Run ID: a2dcf15a-3170-48e5-8d01-999e3a4f5c5e
Sample name:
Date: 25-05-2023 17:35:06
Number of reads: 7220164
Percentage reads mapped: 98.7
Median coverage: 224
Strain: lineage6.3.1;lineage6.2;lineage6.1.3
Spoligotype:
Drug-resistance: Other
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage6 | West-Africa 2 | RD702 | 1.0 |
| lineage6.2 | West-Africa 2 | RD702 | 0.31 |
| lineage6.3 | West-Africa 2 | RD702 | 0.35 |
| lineage6.1.3 | West-Africa 2 | RD702 | 0.32 |
| lineage6.3.1 | West-Africa 2 | RD702 | 0.37 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | embC | p.Ala307Thr | Uncertain significance | |
| pyrazinamide | ||||
| 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 |
|---|---|---|---|---|---|---|---|
| embC | 4240781 | p.Ala307Thr | missense_variant | 0.36 | ethambutol | Uncertain significance |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 5072 | c.-168G>T | upstream_gene_variant | 0.38 | 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 | 7373 | p.Met24Ile | missense_variant | 0.33 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 8333 | c.1032C>T | synonymous_variant | 0.36 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 8493 | p.Leu398Phe | missense_variant | 0.6 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 8806 | p.Asp502Gly | missense_variant | 0.32 | 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 | ||||||
| fgd1 | 491668 | p.Lys296Glu | missense_variant | 1.0 | delamanid | Uncertain significance |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | delamanid | |
| rpoB | 760855 | p.Thr350Ile | missense_variant | 0.35 | rifampicin | Uncertain significance |
| rpoB | 760969 | p.Ser388Leu | missense_variant | 1.0 | rifampicin | Uncertain significance |
| rpoB | 761723 | p.Glu639Asp | missense_variant | 1.0 | rifampicin | Uncertain significance |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 | rifampicin | |
| rpoC | 764731 | c.1362G>T | synonymous_variant | 0.26 | rifampicin | |
| rpoC | 766231 | c.2862T>C | synonymous_variant | 0.34 | 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 | 779469 | c.-989T>C | upstream_gene_variant | 0.38 | 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 |
| Rv1258c | 1406685 | p.Val219Ala | missense_variant | 0.68 | streptomycin | Uncertain significance |
| pyrazinamide | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| embR | 1416633 | p.Leu239Val | missense_variant | 0.6 | ethambutol | Uncertain significance |
| atpE | 1461251 | c.207G>T | synonymous_variant | 1.0 | bedaquiline | |
| rrs | 1471649 | n.-197C>A | upstream_gene_variant | 0.37 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472912 | n.1067C>T | non_coding_transcript_exon_variant | 0.31 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1473049 | n.1205dupA | non_coding_transcript_exon_variant | 0.26 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrl | 1473633 | n.-25C>T | upstream_gene_variant | 0.31 | linezolid | |
| inhA | 1674434 | p.Val78Ala | missense_variant | 1.0 | ethionamide | Uncertain significance |
| isoniazid | Uncertain significance | |||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 0.99 | capreomycin | |
| ndh | 2102694 | p.Val117Ile | missense_variant | 0.36 | ethionamide | Uncertain significance |
| isoniazid | Uncertain significance | |||||
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
| katG | 2155503 | c.609C>T | synonymous_variant | 1.0 | isoniazid | |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2168731 | p.Pro628Thr | missense_variant | 0.27 | pyrazinamide | |
| PPE35 | 2170065 | p.Ala183Gly | missense_variant | 0.28 | pyrazinamide | |
| PPE35 | 2170464 | p.Ala50Val | missense_variant | 0.34 | pyrazinamide | |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| Rv1979c | 2222852 | p.Ala105Thr | missense_variant | 0.36 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| pncA | 2288879 | c.363G>A | synonymous_variant | 0.37 | pyrazinamide | |
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| ahpC | 2726265 | p.Lys25* | stop_gained | 0.36 | isoniazid | |
| ald | 3086728 | c.-92C>T | upstream_gene_variant | 0.99 | cycloserine | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | |
| ald | 3087412 | p.Asp198Val | missense_variant | 0.3 | cycloserine | |
| fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.64 | delamanid | |
| Rv3083 | 3449781 | c.1278G>A | synonymous_variant | 0.33 | ethionamide | |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| whiB7 | 3568428 | c.252A>G | synonymous_variant | 0.26 | streptomycin | |
| kanamycin | ||||||
| amikacin | ||||||
| Rv3236c | 3612143 | p.Arg325His | missense_variant | 0.26 | pyrazinamide | Uncertain significance |
| Rv3236c | 3612800 | p.Val106Ala | missense_variant | 0.3 | pyrazinamide | Uncertain significance |
| fbiB | 3640794 | c.-741A>G | upstream_gene_variant | 0.32 | delamanid | |
| fbiB | 3641879 | c.345G>A | synonymous_variant | 0.35 | delamanid | |
| alr | 3840559 | p.Arg288Ser | missense_variant | 0.27 | cycloserine | |
| alr | 3840618 | p.Asp268Gly | missense_variant | 0.29 | cycloserine | |
| rpoA | 3877696 | p.Thr271Ile | missense_variant | 0.25 | rifampicin | Uncertain significance |
| rpoA | 3877740 | c.768G>C | synonymous_variant | 0.35 | rifampicin | |
| rpoA | 3878291 | p.Val73Ile | missense_variant | 0.3 | rifampicin | Uncertain significance |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embC | 4241843 | p.Leu661Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 | ethambutol | |
| embC | 4242905 | p.Arg1015Trp | missense_variant | 0.3 | ethambutol | |
| embA | 4243541 | c.309C>T | synonymous_variant | 0.33 | ethambutol | |
| embA | 4244220 | c.988C>T | synonymous_variant | 1.0 | ethambutol | |
| embA | 4244379 | p.Pro383Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4246584 | p.Arg24Pro | missense_variant | 0.25 | ethambutol | |
| embB | 4246864 | c.351C>T | synonymous_variant | 1.0 | ethambutol | |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4248324 | p.Ala604Gly | missense_variant | 0.24 | ethambutol | |
| aftB | 4268477 | c.360C>T | synonymous_variant | 0.37 | 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 | 4269522 | c.-686C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| ethA | 4326465 | p.Ile337Val | missense_variant | 1.0 | ethionamide | Uncertain significance |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| whiB6 | 4338602 | c.-81A>C | upstream_gene_variant | 0.26 | streptomycin | Uncertain significance |
| capreomycin | ||||||
| amikacin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | |
| gid | 4408034 | p.Glu57Lys | missense_variant | 0.35 | streptomycin | Uncertain significance |
