Run ID: e2627943-2c91-4f00-b46e-d80609bbe405
Sample name:
Date: 13-07-2023 08:54:49
Number of reads: 159257
Percentage reads mapped: 9.65
Median coverage: 3
Strain: lineage4;lineage1.2.1.2.1
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 0.12 |
| lineage1 | Indo-Oceanic | RD239 | 0.91 |
| lineage1.2.1 | Indo-Oceanic | RD239 | 0.94 |
| lineage1.2.1.2 | Indo-Oceanic | RD239 | 0.96 |
| lineage1.2.1.2.1 | Indo-Oceanic | RD239 | 0.97 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| moxifloxacin | ||||
| levofloxacin | ||||
| bedaquiline | ||||
| delamanid | ||||
| pretomanid | ||||
| linezolid | ||||
| streptomycin | ||||
| amikacin | ||||
| kanamycin | ||||
| capreomycin | ||||
| clofazimine | ||||
| ethionamide | ||||
| para-aminosalicylic_acid | ||||
| cycloserine |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrA | 7541 | c.240C>G | synonymous_variant | 0.2 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 7547 | c.246C>T | synonymous_variant | 0.2 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| fbiC | 1303708 | c.778T>C | synonymous_variant | 0.2 | delamanid | |
| fbiC | 1303750 | c.820_822delTTAinsCTG | synonymous_variant | 0.15 | delamanid | |
| fbiC | 1303764 | c.834C>T | synonymous_variant | 0.17 | delamanid | |
| fbiC | 1303769 | p.Ser280Leu | missense_variant | 0.17 | delamanid | |
| fbiC | 1303776 | c.846G>A | synonymous_variant | 0.14 | delamanid | |
| fbiC | 1303782 | c.852C>T | synonymous_variant | 0.14 | delamanid | |
| fbiC | 1303785 | c.855G>C | synonymous_variant | 0.14 | delamanid | |
| fbiC | 1303788 | c.858T>C | synonymous_variant | 0.17 | delamanid | |
| fbiC | 1303789 | p.Ile287Val | missense_variant | 0.17 | delamanid | |
| fbiC | 1303794 | c.864A>G | synonymous_variant | 0.14 | delamanid | |
| fbiC | 1303809 | c.879G>A | synonymous_variant | 0.17 | delamanid | |
| fbiC | 1303811 | p.Asn294Ser | missense_variant | 0.17 | delamanid | |
| fbiC | 1303818 | c.888C>G | synonymous_variant | 0.14 | delamanid | |
| fbiC | 1303836 | c.906G>A | synonymous_variant | 0.17 | delamanid | |
| fbiC | 1303842 | c.912C>A | synonymous_variant | 0.17 | delamanid | |
| fbiC | 1303845 | c.915C>G | synonymous_variant | 0.17 | delamanid | |
| fbiC | 1303846 | p.Phe306Val | missense_variant | 0.17 | delamanid | |
| fbiC | 1303854 | c.924T>C | synonymous_variant | 0.17 | delamanid | |
| fbiC | 1303884 | c.954T>C | synonymous_variant | 0.17 | delamanid | |
| fbiC | 1303890 | c.960G>C | synonymous_variant | 0.2 | delamanid | |
| fbiC | 1303893 | c.963G>C | synonymous_variant | 0.2 | delamanid | |
| fbiC | 1305320 | p.Gln797Arg | missense_variant | 0.14 | delamanid | |
| rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.55 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.7 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472541 | n.696T>G | non_coding_transcript_exon_variant | 0.73 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.77 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472553 | n.708C>T | non_coding_transcript_exon_variant | 0.79 | linezolid | |
| kanamycin | ||||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| aminoglycosides | ||||||
| streptomycin | Uncertain significance | |||||
| rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.79 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472572 | n.727T>C | non_coding_transcript_exon_variant | 0.79 | linezolid | |
| kanamycin | Uncertain significance | |||||
| capreomycin | ||||||
| amikacin | Uncertain significance | |||||
| aminoglycosides | ||||||
| streptomycin | Uncertain significance | |||||
| rrs | 1472574 | n.729T>C | non_coding_transcript_exon_variant | 0.79 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472579 | n.734G>A | non_coding_transcript_exon_variant | 0.92 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472582 | n.737G>A | non_coding_transcript_exon_variant | 0.92 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472583 | n.738T>A | non_coding_transcript_exon_variant | 0.92 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472584 | n.739A>G | non_coding_transcript_exon_variant | 0.92 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472594 | n.749G>C | non_coding_transcript_exon_variant | 0.88 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472598 | n.753A>T | non_coding_transcript_exon_variant | 0.94 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.83 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.79 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472658 | n.813G>T | non_coding_transcript_exon_variant | 0.79 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472659 | n.814G>C | non_coding_transcript_exon_variant | 0.79 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472660 | n.815T>G | non_coding_transcript_exon_variant | 0.78 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472664 | n.819A>T | non_coding_transcript_exon_variant | 0.67 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472664 | n.818_819insTGG | non_coding_transcript_exon_variant | 0.6 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472667 | n.821_822insAGGT | non_coding_transcript_exon_variant | 0.67 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472667 | n.823delG | non_coding_transcript_exon_variant | 0.6 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472707 | n.862A>G | non_coding_transcript_exon_variant | 0.67 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472714 | n.869A>C | non_coding_transcript_exon_variant | 0.78 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472715 | n.870C>G | non_coding_transcript_exon_variant | 0.79 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472716 | n.871C>A | non_coding_transcript_exon_variant | 0.79 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.86 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.79 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.79 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.72 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472805 | n.960C>A | non_coding_transcript_exon_variant | 0.14 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472806 | n.961A>T | non_coding_transcript_exon_variant | 0.14 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472813 | n.968A>G | non_coding_transcript_exon_variant | 0.12 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472824 | n.979T>A | non_coding_transcript_exon_variant | 0.21 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472827 | n.982G>C | non_coding_transcript_exon_variant | 0.22 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472828 | n.983T>C | non_coding_transcript_exon_variant | 0.3 | linezolid | |
| kanamycin | Uncertain significance | |||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | Uncertain significance | |||||
| rrs | 1472887 | n.1042G>C | non_coding_transcript_exon_variant | 0.4 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472895 | n.1050C>T | non_coding_transcript_exon_variant | 0.2 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472896 | n.1051T>G | non_coding_transcript_exon_variant | 0.17 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472912 | n.1067C>T | non_coding_transcript_exon_variant | 0.31 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472917 | n.1072G>A | non_coding_transcript_exon_variant | 0.31 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472951 | n.1106T>C | non_coding_transcript_exon_variant | 0.2 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.25 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.55 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1473191 | n.1346C>T | non_coding_transcript_exon_variant | 0.55 | linezolid | |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.18 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1473198 | n.1354delC | non_coding_transcript_exon_variant | 0.55 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1473201 | n.1356A>G | non_coding_transcript_exon_variant | 0.18 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.73 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.18 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | Uncertain significance | |||||
| rrs | 1473206 | n.1361G>A | non_coding_transcript_exon_variant | 0.55 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.71 | linezolid | |
| rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.78 | linezolid | |
| rrl | 1475858 | n.2201T>C | non_coding_transcript_exon_variant | 0.12 | linezolid | |
| rrl | 1475874 | n.2217C>T | non_coding_transcript_exon_variant | 0.33 | linezolid | |
| rrl | 1475883 | n.2226A>C | non_coding_transcript_exon_variant | 0.4 | linezolid | |
| rrl | 1475884 | n.2227A>G | non_coding_transcript_exon_variant | 0.4 | linezolid | |
| rrl | 1475892 | n.2235A>G | non_coding_transcript_exon_variant | 0.4 | linezolid | |
| rrl | 1475897 | n.2240T>C | non_coding_transcript_exon_variant | 0.4 | linezolid | |
| rrl | 1475900 | n.2243A>G | non_coding_transcript_exon_variant | 0.4 | linezolid | |
| rrl | 1475902 | n.2245T>C | non_coding_transcript_exon_variant | 0.4 | linezolid | |
| rrl | 1475906 | n.2249C>T | non_coding_transcript_exon_variant | 0.4 | linezolid | Uncertain significance |
| rrl | 1475916 | n.2259C>A | non_coding_transcript_exon_variant | 0.4 | linezolid | |
| rrl | 1475919 | n.2262C>T | non_coding_transcript_exon_variant | 0.4 | linezolid | |
| rrl | 1476252 | n.2595T>G | non_coding_transcript_exon_variant | 0.7 | linezolid | |
| rrl | 1476256 | n.2599A>G | non_coding_transcript_exon_variant | 0.4 | linezolid | |
| rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 0.7 | linezolid | |
| rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.4 | linezolid | |
| rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.5 | linezolid | |
| rrl | 1476297 | n.2640C>G | non_coding_transcript_exon_variant | 0.7 | linezolid | |
| rrl | 1476298 | n.2641C>G | non_coding_transcript_exon_variant | 0.7 | linezolid | |
| rrl | 1476300 | n.2643G>T | non_coding_transcript_exon_variant | 0.62 | linezolid | |
| rrl | 1476301 | n.2644A>T | non_coding_transcript_exon_variant | 0.44 | linezolid | |
| rrl | 1476309 | n.2652G>C | non_coding_transcript_exon_variant | 0.78 | linezolid | |
| rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.36 | linezolid | |
| rrl | 1476321 | n.2664A>T | non_coding_transcript_exon_variant | 0.25 | linezolid | |
| rrl | 1476322 | n.2665C>A | non_coding_transcript_exon_variant | 0.25 | linezolid | |
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.54 | linezolid | |
| rrl | 1476337 | n.2680C>T | non_coding_transcript_exon_variant | 0.17 | linezolid | |
| rrl | 1476353 | n.2696G>A | non_coding_transcript_exon_variant | 0.5 | linezolid | |
| rrl | 1476354 | n.2697A>G | non_coding_transcript_exon_variant | 0.5 | linezolid | |
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.56 | linezolid | |
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.33 | linezolid | |
| rrl | 1476368 | n.2711T>C | non_coding_transcript_exon_variant | 0.48 | linezolid | |
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.67 | linezolid | |
| rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.5 | linezolid | |
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.28 | linezolid | |
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.68 | linezolid | |
| rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.65 | linezolid | |
| rrl | 1476388 | n.2731T>C | non_coding_transcript_exon_variant | 0.58 | linezolid | |
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.11 | linezolid | |
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.74 | linezolid | |
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.2 | linezolid | |
| rrl | 1476428 | n.2771C>A | non_coding_transcript_exon_variant | 1.0 | linezolid | |
| rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 1.0 | linezolid | |
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.12 | linezolid | |
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.15 | linezolid | |
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.5 | linezolid | |
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.2 | linezolid | Uncertain significance |
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.32 | linezolid | |
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.54 | linezolid | |
| ald | 3086655 | c.-164delA | upstream_gene_variant | 0.17 | cycloserine | |
| alr | 3841312 | p.Glu37* | stop_gained | 0.17 | cycloserine | |
| embC | 4240204 | c.344delA | frameshift_variant | 0.2 | ethambutol | |
| aftB | 4268105 | c.732T>C | synonymous_variant | 0.18 | capreomycin | |
| amikacin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin |
