TBProfiler report ================= The following report has been generated by TBProfiler. Summary ------- ID: tbprofiler Date: Fri Jan 28 13:14:58 2022 Strain: lineage5.1.1 Drug-resistance: Sensitive Lineage report -------------- Lineage Estimated Fraction Family Spoligotype Rd lineage5 0.969 West-Africa 1 AFRI 2;AFRI 3 RD711 lineage5.1 0.923 West-Africa 1 AFRI 2;AFRI 3 RD711 lineage5.1.1 0.942 West-Africa 1 AFRI 2;AFRI 3 RD711 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 9566 Rv0006 gyrA c.2265C>T 0.971 491742 Rv0407 fgd1 c.960T>C 1.000 763031 Rv0667 rpoB c.3225T>C 1.000 763280 Rv0667 rpoB c.3474C>T 0.935 781395 Rv0682 rpsL c.-165T>C 1.000 1302899 Rv1173 fbiC c.-32A>G 1.000 1417554 Rv1267c embR c.-207C>G 1.000 1673338 Rv1483 fabG1 c.-102G>A 1.000 1917972 Rv1694 tlyA c.33A>G 1.000 2154724 Rv1908c katG p.Arg463Leu 1.000 2518132 Rv2245 kasA c.18C>T 1.000 3087084 Rv2780 ald c.266 266del 1.000 3840932 Rv3423c alr c.489G>A 0.959 3841662 Rv3423c alr c.-242A>G 0.240 3841663 Rv3423c alr c.-243G>A 0.220 3986987 Rv3547 ddn c.144G>T 0.943 3987180 Rv3547 ddn p.Asp113Asn 0.911 4240671 Rv3793 embC p.Thr270Ile 1.000 4242643 Rv3793 embC c.2781C>T 1.000 4244220 Rv3794 embA c.988C>T 1.000 4244635 Rv3794 embA p.Val468Ala 0.970 4245147 Rv3794 embA p.Pro639Ser 1.000 4247646 Rv3795 embB p.Glu378Ala 1.000 4269387 Rv3806c ubiA p.Glu149Asp 1.000 4269522 Rv3806c ubiA c.312G>A 0.128 4269606 Rv3806c ubiA c.228A>G 1.000 4326928 Rv3854c ethA c.546G>A 0.944 4327103 Rv3854c ethA p.Gly124Asp 0.917 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 rrs rrs 618 gene rrs rrs 619 gene rrs rrs 620 gene rrs rrs 621 gene rrs rrs 622 gene rrs rrs 623 gene rrl rrl 109 gene rrl rrl 110 gene rrl rrl 111 gene rrl rrl 112 gene rrl rrl 113 gene rrl rrl 114 gene rrl rrl 115 gene rrl rrl 116 gene rrl rrl 117 gene rrl rrl 118 gene rrl rrl 119 gene rrl rrl 120 gene rrl rrl 121 gene rrl rrl 122 gene rrl rrl 123 gene rrl rrl 124 gene rrl rrl 125 gene rrl rrl 126 gene rrl rrl 127 gene rrl rrl 128 gene rrl rrl 129 gene rrl rrl 130 gene rrl rrl 131 gene rrl rrl 132 gene rrl rrl 133 gene rrl rrl 134 gene rrl rrl 135 gene rrl rrl 136 gene rrl rrl 137 gene rrl rrl 138 gene rrl rrl 139 gene rrl rrl 140 gene rrl rrl 141 gene rrl rrl 142 gene rrl rrl 143 gene rrl rrl 144 gene rrl rrl 145 gene rrl rrl 146 gene rrl rrl 147 gene rrl rrl 148 gene rrl rrl 149 gene rrl rrl 150 gene rrl rrl 151 gene rrl rrl 152 gene rrl rrl 153 gene rrl rrl 154 gene rrl rrl 155 gene rrl rrl 156 gene rrl rrl 157 gene rrl rrl 158 gene rrl rrl 159 gene rrl rrl 160 gene rrl rrl 161 gene rrl rrl 162 gene rrl rrl 163 gene rrl rrl 164 gene rrl rrl 165 gene rrl rrl 166 gene rrl rrl 167 gene rrl rrl 168 gene rrl rrl 169 gene rrl rrl 170 gene rrl rrl 171 gene rrl rrl 172 gene rrl rrl 173 gene rrl rrl 174 gene rrl rrl 175 gene rrl rrl 176 gene rrl rrl 177 gene rrl rrl 178 gene rrl rrl 179 gene rrl rrl 180 gene rrl rrl 181 gene rrl rrl 182 gene rrl rrl 183 gene rrl rrl 184 gene rrl rrl 185 gene rrl rrl 186 gene rrl rrl 559 gene rrl rrl 590 gene rrl rrl 591 gene rrl rrl 592 gene rrl rrl 593 gene rrl rrl 594 gene rrl rrl 595 gene rrl rrl 596 gene rrl rrl 597 gene rrl rrl 598 gene rrl rrl 599 gene rrl rrl 600 gene rrl rrl 609 gene rrl rrl 610 gene rrl rrl 618 gene rrl rrl 621 gene rrl rrl 622 gene rrl rrl 623 gene rrl rrl 625 gene rrl rrl 626 gene rrl rrl 1853 gene rrl rrl 1854 gene rrl rrl 1855 gene rrl rrl 1856 gene rrl rrl 1857 gene rrl rrl 1858 gene rrl rrl 1859 gene rrl rrl 1860 gene rrl rrl 1861 gene rrl rrl 1862 gene rrl rrl 1863 gene rrl rrl 1864 gene rrl rrl 1865 gene rrl rrl 1866 gene rrl rrl 1867 gene rrl rrl 1868 gene rrl rrl 1869 gene rrl rrl 1870 gene rrl rrl 1871 gene rrl rrl 1872 gene rrl rrl 1873 gene rrl rrl 1874 gene rrl rrl 1875 gene rrl rrl 1876 gene rrl rrl 1877 gene rrl rrl 1886 gene rrl rrl 1887 gene rrl rrl 1888 gene rrl rrl 1889 gene rrl rrl 1890 gene rrl rrl 1891 gene rrl rrl 1892 gene rrl rrl 1893 gene rrl rrl 1894 gene rrl rrl 1895 gene rrl rrl 1896 gene rrl rrl 1897 gene rrl rrl 1898 gene rrl rrl 1899 gene rrl rrl 1900 gene rrl rrl 1901 gene rrl rrl 1902 gene rrl rrl 1903 gene rrl rrl 1904 gene rrl rrl 1905 gene rrl rrl 1906 gene rrl rrl 1907 gene rrl rrl 1908 gene rrl rrl 1909 gene rrl rrl 1910 gene rrl rrl 2023 gene rrl rrl 2024 gene rrl rrl 2025 gene rrl rrl 2026 gene rrl rrl 2027 gene rrl rrl 2028 gene rrl rrl 2029 gene rrl rrl 2030 gene rrl rrl 2031 gene rrl rrl 2032 gene rrl rrl 2033 gene rrl rrl 2034 gene rrl rrl 2035 gene rrl rrl 2036 gene rrl rrl 2037 gene rrl rrl 2038 gene rrl rrl 2039 gene rrl rrl 2040 gene rrl rrl 2041 gene rrl rrl 2042 gene rrl rrl 2043 gene rrl rrl 2044 gene rrl rrl 2045 gene rrl rrl 2046 gene rrl rrl 2047 gene rrl rrl 2048 gene rrl rrl 2049 gene rrl rrl 2050 gene rrl rrl 2051 gene rrl rrl 2052 gene rrl rrl 2053 gene rrl rrl 2054 gene rrl rrl 2055 gene rrl rrl 2056 gene rrl rrl 2057 gene rrl rrl 2058 gene rrl rrl 2059 gene rrl rrl 2060 gene rrl rrl 2061 gene rrl rrl 2062 gene rrl rrl 2063 gene rrl rrl 2064 gene rrl rrl 2065 gene rrl rrl 2066 gene rrl rrl 2067 gene rrl rrl 2068 gene rrl rrl 2069 gene rrl rrl 2070 gene rrl rrl 2071 gene rrl rrl 2072 gene rrl rrl 2073 gene rrl rrl 2074 gene rrl rrl 2075 gene rrl rrl 2076 gene rrl rrl 2077 gene rrl rrl 2078 gene rrl rrl 2079 gene rrl rrl 2080 gene rrl rrl 2081 gene rrl rrl 2082 gene rrl rrl 2083 gene rrl rrl 2084 gene rrl rrl 2085 gene rrl rrl 2086 gene rrl rrl 2087 gene rrl rrl 2088 gene rrl rrl 2089 gene rrl rrl 2090 gene rrl rrl 2091 gene rrl rrl 2092 gene rrl rrl 2093 gene rrl rrl 2094 gene rrl rrl 2095 gene rrl rrl 2096 gene rrl rrl 2097 gene rrl rrl 2098 gene rrl rrl 2099 gene rrl rrl 2100 gene rrl rrl 2101 gene rrl rrl 2102 gene rrl rrl 2103 gene rrl rrl 2104 gene rrl rrl 2105 gene rrl rrl 2106 gene rrl rrl 2107 gene rrl rrl 2108 gene rrl rrl 2109 gene rrl rrl 2110 gene rrl rrl 2111 gene rrl rrl 2112 gene rrl rrl 2113 gene rrl rrl 2114 gene rrl rrl 2115 gene rrl rrl 2116 gene rrl rrl 2117 gene rrl rrl 2118 gene rrl rrl 2119 gene rrl rrl 2120 gene rrl rrl 2121 gene rrl rrl 2122 gene rrl rrl 2123 gene rrl rrl 2124 gene rrl rrl 2125 gene rrl rrl 2126 gene rrl rrl 2127 gene rrl rrl 2128 gene rrl rrl 2129 gene rrl rrl 2130 gene rrl rrl 2131 gene rrl rrl 2132 gene rrl rrl 2133 gene rrl rrl 2134 gene rrl rrl 2135 gene rrl rrl 2136 gene rrl rrl 2137 gene rrl rrl 2138 gene rrl rrl 2139 gene rrl rrl 2140 gene rrl rrl 2141 gene rrl rrl 2142 gene rrl rrl 2143 gene rrl rrl 2144 gene rrl rrl 2145 gene rrl rrl 2146 gene rrl rrl 2147 gene rrl rrl 2148 gene rrl rrl 2149 gene rrl rrl 2150 gene rrl rrl 2151 gene rrl rrl 2152 gene rrl rrl 2153 gene rrl rrl 2154 gene rrl rrl 2155 gene rrl rrl 2156 gene rrl rrl 2157 gene rrl rrl 2158 gene rrl rrl 2159 gene rrl rrl 2160 gene rrl rrl 2161 gene rrl rrl 2162 gene rrl rrl 2163 gene rrl rrl 2164 gene rrl rrl 2165 gene rrl rrl 2166 gene rrl rrl 2167 gene rrl rrl 2168 gene rrl rrl 2169 gene rrl rrl 2170 gene rrl rrl 2171 gene rrl rrl 2172 gene rrl rrl 2173 gene rrl rrl 2174 gene rrl rrl 2175 gene rrl rrl 2176 gene rrl rrl 2177 gene rrl rrl 2178 gene rrl rrl 2179 gene rrl rrl 2180 gene rrl rrl 2181 gene rrl rrl 2182 gene rrl rrl 2183 gene rrl rrl 2184 gene rrl rrl 2185 gene rrl rrl 2186 gene rrl rrl 2187 gene rrl rrl 2188 gene rrl rrl 2189 gene rrl rrl 2190 gene rrl rrl 2191 gene rrl rrl 2192 gene rrl rrl 2193 gene rrl rrl 2194 gene rrl rrl 2195 gene rrl rrl 2196 gene rrl rrl 2197 gene rrl rrl 2198 gene rrl rrl 2199 gene rrl rrl 2200 gene rrl rrl 2201 gene rrl rrl 2202 gene rrl rrl 2203 gene rrl rrl 2204 gene rrl rrl 2205 gene rrl rrl 2206 gene rrl rrl 2207 gene rrl rrl 2208 gene rrl rrl 2209 gene rrl rrl 2210 gene rrl rrl 2211 gene rrl rrl 2212 gene rrl rrl 2213 gene rrl rrl 2214 gene rrl rrl 2215 gene rrl rrl 2216 gene rrl rrl 2217 gene rrl rrl 2218 gene rrl rrl 2219 gene rrl rrl 2220 gene rrl rrl 2221 gene rrl rrl 2222 gene rrl rrl 2223 gene rrl rrl 2224 gene rrl rrl 2243 gene rrl rrl 2244 gene rrl rrl 2245 gene rrl rrl 2246 gene rrl rrl 2247 gene rrl rrl 2248 gene rrl rrl 2249 gene rrl rrl 2250 gene rrl rrl 2251 gene rrl rrl 2252 gene rrl rrl 2253 gene rrl rrl 2254 gene rrl rrl 2255 gene rrl rrl 2257 gene rrl rrl 2258 gene rrl rrl 2259 gene rrl rrl 2260 gene rrl rrl 2261 gene rrl rrl 2262 gene rrl rrl 2263 gene rrl rrl 2264 gene rrl rrl 2265 gene rrl rrl 2266 gene rrl rrl 2356 gene rrl rrl 2357 gene rrl rrl 2358 gene rrl rrl 2359 gene rrl rrl 2360 gene rrl rrl 2361 gene rrl rrl 2362 gene rrl rrl 2363 gene rrl rrl 2364 gene rrl rrl 2365 gene rrl rrl 2366 gene rrl rrl 2367 gene rrl rrl 2368 gene rrl rrl 2369 gene rrl rrl 2370 gene rrl rrl 2371 gene rrl rrl 2372 gene rrl rrl 2373 gene rrl rrl 2376 gene rrl rrl 2377 gene rrl rrl 2378 gene rrl rrl 2419 gene rrl rrl 2420 gene rrl rrl 2559 gene rrl rrl 2560 gene rrl rrl 2561 gene rrl rrl 2562 gene rrl rrl 2563 gene rrl rrl 2564 gene rrl rrl 2565 gene rrl rrl 2566 gene rrl rrl 2567 gene rrl rrl 2568 gene rrl rrl 2569 gene rrl rrl 2570 gene rrl rrl 2571 gene rrl rrl 2572 gene rrl rrl 2573 gene rrl rrl 2574 gene rrl rrl 2575 gene rrl rrl 2576 gene rrl rrl 2577 gene rrl rrl 2578 gene rrl rrl 2579 gene rrl rrl 2580 gene rrl rrl 2581 gene rrl rrl 2582 gene rrl rrl 2583 gene rrl rrl 2584 gene rrl rrl 2585 gene rrl rrl 2586 gene rrl rrl 2587 gene rrl rrl 2588 gene rrl rrl 2589 gene rrl rrl 2590 gene rrl rrl 2591 gene rrl rrl 2592 gene rrl rrl 2593 gene rrl rrl 2594 gene rrl rrl 2595 gene rrl rrl 2596 gene rrl rrl 2597 gene rrl rrl 2598 gene rrl rrl 2599 gene rrl rrl 2600 gene rrl rrl 2601 gene rrl rrl 2602 gene rrl rrl 2603 gene rrl rrl 2604 gene rrl rrl 2605 gene rrl rrl 2606 gene rrl rrl 2607 gene rrl rrl 2608 gene rrl rrl 2609 gene rrl rrl 2610 gene rrl rrl 2611 gene rrl rrl 2612 gene rrl rrl 2613 gene rrl rrl 2614 gene rrl rrl 2615 gene rrl rrl 2616 gene rrl rrl 2617 gene rrl rrl 2618 gene rrl rrl 2619 gene rrl rrl 2620 gene rrl rrl 2621 gene rrl rrl 2622 gene rrl rrl 2623 gene rrl rrl 2624 gene rrl rrl 2625 gene rrl rrl 2626 gene rrl rrl 2627 gene rrl rrl 2628 gene rrl rrl 2629 gene rrl rrl 2630 gene rrl rrl 2631 gene rrl rrl 2632 gene rrl rrl 2633 gene rrl rrl 2634 gene rrl rrl 2635 gene rrl rrl 2636 gene rrl rrl 2637 gene rrl rrl 2638 gene rrl rrl 2639 gene rrl rrl 2640 gene rrl rrl 2641 gene rrl rrl 2642 gene rrl rrl 2643 gene rrl rrl 2644 gene rrl rrl 2645 gene rrl rrl 2646 gene rrl rrl 2647 gene rrl rrl 2648 gene rrl rrl 2649 gene rrl rrl 2650 gene rrl rrl 2651 gene rrl rrl 2652 gene rrl rrl 2653 gene rrl rrl 2654 gene rrl rrl 2655 gene rrl rrl 2656 gene rrl rrl 2657 gene rrl rrl 2658 gene rrl rrl 2659 gene rrl rrl 2660 gene rrl rrl 2661 gene rrl rrl 2662 gene rrl rrl 2663 gene rrl rrl 2664 gene rrl rrl 2665 gene rrl rrl 2666 gene rrl rrl 2667 gene rrl rrl 2668 gene rrl rrl 2669 gene rrl rrl 2670 gene rrl rrl 2671 gene rrl rrl 2672 gene rrl rrl 2673 gene rrl rrl 2674 gene rrl rrl 2675 gene rrl rrl 2676 gene rrl rrl 2677 gene rrl rrl 2678 gene rrl rrl 2679 gene rrl rrl 2680 gene rrl rrl 2681 gene rrl rrl 2682 gene rrl rrl 2683 gene rrl rrl 2684 gene rrl rrl 2685 gene rrl rrl 2686 gene rrl rrl 2687 gene rrl rrl 2688 gene rrl rrl 2689 gene rrl rrl 2690 gene rrl rrl 2691 gene rrl rrl 2692 gene rrl rrl 2693 gene rrl rrl 2694 gene rrl rrl 2695 gene rrl rrl 2696 gene rrl rrl 2697 gene rrl rrl 2698 gene rrl rrl 2699 gene rrl rrl 2700 gene rrl rrl 2701 gene rrl rrl 2702 gene rrl rrl 3010 gene rrl rrl 3011 gene rrl rrl 3012 gene rrl rrl 3013 gene rrl rrl 3014 gene rrl rrl 3015 gene rrl rrl 3016 gene rrl rrl 3017 gene rrl rrl 3018 gene rrl rrl 3019 gene rrl rrl 3020 gene rrl rrl 3021 gene rrl rrl 3022 gene rrl rrl 3023 gene rrl rrl 3024 gene rrl rrl 3025 gene rrl rrl 3026 gene rrl rrl 3027 gene rrl rrl 3028 gene rrl rrl 3029 gene rrl rrl 3030 gene rrl rrl 3031 gene rrl rrl 3032 gene rrl rrl 3033 gene rrl rrl 3034 gene rrl rrl 3035 gene rrl rrl 3036 gene rrl rrl 3037 gene rrl rrl 3038 gene rrl rrl 3039 gene rrl rrl 3040 gene rrl rrl 3041 gene rrl rrl 3042 gene rrl rrl 3043 gene rrl rrl 3044 gene rrl rrl 3045 gene rrl rrl 3046 gene rrl rrl 3047 gene rrl rrl 3048 gene rrl rrl 3049 gene rrl rrl 3050 gene rrl rrl 3051 gene rrl rrl 3052 gene rrl rrl 3053 gene rrl rrl 3054 gene rrl rrl 3055 gene rrl rrl 3056 gene rrl rrl 3057 gene rpsA Rv1630 19 codon rpsA Rv1630 20 codon rpsA Rv1630 22 codon rpsA Rv1630 23 codon rpsA Rv1630 24 codon ahpC Rv2428 21 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