Created
October 12, 2020 16:34
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| TBProfiler report | |
| ================= | |
| The following report has been generated by TBProfiler. | |
| Summary | |
| ------- | |
| ID: SRR6824414 | |
| Date: Mon Oct 12 17:33:42 2020 | |
| Strain: lineage4.5;lineage3 | |
| Drug-resistance: Pre-MDR | |
| Lineage report | |
| -------------- | |
| Lineage Estimated Fraction Family Spoligotype Rd | |
| lineage3 0.190 East-African-Indian CAS RD750 | |
| lineage4 0.754 Euro-American LAM;T;S;X;H None | |
| lineage4.5 0.762 Euro-American H;T RD122 | |
| Resistance report | |
| ----------------- | |
| Drug Genotypic Resistance Mutations | |
| Rifampicin R rpoB p.Ser450Leu (0.19) | |
| Isoniazid | |
| Ethambutol | |
| Pyrazinamide | |
| Streptomycin | |
| Fluoroquinolones | |
| Amikacin | |
| Capreomycin | |
| Kanamycin | |
| Cycloserine | |
| Ethionamide | |
| Clofazimine | |
| Para-aminosalicylic acid | |
| Delamanid | |
| Bedaquiline | |
| Linezolid | |
| Resistance variants report | |
| ----------------- | |
| Genome Position Locus Tag Gene Change Estimated Fraction Drug | |
| 761155 Rv0667 rpoB p.Ser450Leu 0.186 rifampicin | |
| 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 | |
| 7892 Rv0006 gyrA c.591G>A 0.774 | |
| 9304 Rv0006 gyrA p.Gly668Asp 1.000 | |
| 491742 Rv0407 fgd1 c.960T>C 0.250 | |
| 759746 Rv0667 rpoB c.-61C>T 0.197 | |
| 760688 Rv0667 rpoB p.Phe294Leu 0.796 | |
| 762434 Rv0667 rpoB c.2628T>G 0.193 | |
| 763031 Rv0667 rpoB c.3225T>C 0.199 | |
| 775639 Rv0676c mmpL5 p.Ile948Val 1.000 | |
| 776100 Rv0676c mmpL5 p.Thr794Ile 0.221 | |
| 781395 Rv0682 rpsL c.-165T>C 1.000 | |
| 1473610 rrl rrl c.-48C>T 0.744 | |
| 1917972 Rv1694 tlyA c.33A>G 1.000 | |
| 2223293 Rv1979c . c.-129A>G 1.000 | |
| 2726105 Rv2428 ahpC c.-88G>A 0.254 | |
| 3086788 Rv2780 ald c.-32T>C 0.255 | |
| 4242075 Rv3793 embC p.Arg738Gln 0.223 | |
| 4242643 Rv3793 embC c.2781C>T 1.000 | |
| 4407588 Rv3919c gid c.615T>C 0.264 | |
| Coverage report | |
| --------------------- | |
| NA | |
| Missing positions report | |
| --------------------- | |
| NA | |
| Analysis pipeline specifications | |
| -------------------------------- | |
| Pipeline version: 3.0.0 | |
| Database version: pepi_list_eaeded53d95c4f9ddbf5d3eaf6ec7df8f2966ce0_jodyphelan <[email protected]>_Thu Apr 2 09:31:01 2020 +0100 | |
| 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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