Run ID: 728a3ffc-b892-445c-9234-b360aaf336d8
Sample name:
Date: 07-05-2024 22:24:24
Number of reads: 5787323
Percentage reads mapped: 98.49
Median coverage: 165
Strain: lineage6.3.1
Spoligotype:
Drug-resistance: HR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage6 | West-Africa 2 | RD702 | 1.0 |
| lineage6.3 | West-Africa 2 | RD702 | 1.0 |
| lineage6.3.1 | West-Africa 2 | RD702 | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | inhA | c.-154G>A | Assoc w R | |
| katG | p.Ser315Thr | Assoc w R | ||
| ethambutol | ||||
| pyrazinamide | ||||
| moxifloxacin | ||||
| levofloxacin | ||||
| bedaquiline | ||||
| delamanid | ||||
| pretomanid | ||||
| linezolid | ||||
| streptomycin | ||||
| amikacin | ||||
| kanamycin | ||||
| capreomycin | ||||
| clofazimine | ||||
| ethionamide | inhA | c.-154G>A | Assoc w R - interim | |
| para-aminosalicylic_acid | ||||
| cycloserine |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| inhA | 1674048 | c.-154G>A | upstream_gene_variant | 0.99 | isoniazid | Assoc w R | |
| ethionamide | Assoc w R - interim | ||||||
| katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 6446 | p.Ala403Ser | missense_variant | 0.99 | 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 | 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 | 760969 | p.Ser388Leu | missense_variant | 0.99 | 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 | |
| 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 | 777686 | c.795G>A | synonymous_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| mmpL5 | 777986 | c.495C>A | synonymous_variant | 0.99 | 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 | 1305458 | p.Pro843Gln | missense_variant | 0.99 | delamanid | |
| atpE | 1461251 | c.207G>T | synonymous_variant | 1.0 | bedaquiline | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.99 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| inhA | 1674434 | p.Val78Ala | missense_variant | 0.99 | ethionamide | Uncertain significance |
| isoniazid | Uncertain significance | |||||
| tlyA | 1917771 | c.-169G>A | upstream_gene_variant | 1.0 | capreomycin | |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | |
| ndh | 2102694 | p.Val117Ile | missense_variant | 1.0 | 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 |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| Rv1979c | 2222852 | p.Ala105Thr | 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 | 0.99 | 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 | |
| Rv3083 | 3449781 | c.1278G>A | synonymous_variant | 1.0 | ethionamide | |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.99 | capreomycin | |
| amikacin | ||||||
| fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| rpoA | 3877696 | p.Thr271Ile | missense_variant | 1.0 | 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 | |
| embA | 4244220 | c.988C>T | synonymous_variant | 1.0 | ethambutol | |
| embA | 4244379 | p.Pro383Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4246864 | c.351C>T | synonymous_variant | 0.99 | ethambutol | |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
| aftB | 4268477 | c.360C>T | synonymous_variant | 0.99 | capreomycin | |
| amikacin | ||||||
| aftB | 4268651 | c.186G>A | synonymous_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| aftB | 4269351 | c.-515C>T | upstream_gene_variant | 0.99 | capreomycin | |
| amikacin | ||||||
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.99 | ethambutol | Uncertain significance |
| aftB | 4269522 | c.-686C>T | upstream_gene_variant | 0.99 | 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 |
| ethA | 4326711 | p.Lys255Gln | missense_variant | 0.99 | 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 |
