TBProfiler report ================= The following report has been generated by TBProfiler. Summary ------- ID: tbprofiler Date: Fri Jan 28 13:14:27 2022 Strain: lineage6.3.1 Drug-resistance: Sensitive Lineage report -------------- Lineage Estimated Fraction Family Spoligotype Rd lineage6 1.000 West-Africa 2 AFRI 1 RD702 lineage6.3 1.000 West-Africa 2 AFRI 1 RD702 lineage6.3.1 1.000 West-Africa 2 AFRI 1 RD702 Resistance report ----------------- Drug Genotypic Resistance Mutations Rifampicin 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 Other variants report --------------------- Genome Position Locus Tag Gene Change Estimated Fraction 6446 Rv0005 gyrB p.Ala403Ser 1.000 7362 Rv0006 gyrA p.Glu21Gln 1.000 7585 Rv0006 gyrA p.Ser95Thr 1.000 9143 Rv0006 gyrA c.1842T>C 1.000 9304 Rv0006 gyrA p.Gly668Asp 1.000 491668 Rv0407 fgd1 p.Lys296Glu 1.000 491742 Rv0407 fgd1 c.960T>C 1.000 760969 Rv0667 rpoB p.Ser388Leu 1.000 761723 Rv0667 rpoB p.Glu639Asp 1.000 763031 Rv0667 rpoB c.3225T>C 1.000 781395 Rv0682 rpsL c.-165T>C 1.000 1302899 Rv1173 fbiC c.-32A>G 1.000 1417554 Rv1267c embR c.-207C>G 1.000 1461251 Rv1305 atpE c.207G>T 1.000 1673380 Rv1483 fabG1 c.-60C>G 0.200 1674434 Rv1484 inhA p.Val78Ala 1.000 1917972 Rv1694 tlyA c.33A>G 1.000 1918692 Rv1694 tlyA c.753G>A 1.000 2154724 Rv1908c katG p.Arg463Leu 1.000 2155503 Rv1908c katG c.609G>A 1.000 2518132 Rv2245 kasA c.18C>T 1.000 3086788 Rv2780 ald c.-32T>C 1.000 3087084 Rv2780 ald c.266 266del 1.000 3841662 Rv3423c alr c.-242A>G 1.000 3841663 Rv3423c alr c.-243G>A 0.975 4240671 Rv3793 embC p.Thr270Ile 1.000 4241843 Rv3793 embC p.Leu661Ile 1.000 4242643 Rv3793 embC c.2781C>T 1.000 4244220 Rv3794 embA c.988C>T 1.000 4244379 Rv3794 embA p.Pro383Ser 1.000 4245535 Rv3794 embA p.Ser768Ile 1.000 4246864 Rv3795 embB c.351C>T 1.000 4247646 Rv3795 embB p.Glu378Ala 1.000 4269351 Rv3806c ubiA c.483G>A 1.000 4269387 Rv3806c ubiA p.Glu149Asp 1.000 4269522 Rv3806c ubiA c.312G>A 1.000 4269606 Rv3806c ubiA c.228A>G 1.000 4326465 Rv3854c ethA p.Ile337Val 1.000 4407588 Rv3919c gid c.615T>C 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 thyX Rv2754c 174 codon thyX Rv2754c 173 codon thyX Rv2754c 172 codon thyX Rv2754c 171 codon thyX Rv2754c 170 codon thyX Rv2754c 169 codon thyX Rv2754c 167 codon thyX Rv2754c 166 codon thyX Rv2754c 165 codon thyX Rv2754c 164 codon thyX Rv2754c 163 codon 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