Run ID: 608ee43f-1f8d-4e39-adc0-5b7ddaff292f
Sample name:
Date: 01-03-2023 14:30:05
Number of reads: 2958335
Percentage reads mapped: 96.44
Median coverage: 76
Strain: La1.4
Spoligotype:
Drug-resistance: Other
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| La1 | M.bovis | None | 0.99 |
| La1.4 | M.bovis | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | pncA | p.His57Asp | Assoc w R | |
| 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 |
|---|---|---|---|---|---|---|---|
| pncA | 2289073 | p.His57Asp | missense_variant | 1.0 | pyrazinamide | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 5752 | c.513G>A | synonymous_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 6406 | c.-896C>T | upstream_gene_variant | 0.97 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrB | 6446 | p.Ala403Ser | missense_variant | 0.97 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 8285 | c.984C>T | synonymous_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 8864 | c.1563C>T | synonymous_variant | 0.99 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 9143 | c.1842T>C | synonymous_variant | 0.99 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | delamanid | |
| mshA | 576108 | p.Ala254Gly | missense_variant | 0.3 | ethionamide | Uncertain significance |
| isoniazid | ||||||
| mshA | 576613 | c.1266A>C | synonymous_variant | 0.3 | ethionamide | |
| isoniazid | ||||||
| mshA | 576616 | c.1269G>C | synonymous_variant | 0.17 | ethionamide | |
| isoniazid | ||||||
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.97 | rifampicin | |
| rpoC | 764367 | p.Gly333Ala | missense_variant | 0.21 | rifampicin | |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 0.98 | delamanid | Uncertain significance |
| fbiC | 1303545 | c.615A>G | synonymous_variant | 1.0 | delamanid | |
| embR | 1416989 | c.358delA | frameshift_variant | 0.97 | ethambutol | Uncertain significance |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| fabG1 | 1673553 | p.Asp38Glu | missense_variant | 0.23 | ethionamide | |
| isoniazid | ||||||
| rpsA | 1834859 | p.Ala440Thr | missense_variant | 1.0 | pyrazinamide | |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | |
| ndh | 2103173 | c.-132delG | upstream_gene_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
| katG | 2155503 | c.609C>T | synonymous_variant | 1.0 | isoniazid | |
| katG | 2156025 | c.87C>A | synonymous_variant | 0.95 | isoniazid | |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2168011 | p.Ser868Arg | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2168814 | c.1798dupA | frameshift_variant | 0.99 | pyrazinamide | |
| PPE35 | 2170035 | p.Val193Gly | missense_variant | 0.26 | pyrazinamide | |
| PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.12 | pyrazinamide | |
| PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.11 | pyrazinamide | |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.99 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| pepQ | 2859931 | p.Leu163Arg | missense_variant | 0.26 | clofazimine | |
| bedaquiline | ||||||
| pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.25 | clofazimine | |
| bedaquiline | ||||||
| ald | 3086728 | c.-92C>T | upstream_gene_variant | 0.97 | cycloserine | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.99 | cycloserine | |
| ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | |
| ald | 3087364 | p.Asn182Thr | missense_variant | 1.0 | cycloserine | |
| ald | 3087816 | p.Cys333Gly | missense_variant | 0.16 | cycloserine | |
| fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.36 | delamanid | |
| fbiD | 3339749 | p.Val211Ala | missense_variant | 0.27 | delamanid | |
| Rv3083 | 3448783 | p.Val94Ile | missense_variant | 1.0 | ethionamide | Uncertain significance |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| fprA | 3474427 | p.Val141Ile | missense_variant | 0.97 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| fprA | 3474651 | c.645G>T | synonymous_variant | 0.98 | capreomycin | |
| amikacin | ||||||
| fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| clpC1 | 4038403 | c.2302T>C | synonymous_variant | 1.0 | pyrazinamide | |
| embC | 4240409 | p.Pro183Ala | missense_variant | 0.28 | ethambutol | |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 | ethambutol | |
| embA | 4242970 | c.-263C>T | upstream_gene_variant | 1.0 | ethambutol | |
| embA | 4244220 | c.988C>T | synonymous_variant | 1.0 | ethambutol | |
| embB | 4246544 | p.Thr11Pro | missense_variant | 0.1 | ethambutol | Uncertain significance |
| embB | 4246548 | p.Pro12Gln | missense_variant | 0.11 | ethambutol | Uncertain significance |
| embB | 4246551 | p.Asn13Ser | missense_variant | 0.88 | ethambutol | Uncertain significance |
| embB | 4246864 | c.351C>T | synonymous_variant | 1.0 | ethambutol | |
| embB | 4247028 | p.Leu172Arg | missense_variant | 0.38 | ethambutol | Uncertain significance |
| embB | 4247041 | p.Phe176Leu | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4248328 | c.1815G>C | synonymous_variant | 0.15 | ethambutol | |
| aftB | 4267858 | p.Ile327Val | missense_variant | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| aftB | 4268619 | p.Val73Gly | missense_variant | 0.24 | capreomycin | |
| amikacin | ||||||
| aftB | 4269351 | c.-515C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Uncertain significance |
| aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin |
