TBProfiler report ================= The following report has been generated by TBProfiler. Summary ------- ID: tbprofiler Date: Fri Jan 28 13:14:37 2022 Strain: lineage2.2.1 Drug-resistance: Pre-XDR Lineage report -------------- Lineage Estimated Fraction Family Spoligotype Rd lineage2 1.000 East-Asian Beijing RD105 lineage2.2 1.000 East-Asian (Beijing) Beijing-RD207 RD105;RD207 lineage2.2.1 0.998 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 Resistance report ----------------- Drug Genotypic Resistance Mutations Rifampicin R rpoB p.Ser450Leu (1.00) Isoniazid R fabG1 c.-15C>T (1.00) Ethambutol R embB p.Met306Val (1.00) Pyrazinamide R pncA c.459 466del (1.00) Streptomycin R rrs r.514a>c (1.00) Fluoroquinolones R gyrA p.Asp94Gly (1.00) Amikacin Capreomycin Kanamycin Cycloserine Ethionamide R fabG1 c.-15C>T (1.00), ethA c.65 65del (0.99), ethR p.Ala95Thr (1.00) Clofazimine Para-aminosalicylic acid Delamanid Bedaquiline Linezolid Resistance variants report ----------------- Genome Position Locus Tag Gene Change Estimated Fraction Drugs.Drug 7582 Rv0006 gyrA p.Asp94Gly 1.000 ciprofloxacin,fluoroquinolones,levofloxacin,moxifloxacin,ofloxacin 761155 Rv0667 rpoB p.Ser450Leu 1.000 rifampicin 1472359 rrs rrs r.514a>c 1.000 streptomycin 1673425 Rv1483 fabG1 c.-15C>T 1.000 ethionamide,isoniazid 2288775 Rv2043c pncA c.459 466del 1.000 pyrazinamide 4247429 Rv3795 embB p.Met306Val 1.000 ethambutol 4327408 Rv3854c ethA c.65 65del 0.988 ethionamide 4327831 Rv3855 ethR p.Ala95Thr 1.000 ethionamide 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 491742 Rv0407 fgd1 c.960T>C 1.000 575907 Rv0486 mshA p.Ala187Val 1.000 763031 Rv0667 rpoB c.3225T>C 1.000 763555 Rv0668 rpoC c.186C>T 1.000 778979 Rv0678 mmpR5 c.-11C>A 1.000 779275 Rv0678 mmpR5 p.Arg96Trp 1.000 781395 Rv0682 rpsL c.-165T>C 0.982 1834177 Rv1630 rpsA c.636A>C 1.000 1917972 Rv1694 tlyA c.33A>G 1.000 2154724 Rv1908c katG p.Arg463Leu 1.000 3086788 Rv2780 ald c.-32T>C 1.000 4242643 Rv3793 embC c.2781C>T 1.000 4243460 Rv3794 embA c.228C>T 1.000 4407588 Rv3919c gid c.615T>C 1.000 4407927 Rv3919c gid p.Glu92Asp 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 0.002 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 alr Rv3423c -273 gene alr Rv3423c -274 gene alr Rv3423c -275 gene alr Rv3423c -276 gene alr Rv3423c -277 gene alr Rv3423c -278 gene alr Rv3423c -279 gene alr Rv3423c -280 gene alr Rv3423c -281 gene alr Rv3423c -282 gene alr Rv3423c -283 gene alr Rv3423c -284 gene alr Rv3423c -285 gene alr Rv3423c -286 gene alr Rv3423c -287 gene alr Rv3423c -288 gene alr Rv3423c -289 gene alr Rv3423c -290 gene alr Rv3423c -291 gene alr Rv3423c -292 gene 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