Run ID: SRR28467020
Sample name:
Date: 2024-05-22T11:26:44.607712
Number of reads: 88792752
Percentage reads mapped: 99.18
Median coverage: 2884.0
Strain: lineage2.2.2
Spoligotype:
Drug-resistance: Pre-XDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage2 | East-Asian | RD105 | 1.0 |
| lineage2.2.2 | East-Asian (Beijing) | RD105;RD207 | 1.0 |
| lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
| isoniazid | ahpC | c.-48G>A | Uncertain significance | Mutation from literature |
| ethambutol | embB | p.Met306Val | Assoc w R | |
| pyrazinamide | pncA | c.-11A>G | Assoc w R | |
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | gyrA | p.Ala90Val | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
| ofloxacin | ||||
| levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | rrs | n.1401A>G | Assoc w R | |
| capreomycin | rrs | n.1401A>G | Assoc w R | |
| kanamycin | rrs | n.1401A>G | Assoc w R | |
| cycloserine | ||||
| ethionamide | ethA | c.1308delAinsCG | Assoc w R | |
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
| levofloxacin | Assoc w R | ||||||
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Assoc w R | |
| amikacin | Assoc w R | ||||||
| kanamycin | Assoc w R | ||||||
| pncA | 2289252 | c.-11A>G | upstream_gene_variant | 1.0 | pyrazinamide | Assoc w R | |
| ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
| embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol | Assoc w R | |
| ethA | 4326166 | c.1308delAinsCG | frameshift_variant&synonymous_variant | 1.0 | ethionamide | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| Rv0010c | 13504 | p.Gly19Arg | missense_variant | 1.0 | isoniazid | Uncertain significance |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
| pretomanid | ||||||
| delamanid | Not assoc w R - Interim | |||||
| Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| Rv0565c | 657142 | p.Arg110His | missense_variant | 1.0 | ethionamide | Uncertain significance |
| Rv0565c | 657439 | p.Asp11Ala | missense_variant | 1.0 | ethionamide | |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 767123 | p.Val1252Leu | missense_variant | 1.0 | rifampicin | Uncertain significance |
| 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 | |||||
| mmpS5 | 778743 | p.Val55Met | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rpsL | 781406 | c.-154_-153insC | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| Rv1129c | 1254039 | p.Asn166Asp | missense_variant | 1.0 | moxifloxacin | Uncertain significance |
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| 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 | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1471786 | n.-60T>G | upstream_gene_variant | 0.13 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1475954 | n.2297A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rpsA | 1833909 | p.Asp123Ala | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| 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 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv2477c | 2784617 | c.-575T>C | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| thyX | 3067949 | c.-4C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| thyA | 3074122 | p.Asp117Gly | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3083 | 3449688 | p.Trp395* | stop_gained | 1.0 | ethionamide | Uncertain significance |
| whiB7 | 3568428 | c.252A>C | synonymous_variant | 0.14 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| fbiA | 3640366 | c.-177G>A | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| alr | 3841362 | p.Thr20Met | missense_variant | 1.0 | cycloserine | |
| rpoA | 3878613 | c.-106A>C | upstream_gene_variant | 0.15 | rifampicin | |
| glpK | 4138973 | c.782delA | frameshift_variant | 0.77 | ethambutol | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| glpK | 4139183 | c.572dupG | frameshift_variant | 0.21 | ethambutol | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4243460 | c.228C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4247028 | p.Leu172Arg | missense_variant | 0.24 | ethambutol | |
| embB | 4247033 | p.Ser174Arg | missense_variant | 0.18 | ethambutol | |
| embB | 4247039 | p.Phe176Val | missense_variant | 0.16 | ethambutol | |
| aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338286 | c.235delG | frameshift_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 | 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 | 4407797 | p.Ser136Pro | missense_variant | 1.0 | streptomycin | Uncertain significance |
| gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 | streptomycin | Not assoc w R |
