Run ID: ERR11268039
Sample name:
Date: 2024-10-05T10:43:19.156733
Number of reads: 271881
Percentage reads mapped: 96.6
Median coverage: 13.0
Strain: La1.6
Spoligotype:
Drug-resistance: Other
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| La1.6 | M.bovis | None | 1.0 |
| La1 | M.bovis | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | pncA | p.His57Asp | Assoc w R | |
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| pncA | 2289073 | p.His57Asp | missense_variant | 1.0 | pyrazinamide | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| dnaA | 467 | p.His156Arg | missense_variant | 1.0 | isoniazid | Not assoc w R |
| gyrB | 5752 | c.513G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrB | 6406 | c.1167C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrB | 6446 | p.Ala403Ser | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Uncertain significance | |||||
| gyrB | 7042 | c.1803C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 8285 | c.984C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9217 | p.Asp639Ala | missense_variant | 0.77 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| gyrA | 9304 | p.Gly668Glu | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| Rv0010c | 13197 | p.Thr121Ser | missense_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13228 | c.330delG | frameshift_variant | 1.0 | isoniazid | Uncertain significance |
| Rv0010c | 13460 | c.99T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
| delamanid | Not assoc w R - Interim | |||||
| clofazimine | Not assoc w R | |||||
| Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| Rv1129c | 1254582 | c.-48A>G | upstream_gene_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | Uncertain significance | |||||
| clofazimine | Uncertain significance | |||||
| embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1474045 | n.388C>T | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1474054 | n.397T>C | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1474083 | n.426C>T | non_coding_transcript_exon_variant | 0.58 | capreomycin | Uncertain significance |
| linezolid | ||||||
| inhA | 1674342 | c.141T>C | synonymous_variant | 0.26 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674353 | p.Thr51Ile | missense_variant | 0.27 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674368 | p.Ala56Glu | missense_variant | 0.25 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674370 | p.Lys57Pro | missense_variant | 0.25 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674375 | c.174C>G | synonymous_variant | 0.28 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674399 | c.198A>G | synonymous_variant | 0.27 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674403 | p.Glu68Asn | missense_variant | 0.29 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674414 | c.213G>C | synonymous_variant | 0.26 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674416 | p.Ala72Asp | missense_variant | 0.26 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674419 | p.Ser73Thr | missense_variant | 0.26 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674421 | c.220T>C | synonymous_variant | 0.26 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674428 | p.Gly76Asp | missense_variant | 0.3 | isoniazid | Uncertain significance |
| ethionamide | Uncertain significance | |||||
| inhA | 1674435 | c.234G>C | synonymous_variant | 0.3 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674471 | c.270G>T | synonymous_variant | 0.35 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674507 | c.306G>C | synonymous_variant | 0.41 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674534 | c.333G>C | synonymous_variant | 0.44 | isoniazid | Not assoc w R - Interim |
| ethionamide | ||||||
| inhA | 1674539 | p.Tyr113Phe | missense_variant | 0.44 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674542 | p.Ala114Glu | missense_variant | 0.44 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674546 | c.345T>C | synonymous_variant | 0.47 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674549 | c.348G>C | synonymous_variant | 0.47 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674550 | p.Ser117Ala | missense_variant | 0.44 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674579 | c.378G>C | synonymous_variant | 0.45 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674585 | c.384T>C | synonymous_variant | 0.45 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674589 | p.Met130Leu | missense_variant | 0.43 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674597 | c.396G>A | synonymous_variant | 0.48 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674600 | c.399G>C | synonymous_variant | 0.48 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674618 | c.417C>T | synonymous_variant | 0.46 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674624 | c.423A>C | synonymous_variant | 0.48 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674627 | c.426T>C | synonymous_variant | 0.45 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674628 | p.Ser143Gly | missense_variant | 0.45 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674654 | c.453G>C | synonymous_variant | 0.52 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674656 | p.Ser152Thr | missense_variant | 0.55 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674690 | c.489C>G | synonymous_variant | 0.48 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674693 | c.492C>A | synonymous_variant | 0.46 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674702 | c.501G>A | synonymous_variant | 0.42 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674703 | c.502T>C | synonymous_variant | 0.39 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674714 | c.513C>G | synonymous_variant | 0.41 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674718 | c.517A>C | synonymous_variant | 0.41 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674729 | c.528G>A | synonymous_variant | 0.47 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674745 | p.Tyr182Val | missense_variant | 0.53 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674750 | c.549T>C | synonymous_variant | 0.5 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674756 | c.555T>G | synonymous_variant | 0.53 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674765 | c.564C>G | synonymous_variant | 0.56 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674774 | c.573A>C | synonymous_variant | 0.53 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674777 | c.576C>G | synonymous_variant | 0.53 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674780 | c.579T>G | synonymous_variant | 0.56 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674801 | c.600T>C | synonymous_variant | 0.47 | isoniazid | |
| ethionamide | ||||||
| rpsA | 1834859 | p.Ala440Thr | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| tsnR | 1854289 | c.684C>T | synonymous_variant | 1.0 | linezolid | |
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| bacA | 2064293 | p.Thr146Ala | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| ndh | 2102121 | p.Asp308Asn | missense_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| ndh | 2103173 | c.-132delG | upstream_gene_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| katG | 2155503 | c.609C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| katG | 2156025 | c.87C>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2168011 | p.Ser868Arg | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2168814 | c.1798dupA | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv1979c | 2223062 | p.Thr35Ala | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| folC | 2746245 | p.Ala452Thr | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ribD | 2987615 | c.777A>G | stop_lost&splice_region_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2681 | 2997325 | p.Ala196Val | missense_variant | 1.0 | capreomycin | Uncertain significance |
| ald | 3086728 | c.-92C>T | upstream_gene_variant | 1.0 | cycloserine | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| lpqB | 3624350 | c.561G>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| lpqB | 3624710 | c.201G>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| rpoA | 3878630 | c.-124delC | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| clpC1 | 4038403 | c.2302T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| ethambutol | Not assoc w R | |||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4244220 | c.988C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4246864 | c.351C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269351 | c.483C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269606 | c.228T>C | synonymous_variant | 0.95 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
| gid | 4408265 | c.-63T>C | upstream_gene_variant | 1.0 | streptomycin |
