Run ID: SRR23310991
Sample name:
Date: 2024-04-14T13:59:58.039060
Number of reads: 1552882
Percentage reads mapped: 99.64
Median coverage: 46.0
Strain: lineage4.1.2.1;lineage4.3.4.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.3 |
lineage4.1 | Euro-American | None | 0.68 |
lineage4.1.2 | Euro-American | None | 0.68 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 0.7 |
lineage4.3.4.1 | Euro-American (LAM) | RD174 | 0.28 |
lineage4 | Euro-American | None | 1.0 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 0.28 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
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 |
---|
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 | |||||
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.5 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
mshA | 575679 | p.Asn111Ser | missense_variant | 0.77 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.65 | ethionamide | Uncertain significance |
rpoB | 760106 | c.300G>A | synonymous_variant | 0.52 | rifampicin | Not assoc w R |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.58 | rifampicin | Not assoc w R |
rpoC | 763783 | c.414G>A | synonymous_variant | 0.36 | rifampicin | Not assoc w R - Interim |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.24 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.58 | rifampicin | Not assoc w R |
rpoC | 765325 | c.1956C>T | synonymous_variant | 0.34 | rifampicin | Not assoc w R - Interim |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781276 | c.-284A>C | upstream_gene_variant | 0.67 | streptomycin | |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.98 | streptomycin | Not assoc w R |
Rv1129c | 1254583 | c.-49A>C | upstream_gene_variant | 0.57 | moxifloxacin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
sigE | 1364434 | p.Arg8Trp | missense_variant | 0.28 | pyrazinamide | Not assoc w R |
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 | 2223123 | c.42G>A | synonymous_variant | 0.41 | clofazimine | Not assoc w R - Interim |
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 | 2518076 | c.-39C>T | upstream_gene_variant | 0.65 | isoniazid | |
folC | 2746540 | c.1059G>A | synonymous_variant | 0.41 | para-aminosalicylic_acid | |
Rv2680 | 2996034 | c.-71G>A | upstream_gene_variant | 0.1 | capreomycin | Uncertain significance |
Rv2680 | 2996136 | p.Ser11Asn | missense_variant | 0.14 | capreomycin | |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.37 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.98 | cycloserine | |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.32 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.18 | pyrazinamide | Not assoc w R |
embC | 4239298 | c.-565C>T | upstream_gene_variant | 0.59 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.75 | ethambutol | Not assoc w R |
embB | 4247542 | c.1029C>A | synonymous_variant | 0.62 | ethambutol | Not assoc w R - Interim |
whiB6 | 4338513 | c.9C>T | synonymous_variant | 0.64 | capreomycin | Not assoc w R - Interim |
amikacin | Not assoc w R - Interim | |||||
kanamycin | Not assoc w R - Interim | |||||
whiB6 | 4338550 | c.-29A>T | upstream_gene_variant | 0.23 | 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 | ||||||
whiB6 | 4338735 | c.-214C>G | upstream_gene_variant | 0.31 | capreomycin | |
amikacin | ||||||
kanamycin |