Run ID: 4af3ebef-9c1e-41d1-a02e-e48b46af3b4c
Sample name:
Date: 30-11-2023 07:25:15
Number of reads: 1088261
Percentage reads mapped: 93.84
Median coverage: 23
Strain: La1.4
Spoligotype:
Drug-resistance: Other
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| La1 | M.bovis | None | 1.0 |
| La1.4 | M.bovis | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | pncA | p.His57Asp | Assoc w R | |
| p.Leu35Pro | Uncertain significance | |||
| 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 | 0.97 | pyrazinamide | Assoc w R | |
| pncA | 2289138 | p.Leu35Pro | missense_variant | 0.14 | pyrazinamide | Uncertain significance |
| 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 | 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 | 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 | 8570 | p.Glu423Asp | missense_variant | 0.12 | 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 | 9688 | p.Arg796Gln | missense_variant | 0.29 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| fgd1 | 490840 | p.Leu20Ile | missense_variant | 0.11 | delamanid | |
| fgd1 | 491528 | p.Trp249* | stop_gained | 0.12 | delamanid | |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | delamanid | |
| mshA | 575651 | p.Arg102Trp | missense_variant | 0.11 | ethionamide | |
| isoniazid | ||||||
| rpoB | 759817 | p.Ser4Tyr | missense_variant | 0.12 | rifampicin | |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 | 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 | 777290 | c.1191G>A | synonymous_variant | 0.14 | clofazimine | |
| bedaquiline | ||||||
| mmpS5 | 778526 | p.Thr127Ile | missense_variant | 0.15 | 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 | 1.0 | delamanid | |
| Rv1258c | 1407446 | c.-106G>T | upstream_gene_variant | 0.11 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| Rv1258c | 1407466 | c.-126G>T | upstream_gene_variant | 0.14 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| embR | 1416989 | c.358delA | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrl | 1474519 | n.862G>T | non_coding_transcript_exon_variant | 0.18 | linezolid | |
| rrl | 1476088 | n.2431A>C | non_coding_transcript_exon_variant | 0.13 | linezolid | |
| rrl | 1476095 | n.2438C>T | non_coding_transcript_exon_variant | 0.13 | linezolid | |
| rrl | 1476103 | n.2446C>G | non_coding_transcript_exon_variant | 0.13 | linezolid | |
| rrl | 1476105 | n.2448G>A | non_coding_transcript_exon_variant | 0.13 | linezolid | |
| rrl | 1476106 | n.2449A>T | non_coding_transcript_exon_variant | 0.13 | linezolid | |
| rrl | 1476110 | n.2453G>C | non_coding_transcript_exon_variant | 0.13 | linezolid | |
| rrl | 1476115 | n.2458T>C | non_coding_transcript_exon_variant | 0.11 | linezolid | |
| rrl | 1476131 | n.2474C>T | non_coding_transcript_exon_variant | 0.12 | linezolid | |
| rpsA | 1834859 | p.Ala440Thr | missense_variant | 1.0 | pyrazinamide | |
| rpsA | 1834964 | c.1428delA | frameshift_variant | 0.14 | pyrazinamide | |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | |
| ndh | 2102353 | p.Gln230His | missense_variant | 0.12 | ethionamide | |
| isoniazid | Uncertain significance | |||||
| ndh | 2103173 | c.-132delG | upstream_gene_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| katG | 2154724 | p.Arg463Leu | missense_variant | 0.97 | isoniazid | Uncertain significance |
| katG | 2155158 | c.954G>A | synonymous_variant | 0.12 | isoniazid | |
| katG | 2155461 | c.651G>A | synonymous_variant | 0.1 | isoniazid | |
| katG | 2155503 | c.609C>T | synonymous_variant | 1.0 | isoniazid | |
| katG | 2156025 | c.87C>A | synonymous_variant | 1.0 | isoniazid | |
| katG | 2156262 | c.-151C>T | upstream_gene_variant | 0.15 | 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 | 0.96 | pyrazinamide | |
| 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 | |||||
| pncA | 2290167 | c.-926G>T | upstream_gene_variant | 0.1 | pyrazinamide | |
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| pepQ | 2860342 | p.Asp26Gly | missense_variant | 0.11 | clofazimine | Uncertain significance |
| bedaquiline | 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 | |
| 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 | 3474651 | c.645G>T | synonymous_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| whiB7 | 3568605 | c.75C>G | synonymous_variant | 0.12 | streptomycin | |
| kanamycin | ||||||
| amikacin | ||||||
| rpoA | 3878630 | c.-124delC | upstream_gene_variant | 1.0 | rifampicin | |
| clpC1 | 4038403 | c.2302T>C | synonymous_variant | 1.0 | pyrazinamide | |
| clpC1 | 4040293 | p.Val138Leu | missense_variant | 0.11 | pyrazinamide | |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embC | 4240954 | c.1096delC | frameshift_variant | 0.12 | ethambutol | |
| 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 | 4246551 | p.Asn13Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
| 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 | 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 | ||||||
| ethA | 4326205 | c.1269C>A | synonymous_variant | 0.13 | ethionamide | |
| 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 |
