Run ID: SRR28394028
Sample name:
Date: 2024-05-22T14:30:35.014060
Number of reads: 3968005
Percentage reads mapped: 99.71
Median coverage: 115.0
Strain: lineage4
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Ala713Pro | Uncertain significance | Mutation from literature | |
ethambutol | embB | p.Gly406Ala | Assoc w R | |
pyrazinamide | pncA | p.Leu4Trp | Assoc w R | |
streptomycin | rpsL | p.Lys88Thr | Uncertain significance | Mutation from literature |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>T |
ethA | p.Gln24* | Assoc w R | ||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781822 | p.Lys88Thr | missense_variant | 1.0 | streptomycin | Uncertain significance | Mutation from literature |
inhA | 1673423 | c.-779G>T | upstream_gene_variant | 1.0 | ethionamide | Assoc w R - Interim | Alias fabG1_c.-17G>T |
isoniazid | Assoc w R - Interim | Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2153975 | p.Ala713Pro | missense_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
pncA | 2289231 | p.Leu4Trp | missense_variant | 0.98 | pyrazinamide | Assoc w R | |
embB | 4247730 | p.Gly406Ala | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4327404 | p.Gln24* | stop_gained | 0.26 | 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 | 13636 | c.-78A>C | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
rpoB | 761889 | p.Val695Leu | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 765462 | p.Asn698Ser | 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 | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 801009 | c.201A>G | synonymous_variant | 0.99 | linezolid | Not assoc w R - Interim |
Rv1129c | 1253453 | p.Gly361Asp | missense_variant | 1.0 | moxifloxacin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
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 |
Rv1979c | 2223214 | c.-50A>C | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv2752c | 3065517 | c.675C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
isoniazid | Not assoc w R - Interim | |||||
Rv2752c | 3065929 | p.Gly88Val | missense_variant | 1.0 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
levofloxacin | ||||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
Rv3083 | 3448439 | c.-64delA | upstream_gene_variant | 1.0 | ethionamide | |
rpoA | 3878595 | c.-88C>T | upstream_gene_variant | 0.22 | rifampicin | |
rpoA | 3878635 | c.-128C>T | upstream_gene_variant | 0.27 | rifampicin | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269721 | p.Ala38Val | missense_variant | 1.0 | ethambutol | Uncertain significance |
ethA | 4326092 | p.Tyr461Ser | missense_variant | 0.27 | ethionamide | |
ethA | 4327253 | p.Ala74Glu | missense_variant | 0.15 | ethionamide | Uncertain significance |
ethA | 4328317 | c.-844C>T | upstream_gene_variant | 1.0 | ethionamide | |
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 |