Run ID: SRR13837722
Sample name:
Date: 2024-10-04T00:30:05.708089
Number of reads: 2976570
Percentage reads mapped: 97.26
Median coverage: 101.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| dnaA | 1425 | c.1426dupG | frameshift_variant | 0.98 | isoniazid | Uncertain significance |
| rpoB | 760728 | p.Tyr308Asn | missense_variant | 0.97 | rifampicin | |
| rpoC | 763928 | p.Glu187* | stop_gained | 0.99 | rifampicin | |
| rpoC | 766155 | p.Ala929Val | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 777185 | c.1296G>T | synonymous_variant | 0.99 | bedaquiline | |
| clofazimine | ||||||
| fbiC | 1302932 | p.Val1Gly | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiC | 1303151 | p.Gly74Asp | missense_variant | 0.99 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiC | 1304895 | c.1965C>A | synonymous_variant | 0.95 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiC | 1305298 | p.Lys790Gln | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| Rv1258c | 1406311 | c.1030C>T | synonymous_variant | 1.0 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| rpsA | 1834275 | p.Ile245Thr | missense_variant | 0.92 | pyrazinamide | |
| rpsA | 1834366 | c.825A>G | synonymous_variant | 0.13 | pyrazinamide | Not assoc w R - Interim |
| tlyA | 1917936 | c.-4C>A | upstream_gene_variant | 1.0 | capreomycin | |
| bacA | 2064894 | c.-166C>G | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| ndh | 2101676 | p.Ala456Val | missense_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| PPE35 | 2170823 | c.-212delT | upstream_gene_variant | 1.0 | pyrazinamide | |
| pncA | 2289356 | c.-115G>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| kasA | 2518234 | p.Glu40Asp | missense_variant | 1.0 | isoniazid | |
| Rv2752c | 3064837 | p.Leu452Trp | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| Rv3083 | 3449643 | p.Asn380Lys | missense_variant | 1.0 | ethionamide | Uncertain significance |
| Rv3236c | 3611967 | p.Ser384Pro | missense_variant | 1.0 | pyrazinamide | |
| rpoA | 3877756 | p.Ile251Thr | missense_variant | 0.96 | rifampicin | |
| rpoA | 3878065 | p.Pro148Arg | missense_variant | 1.0 | rifampicin | |
| ddn | 3986977 | p.Pro45Arg | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clpC1 | 4040538 | p.Leu56Arg | missense_variant | 0.99 | pyrazinamide | |
| glpK | 4138636 | p.Arg374Gly | missense_variant | 0.97 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| embA | 4245342 | p.Ser704Pro | missense_variant | 1.0 | ethambutol | |
| embB | 4248711 | c.2198_2199insT | frameshift_variant | 1.0 | ethambutol | |
| aftB | 4267498 | p.Glu447Lys | missense_variant | 0.99 | ethambutol | Uncertain significance |
| aftB | 4268559 | p.Leu93Gln | missense_variant | 1.0 | ethambutol | |
| whiB6 | 4338743 | c.-223_-222insC | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin |
