.952
gyrA	8672	c.1371A>G	0.952
gyrA	8693	c.1392T>C	0.929
gyrA	8696	c.1395G>C	0.923
gyrA	8699	c.1398A>G	0.909
gyrA	8799	p.Ala500Ser	1.000
gyrA	8810	c.1509A>G	0.929
gyrA	8817	p.Ser506Ala	1.000
gyrA	8828	c.1527T>C	1.000
gyrA	8829	c.1528T>C	1.000
gyrA	8837	c.1536C>G	1.000
gyrA	8840	c.1539C>T	0.955
gyrA	8846	c.1545C>T	1.000
gyrA	8852	c.1551T>C	1.000
gyrA	8858	c.1557T>C	1.000
gyrA	8870	c.1569G>C	0.963
gyrA	8873	c.1572A>G	1.000
gyrA	8897	c.1596T>C	1.000
gyrA	8903	c.1602T>C	1.000
gyrA	8915	c.1614A>G	1.000
gyrA	8924	c.1623C>T	0.984
gyrA	8942	c.1641G>C	1.000
gyrA	8945	c.1644G>C	1.000
gyrA	8946	c.1645T>C	1.000
gyrA	8967	p.Ala556Lys	1.000
gyrA	8978	c.1677C>T	1.000
gyrA	8987	c.1686C>G	1.000
gyrA	8990	c.1689C>G	1.000
gyrA	8993	c.1692C>T	1.000
gyrA	8996	c.1695T>C	1.000
gyrA	8998	p.Leu566Trp	1.000
rpoB	760079	c.273G>A	1.000
rpoB	760091	c.285G>C	1.000
rpoB	760101	c.295T>C	1.000
rpoB	760110	c.304T>A	1.000
rpoB	760118	c.312T>G	1.000
rpoB	760121	c.315T>C	1.000
rpoB	760130	p.Asp108Glu	0.975
rpoB	760139	c.333A>G	1.000
rpoB	760142	c.336C>T	1.000
rpoB	760181	c.375T>C	1.000
rpoB	760184	c.378A>G	1.000
rpoB	760196	c.390C>G	1.000
rpoB	760235	c.429T>C	1.000
rpoB	760244	c.438G>C	1.000
rpoB	760256	c.450C>T	1.000
rpoB	760274	p.Glu156Asp	1.000
rpoB	760276	p.Lys157Met	1.000
rpoB	760283	c.477G>C	1.000
rpoB	760298	c.492G>C	1.000
rpoB	760307	c.501T>C	1.000
rpoB	760357	p.Thr184Ser	1.000
rpoB	760361	c.555T>C	1.000
rpoB	760370	c.564C>G	1.000
rpoB	760376	p.Asp190Glu	1.000
rpoB	760382	c.576G>C	1.000
rpoB	760400	c.594G>C	1.000
rpoB	760406	c.600G>C	0.976
rpoB	760406	r.600ga>g	1.000
rpoB	760407	p.Ser201Gly	1.000
rpoB	760415	c.609C>T	1.000
rpoB	760418	c.612G>C	1.000
rpoB	760430	c.624T>C	0.964
rpoB	760460	c.654G>C	0.970
rpoB	760475	c.669A>G	0.971
rpoB	760481	c.675G>T	0.957
rpoB	760484	c.678A>G	0.956
rpoB	760499	c.693G>A	0.955
rpoB	760502	c.696C>G	0.958
rpoB	760522	p.Ser239Asn	0.955
rpoB	760532	c.726T>C	0.955
rpoB	760541	c.735G>C	0.950
rpoB	760553	c.747C>G	0.946
rpoB	760567	p.Ser254Trp	0.900
rpoB	760571	c.765G>C	0.967
rpoB	760588	p.Thr261Ile	0.978
rpoB	760591	p.Val262Ala	0.978
rpoB	760595	c.789C>T	0.978
rpoB	760596	p.Thr264Pro	0.979
rpoB	760608	c.802C>T	0.983
rpoB	760611	c.805T>C	0.984
rpoB	760634	c.828T>C	1.000
rpoB	760646	c.840C>G	1.000
rpoB	760655	c.849A>G	1.000
rpoB	760661	c.855A>G	1.000
rpoB	760668	p.Thr288Ala	1.000
rpoB	760674	c.868T>C	1.000
rpoB	760679	c.873A>G	1.000
rpoB	760683	c.877T>C	1.000
rpoB	760703	c.897C>T	0.978
rpoB	760721	c.915C>G	1.000
rpoB	760727	c.921C>G	0.962
rpoB	760730	c.924T>C	1.000
rpoB	760736	c.930C>G	1.000
rpoB	760793	c.987A>G	1.000
rpoB	760799	c.993C>T	1.000
rpoB	760805	c.999G>C	1.000
rpoB	760817	c.1011A>G	1.000
rpoB	760820	c.1014T>C	1.000
rpoB	760826	c.1020C>G	1.000
rpoB	760830	c.1024T>C	1.000
rpoB	760841	c.1035T>C	1.000
rpoB	760858	p.Val351Ala	1.000
rpoB	760862	c.1056G>C	1.000
rpoB	760886	p.Glu360Asp	1.000
rpoB	760887	p.Thr361Val	1.000
rpoB	760910	c.1104C>T	1.000
rpoB	760916	c.1110C>T	1.000
rpoB	760928	c.1122G>C	1.000
rpoB	760946	c.1140A>G	1.000
rpoB	760965	p.Met387Leu	1.000
rpoB	760970	c.1164G>C	1.000
rpoB	760973	c.1167G>T	1.000
rpoB	760979	c.1173G>A	1.000
rpoB	760982	c.1176G>T	1.000
rpoB	760985	c.1179G>C	1.000
rpoB	760988	c.1182C>G	1.000
rpoB	760991	c.1185G>C	1.000
rpoB	760997	c.1191G>C	1.000
rpoB	761006	c.1200C>G	1.000
rpoB	761015	c.1209G>C	1.000
rpoB	761027	c.1221A>C	1.000
rpoB	761036	c.1230G>C	1.000
rpoB	761037	c.1231T>C	1.000
rpoB	761051	c.1245G>T	0.985
rpoB	761054	c.1248G>C	1.000
rpoB	761060	c.1254C>G	1.000
rpoB	761063	c.1257C>G	1.000
rpoB	761084	c.1278C>A	1.000
rpoB	761097	c.1291A>T	1.000
rpoB	761102	c.1296A>G	1.000
rpoB	761132	c.1326G>T	1.000
rpoB	761133	c.1327T>C	1.000
rpoB	761147	c.1341C>T	1.000
rpoB	761150	c.1344A>T	1.000
rpoB	761165	c.1359G>C	1.000
rpoB	761171	c.1365C>T	1.000
rpoB	761178	p.Ser458Thr	1.000
rpoB	761186	p.Glu460Asp	1.000
rpoB	761189	c.1383T>C	1.000
rpoB	761195	c.1389G>C	1.000
rpoB	761198	c.1392G>T	1.000
rpoB	761219	c.1413G>C	1.000
rpoB	761231	c.1425C>T	0.987
rpoB	761234	c.1428G>T	0.987
rpoB	761249	c.1443A>G	0.987
rpoB	761255	c.1449T>G	0.984
rpoB	761258	c.1452G>A	0.984
rpoB	761261	c.1455G>C	0.983
rpoB	761264	c.1458C>G	0.952
rpoB	761273	c.1467T>C	0.985
rpoB	761297	c.1491C>T	0.984
rpoB	761318	c.1512G>C	0.979
rpoB	761327	c.1521A>G	0.977
rpoB	761339	c.1533C>G	0.974
rpoB	761516	c.1710G>C	1.000
rpoB	761528	c.1722C>T	1.000
rpoB	761537	c.1731C>G	1.000
rpoB	761555	c.1749G>C	1.000
rpoB	761558	c.1752C>G	1.000
rpoB	761564	c.1758G>C	1.000
rpoB	761573	c.1767C>G	1.000
rpoB	761579	c.1773G>C	1.000
rpoB	761606	c.1800C>G	0.990
rpoB	761612	c.1806G>T	1.000
rpoB	761615	c.1809A>C	1.000
rpoB	761636	c.1830G>T	1.000
rpoB	761645	c.1839C>G	1.000
rpoB	761648	c.1842T>C	0.987
rpoB	761657	c.1851C>T	1.000
rpoB	761669	c.1863C>T	1.000
rpoB	761675	c.1869G>C	1.000
rpoB	761687	c.1881C>T	1.000
rpoB	761690	c.1884G>C	1.000
rpoB	761693	c.1887G>C	1.000
rpoB	761705	c.1899C>A	0.980
rpoB	761720	c.1914C>G	0.150
rpoB	761722	p.Glu639Gly	0.941
rpoB	761727	p.Ser641Gly	0.941
rpoB	761741	c.1935G>A	0.941
rpoB	761750	c.1944G>T	0.938
rpoB	761863	p.Ala686Glu	0.900
rpoB	761868	p.Asp688Gln	0.900
rpoB	761873	c.2067A>G	0.917
rpoB	761891	c.2085G>C	1.000
rpoB	761892	p.Ile696Val	1.000
rpoB	761909	c.2103T>C	1.000
rpoB	761912	c.2106T>C	1.000
rpoB	761915	p.Asp703Glu	1.000
rpoB	761916	p.Asp704Asn	1.000
rpoB	761924	c.2118G>A	1.000
rpoB	761930	c.2124G>C	1.000
rpoB	761933	c.2127G>C	1.000
rpoB	761936	c.2130C>T	1.000
rpoB	761948	c.2142G>C	1.000
rpoB	761954	c.2148C>A	1.000
rpoB	761955	p.Ile717Val	1.000
rpoB	761969	c.2163G>A	1.000
rpoB	761990	c.2184G>C	1.000
rpoB	762008	c.2202C>T	1.000
rpoB	762014	c.2208C>G	1.000
rpoB	762038	c.2232C>T	1.000
rpoB	762047	c.2241G>A	1.000
rpoB	762053	c.2247T>C	1.000
rpoB	762056	c.2250G>A	1.000
rpoB	762065	c.2259T>G	1.000
rpoB	762083	c.2277T>C	1.000
rpoB	762086	c.2280G>C	1.000
rpoB	762101	c.2295C>G	0.980
rpoB	762114	p.Ile770Val	0.982
rpoB	762122	c.2316C>T	0.982
rpoB	762131	c.2325C>G	0.982
rpoB	762134	c.2328C>A	0.982
rpoB	762140	c.2334G>C	0.981
rpoB	762143	c.2337T>C	0.981
rpoB	762158	c.2352G>C	0.986
rpoB	762167	c.2361T>C	0.986
rpoB	762176	c.2370T>C	0.986
rpoB	762185	c.2379G>C	1.000
rpoB	762194	c.2388G>C	1.000
rpoB	762233	c.2427G>C	1.000
rpoB	762236	c.2430G>C	1.000
rpoB	762239	c.2433G>A	1.000
rpoB	762245	c.2439G>C	1.000
rpoB	762254	c.2448T>C	1.000
rpoB	762284	c.2478G>T	1.000
rpoB	762293	c.2487T>C	1.000
rpoB	762296	c.2490G>C	1.000
rpoB	762314	c.2508C>T	1.000
rpoB	762317	c.2511A>G	1.000
rpoB	762323	c.2517C>A	1.000
rpoB	762329	c.2523G>C	1.000
rpoB	762362	p.Glu852Asp	1.000
rpoB	762368	p.Glu854Asp	1.000
rpoB	762374	c.2568G>T	1.000
rpoB	762380	c.2574T>C	1.000
rpoB	762383	c.2577C>G	1.000
rpoB	762392	c.2586G>C	1.000
rpoB	762395	c.2589G>T	1.000
rpoB	762398	c.2592T>C	1.000
rpoB	762404	c.2598T>C	1.000
rpoB	762410	c.2604T>G	1.000
rpoB	762416	c.2610A>G	1.000
rpoB	762449	c.2643C>A	1.000
rpoB	762452	c.2646G>C	1.000
rpoB	762470	c.2664G>C	1.000
rpoB	762488	c.2682G>C	1.000
rpoB	762491	c.2685T>C	0.979
rpoB	762507	c.2702 2702del	1.000
rpoC	763402	c.33C>T	0.889
rpoC	763408	c.39T>C	0.800
rpoC	763411	c.42T>C	0.889
rpoC	763414	c.45T>G	0.889
rpoC	763415	p.Thr16Ser	0.800
rpoC	763423	p.Glu18Asp	0.800
rpoC	763430	c.61A>C	0.800
rpoC	763433	p.Gln22Asn	0.800
rpoC	763443	p.Tyr25Phe	0.800
rpoC	763450	c.81G>A	0.939
rpoC	763456	c.87A>G	0.971
rpoC	763468	c.99G>C	0.972
rpoC	763486	c.117T>C	0.980
rpoC	763492	c.123G>C	0.962
rpoC	763528	c.159G>A	0.981
rpoC	763531	c.162G>T	0.980
rpoC	763546	c.177A>G	1.000
rpoC	763570	c.201G>C	1.000
rpoC	763594	c.225C>T	1.000
rpoC	763609	c.240C>T	0.965
rpoC	763621	c.252C>T	0.965
rpoC	763633	c.264T>C	1.000
rpoC	763657	c.288G>A	1.000
rpoC	763660	c.291T>G	1.000
rpoC	763666	c.297G>C	1.000
rpoC	763669	c.300C>G	1.000
rpoC	763675	c.306C>G	1.000
rpoC	763696	c.327T>C	0.913
rpoC	763699	c.330G>T	1.000
rpoC	763702	c.333C>G	1.000
rpoC	763708	c.339G>C	1.000
rpoC	763711	c.342G>C	1.000
rpoC	763714	c.345G>C	1.000
rpoC	763717	c.348T>C	1.000
rpoC	763723	c.354G>C	1.000
rpoC	763732	c.363C>G	1.000
rpoC	763741	c.372C>T	1.000
rpoC	763744	c.375G>C	1.000
rpoC	763747	c.378G>A	1.000
rpoC	763765	c.396T>C	1.000
rpoC	763774	c.405G>C	1.000
rpoC	763894	c.525A>G	0.900
rpoC	763900	c.531G>C	0.962
rpoC	763933	c.564C>T	1.000
rpoC	763940	p.Ala191Ser	0.967
rpoC	763945	c.576T>C	0.967
rpoC	763947	p.Ala193Val	0.967
rpoC	763951	c.582G>C	0.967
rpoC	763960	c.591T>G	0.967
rpoC	763969	c.600C>T	0.967
rpoC	763987	c.618C>T	0.952
rpoC	763991	p.Ile208Leu	0.950
rpoC	763996	c.627T>C	0.950
rpoC	763999	c.630C>T	0.950
rpoC	764002	c.633C>G	0.950
rpoC	764003	p.Ala212Ser	0.950
rpoC	764024	c.655T>C	0.962
rpoC	764029	p.Glu220Asp	0.962
rpoC	764032	p.Asp221Glu	0.963
rpoC	764040	p.Ser224Thr	0.971
rpoC	764044	c.675T>C	0.973
rpoC	764054	c.685C>T	0.972
rpoC	764059	c.690G>T	0.973
rpoC	764083	c.714A>G	0.974
rpoC	764084	p.Asn239Val	0.974
rpoC	764098	c.729A>G	1.000
rpoC	764110	c.741C>T	1.000
rpoC	764143	c.774G>C	1.000
rpoC	764147	p.Ser260Ala	1.000
rpoC	764150	p.Ile261Val	1.000
rpoC	764165	p.Glu266Gln	1.000
rpoC	764311	c.942C>G	0.889
rpoC	764317	c.948C>G	0.941
rpoC	764320	c.951C>G	0.955
rpoC	764338	c.969G>A	1.000
rpoC	764353	c.984G>T	1.000
rpoC	764362	c.993C>T	1.000
rpoC	764365	c.996C>T	1.000
rpoC	764371	c.1002G>C	1.000
rpoC	764377	c.1008C>G	1.000
rpoC	764380	c.1011G>C	1.000
rpoC	764387	c.1018T>C	1.000
rpoC	764405	c.1036A>C	1.000
rpoC	764428	c.1059G>T	1.000
rpoC	764431	c.1062G>C	1.000
rpoC	764434	c.1065A>G	0.979
rpoC	764435	c.1066A>C	0.979
rpoC	764452	c.1083T>C	1.000
rpoC	764458	c.1089G>C	1.000
rpoC	764461	c.1092A>G	1.000
rpoC	764497	c.1128A>G	1.000
rpoC	764509	c.1140G>A	1.000
rpoC	764510	c.1141C>T	1.000
rpoC	764521	c.1152T>C	1.000
rpoC	764527	c.1158C>T	1.000
rpoC	764530	c.1161C>T	1.000
rpoC	764533	c.1164C>A	1.000
rpoC	764536	c.1167G>T	1.000
rpoC	764539	c.1170C>G	1.000
rpoC	764545	c.1176C>A	1.000
rpoC	764575	c.1206T>G	1.000
rpoC	764593	c.1224C>T	1.000
rpoC	764611	c.1242G>T	1.000
rpoC	764626	c.1257C>T	1.000
rpoC	764632	c.1263T>C	1.000
rpoC	764650	c.1281G>T	1.000
rpoC	764668	c.1299C>T	1.000
rpoC	764683	c.1314G>A	0.969
rpoC	764692	c.1323C>T	1.000
rpoC	764713	c.1344G>T	1.000
rpoC	764716	c.1347G>C	1.000
rpoC	764746	c.1377G>T	1.000
rpoC	764752	c.1383G>C	1.000
rpoC	764758	c.1389C>G	1.000
rpoC	764764	c.1395T>C	0.987
rpoC	764791	c.1422C>G	1.000
rpoC	764803	c.1434C>T	1.000
rpoC	764809	c.1440C>T	1.000
rpoC	764810	p.Pro481Ala	1.000
rpoC	764815	c.1446A>G	1.000
rpoC	764824	c.1455T>C	1.000
rpoC	764827	c.1458G>C	1.000
rpoC	764858	c.1489T>C	1.000
rpoC	764869	c.1500C>T	1.000
rpoC	764875	c.1506C>A	1.000
rpoC	764887	c.1518G>C	1.000
rpoC	764888	c.1519T>C	1.000
rpoC	764911	c.1542A>G	1.000
rpoC	764912	p.Met515Gln	1.000
rpoC	764932	c.1563C>A	1.000
rpoC	764948	c.1579T>C	1.000
rpoC	764968	c.1599T>C	1.000
rpoC	765343	c.1974G>A	1.000
rpoC	765352	c.1983G>C	1.000
rpoC	765356	p.Met663Val	1.000
rpoC	765370	c.2001G>A	1.000
rpoC	765379	c.2010G>C	1.000
rpoC	765382	c.2013G>T	1.000
rpoC	765383	p.Met672Leu	1.000
rpoC	765403	c.2034G>C	1.000
rpoC	765405	p.Leu679His	0.938
rpoC	765408	c.2040 2040del	1.000
rpoC	765409	r.2040t>g	1.000
rpsL	781559	c.-1G>C	1.000
rpsL	781572	p.Gln5Asn	1.000
rpsL	781586	c.27C>T	1.000
rpsL	781595	c.36T>C	1.000
rpsL	781608	p.Ser17Ala	1.000
rpsL	781616	c.57C>G	1.000
rpsL	781628	c.69T>C	1.000
rpsL	781649	c.90T>C	1.000
rpsL	781655	c.96T>C	1.000
rpsL	781658	c.99A>C	1.000
rpsL	781670	c.111G>C	1.000
rpsL	781706	c.147T>C	1.000
rpsL	781715	c.156T>G	1.000
rpsL	781772	c.213C>T	1.000
rpsL	781802	c.243G>C	1.000
rpsL	781814	c.255C>T	1.000
rpsL	781817	c.258G>T	0.982
rpsL	781829	c.270G>C	1.000
rpsL	781832	c.273T>C	1.000
rpsL	781859	c.300T>C	1.000
rpsL	781868	c.309T>C	1.000
rpsL	781871	c.312G>C	1.000
rpsL	781877	c.318T>A	1.000
rpsL	781892	c.333A>G	1.000
rpsL	781898	c.339A>T	1.000
rpsL	781907	c.348T>C	1.000
rpsL	781916	c.357T>C	1.000
rpsL	781929	p.Gly124Ser	1.000
rpsL	781933	374G>A	1.000
rrs	1471922	r.77gt>g	0.957
rrs	1471925	r.80t>c	0.950
rrs	1471931	r.86ga>g	0.952
rrs	1471934	r.89a>g	0.952
rrs	1471985	r.140t>c	0.913
rrs	1471986	r.141c>t	0.957
rrs	1472061	r.216a>t	1.000
rrs	1472106	r.261g>a	0.929
rrs	1472108	r.263c>t	0.929
rrs	1472113	r.268t>c	0.933
rrs	1472150	r.305t>a	0.947
rrs	1472251	r.406g>a	1.000
rrs	1472337	r.492c>g	0.917
rrs	1472380	r.535g>c	0.929
rrs	1472446	r.601t>a	1.000
rrs	1472452	r.607g>a	1.000
rrs	1472464	r.619a>g	1.000
rrs	1472612	r.767g>t	1.000
rrs	1472734	r.889c>t	0.938
rrs	1472741	r.896g>a	0.933
rrs	1472846	r.1001c>t	0.941
rrs	1472847	r.1002g>a	0.941
rrs	1472860	r.1015c>t	0.938
rrs	1472861	r.1016g>a	0.938
rrs	1472969	r.1124a>g	1.000
rrs	1472970	r.1125c>g	1.000
rrs	1472977	r.1132g>c	1.000
rrs	1472978	r.1133t>c	1.000
rrs	1472989	r.1144g>a	1.000
rrs	1472990	r.1145a>g	1.000
rrs	1473082	r.1237g>a	1.000
rrs	1473088	r.1243a>g	1.000
rrs	1473099	r.1254t>a	1.000
rrs	1473121	r.1276t>c	1.000
rrs	1473123	r.1278a>t	0.917
rrs	1473129	r.1284c>t	0.917
rrs	1473145	r.1300c>t	0.909
rrs	1473288	r.1443c>t	1.000
rrs	1473290	r.1445c>t	1.000
rrs	1473291	r.1446g>t	1.000
rrl	1473770	r.113t>c	0.800
rrl	1473815	r.158t>g	0.900
rrl	1473829	r.172g>c	1.000
rrl	1473831	r.174g>t	1.000
rrl	1473832	r.175c>t	1.000
rrl	1473839	r.182g>a	1.000
rrl	1473876	r.219g>a	1.000
rrl	1473887	r.230t>c	1.000
rrl	1473888	r.231t>c	1.000
rrl	1473898	r.241c>t	1.000
rrl	1473899	r.242a>g	1.000
rrl	1474151	r.494c>t	1.000
rrl	1474181	r.524c>ct	0.727
rrl	1474249	r.592g>t	1.000
rrl	1474263	r.606g>a	0.933
rrl	1474282	r.625g>a	0.923
rrl	1474291	r.634tttcctctccggagga>t	1.000
rrl	1474356	r.699t>c	1.000
rrl	1474362	r.705a>g	1.000
rrl	1474387	r.730c>t	1.000
rrl	1474413	r.756a>c	1.000
rrl	1474415	r.758ccacacgcgcatacgcgcgtgtga>c	1.000
rrl	1474496	r.839c>g	1.000
rrl	1474497	r.840g>c	1.000
rrl	1474506	r.849c>g	1.000
rrl	1474507	r.850g>c	1.000
rrl	1474626	r.969t>c	0.929
rrl	1474632	r.975g>t	0.923
rrl	1474636	r.979a>t	0.917
rrl	1474637	r.980c>t	0.917
rrl	1474638	r.981c>g	0.917
rrl	1474639	r.982g>t	0.917
rrl	1474640	r.983c>t	0.917
rrl	1474913	r.1256t>c	0.900
rrl	1475031	r.1374g>c	1.000
rrl	1475061	r.1404ca>c	1.000
rrl	1475076	r.1419c>a	1.000
rrl	1475090	r.1433a>t	1.000
rrl	1475114	r.1457c>t	1.000
rrl	1475120	r.1463g>t	1.000
rrl	1475129	r.1472g>a	1.000
rrl	1475526	r.1869c>a	0.900
rrl	1475531	r.1874c>t	0.900
rrl	1475659	r.2002g>a	0.900
rrl	1475954	r.2297a>g	1.000
rrl	1476131	r.2474c>t	1.000
rrl	1476160	r.2503t>c	1.000
rrl	1476214	r.2557g>t	1.000
rrl	1476215	r.2558c>t	1.000
rrl	1476221	r.2564t>c	1.000
rrl	1476224	r.2567a>g	1.000
rrl	1476251	r.2594t>c	1.000
rrl	1476281	r.2624t>c	1.000
rrl	1476297	r.2640c>t	1.000
rrl	1476299	r.2642c>t	1.000
rrl	1476584	r.2927c>t	1.000
rrl	1476594	r.2937c>t	1.000
rrl	1476597	r.2940g>a	1.000
rrl	1476603	r.2946g>a	1.000
rrl	1476608	r.2951c>g	1.000
rrl	1476619	r.2962c>t	1.000
rrl	1476628	r.2971t>a	1.000
rpsA	1833536	c.-6A>C	0.900
rpsA	1833538	c.-4CA>C	0.900
rpsA	1833541	c.-1T>C	0.900
rpsA	1833547	c.6G>A	0.947
rpsA	1833589	c.48A>C	0.971
rpsA	1833595	c.54T>G	0.971
rpsA	1833596	p.Ser19Ala	0.971
rpsA	1833604	c.63C>T	0.978
rpsA	1833616	c.75A>T	0.979
rpsA	1833619	c.78A>C	0.979
rpsA	1833625	c.84A>G	1.000
rpsA	1833664	c.123C>G	0.983
rpsA	1833676	c.135A>G	0.980
rpsA	1833679	c.138G>T	0.979
rpsA	1833685	c.144G>C	0.978
rpsA	1833691	c.150G>A	0.977
rpsA	1833694	c.153G>T	0.976
rpsA	1833697	c.156C>T	0.976
rpsA	1833700	c.159C>T	0.976
rpsA	1833709	c.168C>T	0.980
rpsA	1833724	c.183C>T	1.000
rpsA	1833727	c.186G>C	1.000
rpsA	1833733	c.192C>G	1.000
rpsA	1833734	p.Ala65Ser	1.000
rpsA	1833745	c.204G>C	1.000
rpsA	1833748	c.207C>G	1.000
rpsA	1833760	c.219C>T	1.000
rpsA	1833787	c.246C>G	1.000
rpsA	1833790	c.249T>C	0.981
rpsA	1833802	c.261A>G	1.000
rpsA	1833811	c.270G>T	1.000
rpsA	1833823	c.282G>A	1.000
rpsA	1833832	c.291G>A	1.000
rpsA	1833835	c.294C>T	1.000
rpsA	1833838	c.297G>C	1.000
rpsA	1833841	c.300C>G	1.000
rpsA	1833847	c.306C>G	1.000
rpsA	1833862	c.321G>T	1.000
rpsA	1833874	c.333T>G	1.000
rpsA	1833877	c.336C>G	0.984
rpsA	1833886	c.345C>G	1.000
rpsA	1833894	p.Ala118Glu	1.000
rpsA	1833928	c.387G>C	1.000
rpsA	1833949	c.408T>C	1.000
rpsA	1833958	c.417C>T	0.981
rpsA	1833961	c.420C>G	1.000
rpsA	1833970	c.429G>T	1.000
rpsA	1833979	c.438T>C	1.000
rpsA	1833991	c.450C>G	1.000
rpsA	1834000	c.459G>C	1.000
rpsA	1834009	c.468C>T	1.000
rpsA	1834012	c.471G>C	1.000
rpsA	1834015	c.474G>C	1.000
rpsA	1834021	c.480C>T	1.000
rpsA	1834030	c.489C>G	1.000
rpsA	1834073	p.Lys178Arg	1.000
rpsA	1834096	c.555G>C	1.000
rpsA	1834099	c.558C>G	1.000
rpsA	1834108	c.567C>G	1.000
rpsA	1834114	c.573G>C	1.000
rpsA	1834177	c.636A>C	1.000
rpsA	1834228	c.687C>A	0.971
rpsA	1834231	c.690T>G	0.969
rpsA	1834234	c.693G>T	0.968
rpsA	1834240	c.699T>C	0.969
rpsA	1834246	c.705G>T	0.968
rpsA	1834249	c.708T>C	0.968
rpsA	1834252	c.711C>G	0.968
rpsA	1834261	c.720A>G	0.974
rpsA	1834264	c.723G>C	0.975
rpsA	1834279	c.738C>T	0.976
rpsA	1834294	c.753G>T	0.977
rpsA	1834297	c.756C>T	0.976
rpsA	1834303	c.762T>G	0.978
rpsA	1834306	c.765T>C	0.978
rpsA	1834327	c.786G>T	0.984
rpsA	1834348	c.807T>C	0.985
rpsA	1834357	c.816T>C	0.985
rpsA	1834366	c.825A>G	0.985
rpsA	1834375	c.834G>T	0.987
rpsA	1834396	c.855G>C	0.987
rpsA	1834411	c.870T>G	0.986
rpsA	1834414	c.873C>T	0.986
rpsA	1834417	c.876G>C	0.986
rpsA	1834423	c.882G>C	0.986
rpsA	1834429	c.888C>T	0.986
rpsA	1834438	c.897C>T	1.000
rpsA	1834451	c.910T>C	1.000
rpsA	1834456	c.915T>G	1.000
rpsA	1834468	c.927A>G	1.000
rpsA	1834477	c.936C>T	1.000
rpsA	1834489	c.948T>C	1.000
rpsA	1834516	c.975G>A	1.000
rpsA	1834519	c.978G>C	1.000
rpsA	1834520	p.Ala327Ser	1.000
rpsA	1834528	c.987T>C	1.000
rpsA	1834543	c.1002C>G	1.000
rpsA	1834546	c.1005T>C	1.000
rpsA	1834552	c.1011G>T	1.000
rpsA	1834555	c.1014T>G	1.000
rpsA	1834557	p.Ala339Gly	1.000
rpsA	1834606	c.1065C>T	1.000
rpsA	1834609	c.1068T>C	1.000
rpsA	1834619	c.1078T>C	1.000
rpsA	1834622	c.1081T>A	1.000
rpsA	1834633	c.1092A>G	1.000
rpsA	1834639	c.1098T>C	1.000
rpsA	1834645	c.1104C>T	1.000
rpsA	1834666	c.1125G>C	1.000
rpsA	1834667	p.Ala376Ser	1.000
rpsA	1834690	c.1149T>C	1.000
rpsA	1834700	p.Gln387Ala	1.000
rpsA	1834705	c.1164C>G	1.000
rpsA	1834720	c.1179C>G	1.000
rpsA	1834732	c.1191T>C	1.000
rpsA	1834738	c.1197A>G	1.000
rpsA	1834747	c.1206A>G	1.000
rpsA	1834759	c.1218A>C	1.000
rpsA	1834765	p.Glu408Asp	1.000
rpsA	1834774	c.1233C>T	1.000
rpsA	1834776	p.Ala412Glu	1.000
rpsA	1834780	c.1239A>G	1.000
rpsA	1834789	c.1248T>C	1.000
rpsA	1834813	c.1272G>T	1.000
rpsA	1834830	p.Ala430Val	0.964
kasA	2518738	c.624G>C	1.000
kasA	2518756	c.642G>C	1.000
kasA	2518768	c.654C>G	1.000
kasA	2518771	c.657C>G	1.000
kasA	2518774	c.660C>T	1.000
kasA	2518783	c.669T>G	1.000
kasA	2518787	p.Arg225Lys	1.000
kasA	2518792	c.678C>T	1.000
kasA	2518795	c.681C>T	1.000
kasA	2518798	c.684G>C	1.000
kasA	2518822	c.708C>A	1.000
kasA	2518825	c.711T>C	1.000
kasA	2518846	c.732G>T	0.984
kasA	2518849	c.735G>C	1.000
kasA	2518853	p.Leu247Val	1.000
kasA	2518864	c.750G>C	0.981
panD	4044138	c.144A>G	0.182
panD	4044150	c.132T>G	1.000
panD	4044156	c.126T>C	0.182
panD	4044167	c.115G>A	1.000
panD	4044171	c.111G>A	1.000
panD	4044174	c.108G>A	1.000
panD	4044180	p.Asp34Glu	1.000
panD	4044188	c.94C>G	1.000
panD	4044189	c.93G>A	1.000
panD	4044194	p.Ala30Pro	1.000
panD	4044195	c.87A>G	1.000
panD	4044219	c.63G>A	0.818
panD	4044233	p.Cys17His	1.000
panD	4044234	c.48G>C	1.000
panD	4044240	c.42C>G	0.818
panD	4044249	c.33G>A	1.000
embC	4240729	c.867C>G	1.000
embC	4240735	c.873C>G	1.000
embC	4240741	c.879C>T	1.000
embC	4240756	c.894G>C	1.000
embC	4240771	c.909G>C	1.000
embC	4240772	p.Ser304Ala	1.000
embC	4240778	p.His306Gly	1.000
embC	4240781	p.Ala307Ser	1.000
embC	4240789	c.927T>C	1.000
embC	4240819	c.957A>C	1.000
embC	4240826	p.Ala322Ser	1.000
embC	4240831	c.969T>G	1.000
embC	4240856	p.Ala332Thr	1.000
embC	4240859	p.Leu333Ile	1.000
embC	4240876	c.1014C>T	1.000
embC	4240879	c.1017G>T	1.000
embC	4240885	c.1023T>C	1.000
embC	4240886	p.Ile342Val	1.000
embC	4240897	c.1035C>G	1.000
embC	4240900	c.1038A>G	1.000