TBProfiler report ================= The following report has been generated by TBProfiler. Summary ------- ID: tbprofiler Date: Fri Jan 28 13:15:14 2022 Strain: lineage4.3.2.1 Drug-resistance: Pre-MDR Lineage report -------------- Lineage Estimated Fraction Family Spoligotype Rd lineage4 1.000 Euro-American LAM;T;S;X;H None lineage4.3 0.995 Euro-American (LAM) mainly-LAM None lineage4.3.2 0.992 Euro-American (LAM) LAM3 None lineage4.3.2.1 0.994 Euro-American (LAM) LAM3 RD761 Resistance report ----------------- Drug Genotypic Resistance Mutations Rifampicin R rpoB p.Ser450Leu (0.99) 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 Drugs.Drug 761155 Rv0667 rpoB p.Ser450Leu 0.989 rifampicin Other variants report --------------------- Genome Position Locus Tag Gene Change Estimated Fraction 5520 Rv0005 gyrB p.Pro94Leu 1.000 6417 Rv0005 gyrB p.Thr393Ser 1.000 7222 Rv0005 gyrB c.1983C>T 1.000 7362 Rv0006 gyrA p.Glu21Gln 1.000 7585 Rv0006 gyrA p.Ser95Thr 1.000 9304 Rv0006 gyrA p.Gly668Asp 1.000 9486 Rv0006 gyrA p.Gly729Arg 1.000 764995 Rv0668 rpoC c.1626C>G 0.990 781395 Rv0682 rpsL c.-165T>C 1.000 1472337 rrs rrs r.492c>t 0.965 1917972 Rv1694 tlyA c.33A>G 1.000 3073868 Rv2764c thyA p.Thr202Ala 0.991 3086788 Rv2780 ald c.-32T>C 1.000 3841652 Rv3423c alr c.-232A>T 0.947 3841654 Rv3423c alr c.-234A>C 0.947 3841662 Rv3423c alr c.-242A>G 0.974 3841663 Rv3423c alr c.-243G>A 0.949 4242643 Rv3793 embC c.2781C>T 1.000 4408156 Rv3919c gid p.Leu16Arg 1.000 Coverage report --------------------- Gene Locus_Tag Cutoff Fraction gyrB Rv0005 0 0.000 gyrA Rv0006 0 0.000 fgd1 Rv0407 0 0.000 mshA Rv0486 0 0.000 rpoB Rv0667 0 0.000 rpoC Rv0668 0 0.000 mmpR5 Rv0678 0 0.000 rpsL Rv0682 0 0.000 rplC Rv0701 0 0.000 fbiC Rv1173 0 0.000 embR Rv1267c 0 0.000 atpE Rv1305 0 0.000 rrs rrs 0 0.000 rrl rrl 0 0.000 fabG1 Rv1483 0 0.000 inhA Rv1484 0 0.000 rpsA Rv1630 0 0.000 tlyA Rv1694 0 0.000 katG Rv1908c 0 0.000 pncA Rv2043c 0 0.000 kasA Rv2245 0 0.000 eis Rv2416c 0 0.000 ahpC Rv2428 0 0.000 folC Rv2447c 0 0.000 pepQ Rv2535c 0 0.000 ribD Rv2671 0 0.000 thyX Rv2754c 0 0.000 thyA Rv2764c 0 0.000 ald Rv2780 0 0.000 fbiD Rv2983 0 0.000 fbiA Rv3261 0 0.000 fbiB Rv3262 0 0.000 alr Rv3423c 0 0.000 ddn Rv3547 0 0.000 panD Rv3601c 0 0.000 embC Rv3793 0 0.000 embA Rv3794 0 0.000 embB Rv3795 0 0.000 ubiA Rv3806c 0 0.000 ethA Rv3854c 0 0.000 ethR Rv3855 0 0.000 gid Rv3919c 0 0.000 Missing positions report --------------------- Gene Locus_Tag Position Position_Type Drug_Resistance_Position Analysis pipeline specifications -------------------------------- Pipeline version: 3.0.8 Database version: tbdb_a2a234b_Jody Phelan _Fri Dec 18 17:32:34 2020 +0000 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