Run ID: SRR5065648
Sample name:
Date: 2024-04-15T17:36:53.950043
Number of reads: 1417714
Percentage reads mapped: 99.27
Median coverage: 47.0
Strain: lineage1.1.1.1
Spoligotype:
Drug-resistance: HR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage1.1 | Indo-Oceanic | RD239 | 1.0 |
| lineage1 | Indo-Oceanic | RD239 | 1.0 |
| lineage1.1.1 | Indo-Oceanic | RD239 | 1.0 |
| lineage1.1.1.1 | Indo-Oceanic | RD239 | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
| 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 |
|---|---|---|---|---|---|---|---|
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 6112 | p.Met291Ile | missense_variant | 0.99 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7944 | p.Thr215Ala | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 8452 | p.Ala384Val | missense_variant | 0.98 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| Rv0010c | 13275 | p.Tyr95Cys | missense_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13298 | p.Ile87Met | missense_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13460 | c.99T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13482 | p.Ala26Val | missense_variant | 1.0 | isoniazid | Not assoc w R |
| fgd1 | 490972 | p.Arg64Ser | missense_variant | 1.0 | clofazimine | Uncertain significance |
| pretomanid | ||||||
| delamanid | Uncertain significance | |||||
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
| pretomanid | ||||||
| delamanid | Not assoc w R - Interim | |||||
| Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | |
| nusG | 734116 | c.-138T>C | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpL5 | 777581 | p.Tyr300* | stop_gained | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rplC | 800357 | c.-452C>A | upstream_gene_variant | 1.0 | linezolid | Not assoc w R |
| Rv1129c | 1254543 | c.-9T>G | upstream_gene_variant | 0.98 | moxifloxacin | Uncertain significance |
| levofloxacin | Uncertain significance | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
| embR | 1417793 | c.-446C>T | upstream_gene_variant | 1.0 | ethambutol | |
| embR | 1417967 | c.-620C>T | upstream_gene_variant | 1.0 | ethambutol | |
| atpE | 1460931 | c.-114A>G | upstream_gene_variant | 1.0 | bedaquiline | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1474709 | n.1052G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rpsA | 1834020 | p.Asp160Ala | missense_variant | 0.99 | pyrazinamide | Uncertain significance |
| rpsA | 1834319 | p.Val260Ile | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| tsnR | 1853974 | c.369C>T | synonymous_variant | 1.0 | linezolid | Not assoc w R |
| tsnR | 1854045 | p.Tyr147Cys | missense_variant | 1.0 | linezolid | Not assoc w R |
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| bacA | 2062922 | p.Ile603Val | missense_variant | 1.0 | streptomycin | Not assoc w R |
| kanamycin | Not assoc w R | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| bacA | 2063106 | c.1623G>A | synonymous_variant | 1.0 | streptomycin | Not assoc w R - Interim |
| kanamycin | Not assoc w R - Interim | |||||
| capreomycin | Not assoc w R - Interim | |||||
| amikacin | Not assoc w R - Interim | |||||
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| katG | 2156389 | c.-278G>C | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.99 | isoniazid | |
| Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 | ethionamide | Uncertain significance |
| lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| fbiB | 3641759 | c.225C>T | synonymous_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| glpK | 4139074 | p.Leu228Val | missense_variant | 1.0 | ethambutol | Not assoc w R |
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| glpK | 4139347 | p.Arg137Cys | missense_variant | 1.0 | ethambutol | Uncertain significance |
| moxifloxacin | ||||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | ||||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4243848 | p.Val206Met | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4244096 | c.864C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4245138 | p.Asp636Asn | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4246393 | p.Trp1054Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| aftB | 4267678 | c.1159C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269606 | c.228T>C | synonymous_variant | 0.98 | ethambutol | Not assoc w R |
| ethR | 4328185 | p.Gly213Arg | missense_variant | 1.0 | ethionamide | |
| ethA | 4328269 | c.-796C>T | upstream_gene_variant | 1.0 | ethionamide | |
| whiB6 | 4338242 | p.Gln94Glu | missense_variant | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
| gid | 4407873 | c.330G>T | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
| gid | 4407967 | p.Leu79Trp | missense_variant | 1.0 | streptomycin | Uncertain significance |
