Run ID: SRR28394203
Sample name:
Date: 2024-05-22T18:27:24.059946
Number of reads: 3841794
Percentage reads mapped: 99.51
Median coverage: 110.0
Strain: lineage4.1.2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 0.99 |
lineage4.1.2 | Euro-American | None | 0.98 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 0.98 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | inhA | c.-154G>A | Assoc w R | Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethambutol | embB | p.Met306Ile | Assoc w R | |
p.Gly406Asp | Assoc w R | |||
pyrazinamide | ||||
streptomycin | gid | c.41delC | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-154G>A | Assoc w R - Interim | Alias fabG1_p.Leu203Leu |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.96 | rifampicin | Assoc w R | |
inhA | 1674048 | c.-154G>A | upstream_gene_variant | 0.98 | isoniazid | Assoc w R | Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethionamide | Assoc w R - Interim | Alias fabG1_p.Leu203Leu | |||||
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | Assoc w R | |
embB | 4247730 | p.Gly406Asp | missense_variant | 0.97 | ethambutol | Assoc w R | |
gid | 4408161 | c.41delC | frameshift_variant | 0.95 | streptomycin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1053 | c.1053C>T | synonymous_variant | 0.97 | isoniazid | Not assoc w R - Interim |
gyrA | 7362 | p.Glu21Gln | missense_variant | 0.99 | 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 | 0.96 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.99 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
mshA | 575679 | p.Asn111Ser | missense_variant | 0.99 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.99 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 765650 | p.Gln761Lys | missense_variant | 0.98 | 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 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1833510 | c.-31delG | upstream_gene_variant | 0.99 | pyrazinamide | Uncertain significance |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.98 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
tlyA | 1918164 | c.225G>A | synonymous_variant | 0.98 | capreomycin | Not assoc w R - Interim |
katG | 2156119 | c.-8G>C | upstream_gene_variant | 0.97 | isoniazid | Uncertain significance |
katG | 2156520 | c.-409G>C | upstream_gene_variant | 0.97 | isoniazid | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 0.99 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 | isoniazid | |
Rv2680 | 2996034 | c.-71G>A | upstream_gene_variant | 0.16 | capreomycin | Uncertain significance |
Rv2680 | 2996085 | c.-20G>A | upstream_gene_variant | 0.2 | capreomycin | Uncertain significance |
Rv2680 | 2996136 | p.Ser11Asn | missense_variant | 0.17 | capreomycin | |
Rv2752c | 3065737 | p.Asp152Ala | missense_variant | 0.97 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.99 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
glpK | 4139231 | c.525A>G | synonymous_variant | 0.98 | ethambutol | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
isoniazid | Not assoc w R - Interim | |||||
embC | 4239298 | c.-565C>T | upstream_gene_variant | 0.97 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 0.96 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.97 | ethambutol | Not assoc w R |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 0.98 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 0.99 | capreomycin | |
amikacin | ||||||
kanamycin |