Run ID: 00daa22b-52d7-44ac-b2ac-c6153d5f38ce
Sample name:
Date: 29-11-2023 03:44:22
Number of reads: 1221954
Percentage reads mapped: 87.2
Median coverage: 26
Strain: La1.4
Spoligotype:
Drug-resistance: Other
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| La1 | M.bovis | None | 1.0 |
| La1.4 | M.bovis | None | 0.99 |
| 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 | ||||||
| gyrB | 6038 | p.Thr267Ala | missense_variant | 0.12 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 6406 | c.-896C>T | upstream_gene_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrB | 6446 | p.Ala403Ser | missense_variant | 1.0 | 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 | 7750 | p.Val150Gly | missense_variant | 0.13 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 7784 | c.483A>G | synonymous_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 8243 | c.942C>T | synonymous_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 8285 | c.984C>T | synonymous_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 9333 | p.Gly678Trp | missense_variant | 0.2 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| fgd1 | 490909 | p.Pro43Ser | missense_variant | 0.11 | delamanid | |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | delamanid | |
| rpoB | 761152 | p.Leu449Gln | missense_variant | 0.12 | rifampicin | |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 | rifampicin | |
| rpoC | 764920 | c.1551G>T | synonymous_variant | 0.11 | rifampicin | |
| rpoC | 766291 | c.2922G>T | synonymous_variant | 0.1 | 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 | |||||
| mmpL5 | 776249 | p.Glu744Asp | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| mmpL5 | 778344 | p.Leu46His | missense_variant | 0.12 | clofazimine | |
| bedaquiline | ||||||
| mmpL5 | 778422 | p.Ala20Glu | missense_variant | 0.12 | clofazimine | |
| bedaquiline | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 | delamanid | Uncertain significance |
| fbiC | 1303545 | c.615A>G | synonymous_variant | 0.96 | delamanid | |
| embR | 1416659 | p.Arg230Leu | missense_variant | 0.12 | ethambutol | |
| embR | 1416989 | c.358delA | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
| embR | 1417259 | p.Ser30Leu | missense_variant | 0.15 | ethambutol | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| 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 | 2155492 | p.Asp207Gly | missense_variant | 0.11 | isoniazid | |
| katG | 2155503 | c.609C>T | synonymous_variant | 1.0 | isoniazid | |
| katG | 2156025 | c.87C>A | synonymous_variant | 1.0 | isoniazid | |
| katG | 2156420 | c.-309A>T | upstream_gene_variant | 0.12 | isoniazid | |
| katG | 2156422 | c.-311C>A | upstream_gene_variant | 0.12 | isoniazid | |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2168007 | p.Ile869Thr | missense_variant | 0.11 | pyrazinamide | |
| PPE35 | 2168011 | p.Ser868Arg | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2168814 | c.1798dupA | frameshift_variant | 1.0 | pyrazinamide | |
| PPE35 | 2170085 | c.528G>T | synonymous_variant | 0.11 | pyrazinamide | |
| Rv1979c | 2221785 | c.1380G>A | synonymous_variant | 0.12 | clofazimine | |
| bedaquiline | ||||||
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | 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 | |
| ahpC | 2726558 | c.366A>T | synonymous_variant | 0.12 | isoniazid | |
| Rv2752c | 3066297 | c.-106G>A | upstream_gene_variant | 0.12 | rifampicin | |
| isoniazid | ||||||
| Rv2752c | 3066349 | c.-158T>C | upstream_gene_variant | 0.15 | rifampicin | |
| isoniazid | ||||||
| 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 | |
| ald | 3087364 | p.Asn182Thr | missense_variant | 1.0 | cycloserine | |
| 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 | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| fprA | 3474651 | c.645G>T | synonymous_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| Rv3236c | 3612072 | p.Pro349Thr | missense_variant | 0.15 | pyrazinamide | |
| Rv3236c | 3612702 | p.Asp139His | missense_variant | 0.1 | pyrazinamide | |
| fbiB | 3641706 | p.Gly58Arg | missense_variant | 0.11 | delamanid | |
| fbiB | 3642603 | p.Ala357Thr | missense_variant | 1.0 | delamanid | |
| rpoA | 3878630 | c.-124delC | upstream_gene_variant | 1.0 | rifampicin | |
| clpC1 | 4038403 | c.2302T>C | synonymous_variant | 1.0 | pyrazinamide | |
| clpC1 | 4040611 | p.His32Tyr | missense_variant | 0.11 | pyrazinamide | |
| embC | 4239852 | c.-11G>A | upstream_gene_variant | 0.12 | 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 | |
| embC | 4243020 | p.Trp1053Leu | missense_variant | 0.2 | ethambutol | |
| embA | 4243621 | p.Thr130Met | missense_variant | 0.12 | ethambutol | |
| embA | 4244220 | c.988C>T | synonymous_variant | 1.0 | ethambutol | |
| embA | 4245685 | p.Pro818Gln | missense_variant | 0.11 | ethambutol | |
| embB | 4246551 | p.Asn13Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4246834 | c.321G>A | synonymous_variant | 0.15 | ethambutol | |
| embB | 4246864 | c.351C>T | synonymous_variant | 1.0 | ethambutol | |
| embB | 4246991 | p.Asn160Asp | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4248027 | p.Ala505Asp | missense_variant | 0.19 | ethambutol | |
| embB | 4248386 | c.1873C>A | synonymous_variant | 0.12 | ethambutol | |
| embB | 4248469 | c.1956C>T | synonymous_variant | 1.0 | ethambutol | |
| aftB | 4267858 | p.Ile327Val | missense_variant | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| 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 | |
| gid | 4408011 | c.192G>A | synonymous_variant | 0.11 | streptomycin |
