Created
May 6, 2019 09:23
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| TBProfiler report | |
| ================= | |
| The following report has been generated by TBProfiler. | |
| Summary | |
| ------- | |
| ID: por7B | |
| Date: Mon May 6 09:31:27 2019 | |
| Strain: lineage4.3.4.1 | |
| Drug-resistance: MDR | |
| Lineage report | |
| -------------- | |
| Lineage Estimated Fraction Family Spoligotype Rd | |
| lineage4 1.000 Euro-American LAM;T;S;X;H None | |
| lineage4.3 1.000 Euro-American (LAM) mainly-LAM None | |
| lineage4.3.4 1.000 Euro-American (LAM) LAM RD174 | |
| lineage4.3.4.1 1.000 Euro-American (LAM) LAM1;LAM2 RD174 | |
| Resistance report | |
| ----------------- | |
| Drug Genotypic Resistance Mutations | |
| Ofloxacin | |
| Amikacin R rrs r.1401a>g (1.00) | |
| Delamanid | |
| Para-aminosalicylic acid | |
| Levofloxacin | |
| Cycloserine | |
| Fluoroquinolones | |
| Ethambutol R embB p.Met306Ile (1.00) | |
| Streptomycin | |
| Ethionamide | |
| Linezolid | |
| Clofazimine | |
| Isoniazid R katG p.Ser315Thr (1.00) | |
| Aminoglycosides R rrs r.1401a>g (1.00) | |
| Capreomycin R rrs r.1401a>g (1.00) | |
| Moxifloxacin | |
| Ciprofloxacin | |
| Kanamycin R rrs r.1401a>g (1.00) | |
| Rifampicin R rpoB p.Ser450Leu (1.00) | |
| Bedaquiline | |
| Pyrazinamide R pncA p.Pro69Leu (1.00) | |
| Resistance variants report | |
| ----------------- | |
| Genome Position Locus Tag Gene Change Estimated Fraction Drug | |
| 761155 Rv0667 rpoB p.Ser450Leu 1.000 rifampicin | |
| 1473246 rrs rrs r.1401a>g 1.000 amikacin, aminoglycosides, capreomycin, kanamycin | |
| 2155168 Rv1908c katG p.Ser315Thr 1.000 isoniazid | |
| 2289036 Rv2043c pncA p.Pro69Leu 1.000 pyrazinamide | |
| 4247431 Rv3795 embB p.Met306Ile 1.000 ethambutol | |
| Other variants report | |
| --------------------- | |
| Genome Position Locus Tag Gene Change Estimated Fraction | |
| 7362 Rv0006 gyrA p.Glu21Gln 1.000 | |
| 7585 Rv0006 gyrA p.Ser95Thr 1.000 | |
| 9304 Rv0006 gyrA p.Gly668Asp 1.000 | |
| 761998 Rv0667 rpoB p.Leu731Pro 1.000 | |
| 764995 Rv0668 rpoC c.1626C>G 1.000 | |
| 781395 Rv0682 rpsL c.-165T>C 1.000 | |
| 1917972 Rv1694 tlyA c.33A>G 1.000 | |
| 2714504 Rv2416c eis p.His277Tyr 1.000 | |
| 3073868 Rv2764c thyA p.Thr202Ala 1.000 | |
| 3086788 Rv2780 ald c.-32T>C 1.000 | |
| 4242159 Rv3793 embC p.Leu766Pro 1.000 | |
| 4242643 Rv3793 embC c.2781C>T 1.000 | |
| 4407899 Rv3919c gid 102R>102* 1.000 | |
| 4408156 Rv3919c gid p.Leu16Arg 1.000 | |
| Analysis pipeline specifications | |
| -------------------------------- | |
| Version: 2.3.0 | |
| Analysis Program | |
| Mapping N/A | |
| Variant Calling BCFtools | |
| Disclaimer | |
| ---------- | |
| This tool is for Research Use Only and is offered free foruse. The London School | |
| of Hygiene and Tropical Medicine shall have no liability for any loss or damages | |
| of any kind, however sustained relating to the use of this tool. | |
| Citation | |
| -------- | |
| Coll, F. et al. Rapid determination of anti-tuberculosis drug resistance from | |
| whole-genome sequences. Genome Medicine 7, 51. 2015 |
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