TBProfiler report ================= The following report has been generated by TBProfiler. Summary ------- ID: tbprofiler Date: Fri Jan 28 13:14:46 2022 Strain: Drug-resistance: Sensitive Lineage report -------------- Lineage Estimated Fraction Family Spoligotype Rd 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 5452 Rv0005 gyrB c.213G>A 1.000 6454 Rv0005 gyrB c.1215C>T 1.000 6721 Rv0005 gyrB c.1482C>T 1.000 7093 Rv0005 gyrB c.1854T>C 1.000 7362 Rv0006 gyrA p.Glu21Gln 1.000 7585 Rv0006 gyrA p.Ser95Thr 1.000 7763 Rv0006 gyrA c.462T>C 1.000 7835 Rv0006 gyrA c.534A>G 1.000 7937 Rv0006 gyrA c.636A>G 1.000 7970 Rv0006 gyrA c.669T>C 1.000 7988 Rv0006 gyrA c.687G>C 1.000 8039 Rv0006 gyrA c.738T>C 1.000 8054 Rv0006 gyrA c.753T>C 1.000 8198 Rv0006 gyrA c.897T>C 1.000 8219 Rv0006 gyrA c.918T>C 1.000 8399 Rv0006 gyrA c.1098T>C 1.000 8756 Rv0006 gyrA c.1455A>G 1.000 8810 Rv0006 gyrA c.1509A>C 1.000 8813 Rv0006 gyrA p.Asp504Glu 1.000 8966 Rv0006 gyrA c.1665C>G 1.000 9089 Rv0006 gyrA c.1788G>A 1.000 9101 Rv0006 gyrA c.1800A>G 1.000 9143 Rv0006 gyrA c.1842T>C 1.000 9182 Rv0006 gyrA c.1881T>C 1.000 9200 Rv0006 gyrA c.1899A>G 1.000 9304 Rv0006 gyrA p.Gly668Asp 1.000 9377 Rv0006 gyrA c.2076A>G 1.000 9716 Rv0006 gyrA c.2415T>C 1.000 9740 Rv0006 gyrA c.2439G>A 1.000 9776 Rv0006 gyrA c.2475T>C 1.000 490744 Rv0407 fgd1 c.-39T>C 0.167 490745 Rv0407 fgd1 c.-38G>C 0.167 491181 Rv0407 fgd1 c.399T>C 1.000 491191 Rv0407 fgd1 p.Gly137Arg 1.000 491196 Rv0407 fgd1 c.414A>G 1.000 491212 Rv0407 fgd1 p.Ser144Arg 1.000 491310 Rv0407 fgd1 c.528C>T 1.000 491742 Rv0407 fgd1 c.960T>C 1.000 575665 Rv0486 mshA c.181G>C 1.000 576757 Rv0486 mshA c.1273C>G 1.000 759741 Rv0667 rpoB c.-66C>T 1.000 763031 Rv0667 rpoB c.3225T>C 1.000 763660 Rv0668 rpoC c.291T>C 1.000 764152 Rv0668 rpoC c.783C>T 1.000 765478 Rv0668 rpoC c.2109T>C 1.000 779283 Rv0678 mmpR5 c.294C>T 1.000 779295 Rv0678 mmpR5 c.306T>C 1.000 779431 Rv0678 mmpR5 p.Asn148Gln 1.000 779472 Rv0678 mmpR5 c.483C>T 1.000 781395 Rv0682 rpsL c.-165T>C 1.000 781456 Rv0682 rpsL c.-104A>G 1.000 800970 Rv0701 rplC c.162T>C 1.000 801003 Rv0701 rplC c.195G>A 1.000 801267 Rv0701 rplC c.459A>G 1.000 1302694 Rv1173 fbiC c.-237C>T 1.000 1302810 Rv1173 fbiC c.-121C>T 1.000 1302860 Rv1173 fbiC c.-71G>A 1.000 1303695 Rv1173 fbiC c.765T>C 1.000 1304598 Rv1173 fbiC c.1668C>T 1.000 1417294 Rv1267c embR c.54T>C 1.000 1417454 Rv1267c embR c.-107C>A 1.000 1417554 Rv1267c embR c.-207C>G 1.000 1471845 rrs rrs c.-1G>GT 0.960 1471851 rrs rrs r.6t>g 1.000 1474438 rrl rrl r.781a>g 1.000 1475266 rrl rrl r.1609t>c 1.000 1674816 Rv1484 inhA c.615T>C 1.000 1833381 Rv1630 rpsA c.-161T>C 1.000 1833554 Rv1630 rpsA p.Thr5Ala 1.000 1833568 Rv1630 rpsA c.27G>C 1.000 1834169 Rv1630 rpsA p.Thr210Ala 1.000 1834912 Rv1630 rpsA c.1371A>G 1.000 1917972 Rv1694 tlyA c.33A>G 1.000 2154724 Rv1908c katG p.Arg463Leu 1.000 2156055 Rv1908c katG c.57G>A 1.000 2289104 Rv2043c pncA c.138T>C 1.000 2518132 Rv2245 kasA c.18C>T 1.000 2519287 Rv2245 kasA c.1173T>C 1.000 2714714 Rv2416c eis p.Ala207Thr 1.000 2714994 Rv2416c eis c.339A>G 1.000 2747205 Rv2447c folC p.Ala132Gln 1.000 2747572 Rv2447c folC c.27A>G 1.000 2747575 Rv2447c folC c.24C>G 1.000 2859490 Rv2535c pepQ p.Val310Ala 1.000 2986929 Rv2671 ribD p.Leu31Phe 1.000 3067355 Rv2754c thyX c.591T>G 1.000 3067770 Rv2754c thyX p.Gly59Ala 1.000 3067980 Rv2754c thyX c.-35T>C 1.000 3074160 Rv2764c thyA c.312T>C 1.000 3074238 Rv2764c thyA c.234G>A 1.000 3074247 Rv2764c thyA c.225G>A 1.000 3086788 Rv2780 ald c.-32T>C 1.000 3087122 Rv2780 ald c.303T>C 1.000 3087140 Rv2780 ald c.321G>A 1.000 3339049 Rv2983 fbiD c.-69C>T 1.000 3339402 Rv2983 fbiD c.285C>T 1.000 3339568 Rv2983 fbiD c.451C>T 1.000 3641840 Rv3262 fbiB c.306T>C 1.000 3642254 Rv3262 fbiB c.720G>A 1.000 3642467 Rv3262 fbiB c.933T>C 1.000 3642852 Rv3262 fbiB p.Pro440Ser 1.000 3642874 Rv3262 fbiB p.Leu447Arg 1.000 3840527 Rv3423c alr c.894T>G 1.000 3840620 Rv3423c alr c.801A>G 1.000 3840719 Rv3423c alr c.702T>C 1.000 3840796 Rv3423c alr p.Asp209Asn 1.000 3840914 Rv3423c alr c.507C>G 0.985 3840994 Rv3423c alr p.His143Asp 1.000 3841112 Rv3423c alr c.309A>G 1.000 3841116 Rv3423c alr p.Ala102Gly 1.000 3841172 Rv3423c alr c.249T>G 1.000 3841365 Rv3423c alr c.55 56insA 1.000 3841419 Rv3423c alr p.Val1Ala 1.000 3841531 Rv3423c alr c.-111A>G 1.000 3841532 Rv3423c alr c.-112A>G 1.000 3841539 Rv3423c alr c.-119C>T 1.000 3841546 Rv3423c alr c.-126C>G 1.000 3841568 Rv3423c alr c.-148G>A 1.000 3841662 Rv3423c alr c.-242A>G 0.187 3986910 Rv3547 ddn c.67C>A 1.000 3987050 Rv3547 ddn c.207C>T 1.000 3987287 Rv3547 ddn c.444T>C 1.000 4043932 Rv3601c panD p.Met117Thr 1.000 4044243 Rv3601c panD c.39G>C 1.000 4240237 Rv3793 embC c.375G>C 1.000 4240671 Rv3793 embC p.Thr270Ile 1.000 4242643 Rv3793 embC c.2781C>T 1.000 4243377 Rv3794 embA p.Ser49Arg 1.000 4243690 Rv3794 embA p.Met153Thr 1.000 4243919 Rv3794 embA c.687G>A 1.000 4244154 Rv3794 embA p.Thr308Pro 1.000 4244312 Rv3794 embA c.1080T>G 1.000 4245023 Rv3794 embA c.1791A>G 1.000 4245701 Rv3794 embA c.2469G>T 1.000 4247590 Rv3795 embB c.1077A>G 1.000 4247646 Rv3795 embB p.Glu378Ala 1.000 4247815 Rv3795 embB c.1302C>T 1.000 4248195 Rv3795 embB p.Lys561Met 1.000 4248206 Rv3795 embB p.Ser565Gly 1.000 4248439 Rv3795 embB c.1926C>T 1.000 4248664 Rv3795 embB c.2151G>A 1.000 4248721 Rv3795 embB c.2208C>T 1.000 4248744 Rv3795 embB p.Val744Ala 1.000 4248853 Rv3795 embB c.2340G>A 1.000 4249069 Rv3795 embB c.2556A>G 1.000 4269387 Rv3806c ubiA p.Glu149Asp 1.000 4269588 Rv3806c ubiA c.246C>T 1.000 4269606 Rv3806c ubiA c.228A>G 1.000 4269811 Rv3806c ubiA p.Gln8Arg 1.000 4326463 Rv3854c ethA c.1011G>A 1.000 4326740 Rv3854c ethA p.Arg245His 1.000 4327547 Rv3854c ethA c.-74C>TC 0.952 4407588 Rv3919c gid c.615T>C 1.000 4408185 Rv3919c gid c.18G>A 0.984 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 gyrA Rv0006 838 codon gyrA Rv0006 839 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