Run ID: ERR2653064
Sample name:
Date: 2024-10-04T19:01:10.731904
Number of reads: 2357391
Percentage reads mapped: 99.17
Median coverage: 67.0
Strain: lineage4.3.4.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 1.0 |
lineage4.3.4.1 | Euro-American (LAM) | RD174 | 0.99 |
lineage4 | Euro-American | None | 1.0 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Gly406Ser | Assoc w R | |
pyrazinamide | pncA | p.Pro62Ser | Assoc w R - Interim | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Asn | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Asn | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | eis | c.-10G>A | Assoc w R | Can only confer resistance if genetically linked to a functional Eis |
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7581 | p.Asp94Asn | missense_variant | 1.0 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289058 | p.Pro62Ser | missense_variant | 1.0 | pyrazinamide | Assoc w R - Interim | |
eis | 2715342 | c.-10G>A | upstream_gene_variant | 1.0 | kanamycin | Assoc w R | Can only confer resistance if genetically linked to a functional Eis |
embB | 4247729 | p.Gly406Ser | missense_variant | 0.98 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6807 | p.Arg523His | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | ||||||
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 | |||||
mshA | 574774 | c.-574C>G | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
ethionamide | Uncertain significance | |||||
mshA | 575876 | c.535_536delAC | frameshift_variant | 1.0 | isoniazid | Uncertain significance |
ethionamide | Uncertain significance | |||||
Rv0565c | 656408 | p.Gly355Arg | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 765113 | p.Val582Met | missense_variant | 1.0 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 778275 | p.Ala69Val | missense_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.97 | streptomycin | Not assoc w R |
sigE | 1364434 | p.Arg8Trp | missense_variant | 0.96 | pyrazinamide | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
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 |
tlyA | 1918711 | p.Asp258Asn | missense_variant | 1.0 | capreomycin | |
katG | 2156197 | c.-86T>C | upstream_gene_variant | 1.0 | isoniazid | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.98 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.98 | cycloserine | |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv3236c | 3613608 | c.-492C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrA | 3626873 | c.477C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
alr | 3841370 | c.51G>A | synonymous_variant | 0.19 | cycloserine | |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243229 | c.-4C>T | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.11 | ethambutol | Uncertain significance |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.11 | ethambutol | Uncertain significance |
embB | 4246567 | c.54G>T | synonymous_variant | 0.15 | ethambutol | Not assoc w R - Interim |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |