Run ID: ERR12976101
Sample name:
Date: 2024-05-22T17:08:27.398015
Number of reads: 1615031
Percentage reads mapped: 99.54
Median coverage: 62.0
Strain: La1.2
Spoligotype:
Drug-resistance: Other
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| La1.2 | M.bovis | None | 0.81 |
| 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 | fbiC | c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| fbiC | 1305494 | c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | frameshift_variant&stop_lost&splice_region_variant | 1.0 | pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance | |||||
| 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 | |||||
| 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 | 8741 | c.1440C>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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| 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 | clofazimine | Not assoc w R |
| pretomanid | ||||||
| delamanid | Not assoc w R - Interim | |||||
| 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 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpS5 | 779592 | c.-687A>G | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| 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 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| Rv1129c | 1254582 | c.-48A>G | upstream_gene_variant | 1.0 | moxifloxacin | Uncertain significance |
| levofloxacin | Uncertain significance | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
| pretomanid | ||||||
| delamanid | Uncertain significance | |||||
| sigE | 1364961 | c.549A>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| Rv1258c | 1406522 | c.819G>A | synonymous_variant | 1.0 | streptomycin | |
| isoniazid | ||||||
| pyrazinamide | ||||||
| embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rpsA | 1834859 | p.Ala440Thr | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| bacA | 2062922 | p.Ile603Val | missense_variant | 0.99 | streptomycin | Not assoc w R |
| kanamycin | Not assoc w R | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| ndh | 2102106 | p.Gly313Arg | missense_variant | 1.0 | ethionamide | Uncertain significance |
| delamanid | Uncertain significance | |||||
| isoniazid | Not assoc w R - Interim | |||||
| ndh | 2103173 | c.-132delG | upstream_gene_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| 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 |
| katG | 2156465 | c.-354C>T | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| 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 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv1979c | 2223264 | c.-100C>T | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| Rv2477c | 2782927 | c.1116A>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| moxifloxacin | Not assoc w R - Interim | |||||
| streptomycin | Not assoc w R | |||||
| levofloxacin | Not assoc w R - Interim | |||||
| kanamycin | Not assoc w R - Interim | |||||
| rifampicin | Not assoc w R | |||||
| amikacin | Not assoc w R - Interim | |||||
| 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 | |
| ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | |
| fbiD | 3339154 | p.Ile13Leu | missense_variant | 1.0 | clofazimine | Uncertain significance |
| pretomanid | ||||||
| delamanid | Uncertain significance | |||||
| Rv3083 | 3448745 | p.Ile81Ser | missense_variant | 1.0 | ethionamide | Uncertain significance |
| Rv3083 | 3448783 | p.Val94Ile | missense_variant | 1.0 | ethionamide | Uncertain significance |
| lpqB | 3623730 | p.Ser394Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| lpqB | 3624350 | c.561G>T | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| rifampicin | Not assoc w R | |||||
| lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| lpqB | 3624593 | c.318G>A | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| rifampicin | Not assoc w R | |||||
| lpqB | 3624710 | c.201G>A | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| rifampicin | Not assoc w R | |||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| 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 | ethambutol | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242970 | c.3108C>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 | 4246551 | p.Asn13Ser | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4246864 | c.351C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4247173 | c.660G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4248342 | p.Thr610Lys | missense_variant | 1.0 | ethambutol | |
| aftB | 4267858 | p.Ile327Val | missense_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 | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
