Run ID: SRR1049737
Sample name:
Date: 2024-04-14T00:35:38.221892
Number of reads: 4227990
Percentage reads mapped: 98.81
Median coverage: 99.0
Strain: lineage4.1.2.1;lineage4.3.3
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.24 |
lineage4.1 | Euro-American | None | 0.8 |
lineage4.1.2 | Euro-American | None | 0.78 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 0.75 |
lineage4 | Euro-American | None | 1.0 |
lineage4.3.3 | Euro-American (LAM) | RD115 | 0.24 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.His445Asn | Assoc w R | |
p.His445Tyr | Assoc w R | |||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
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 |
---|---|---|---|---|---|---|---|
rpoB | 761139 | p.His445Asn | missense_variant | 0.24 | rifampicin | Assoc w R | |
rpoB | 761139 | p.His445Tyr | missense_variant | 0.76 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.33 | isoniazid | Assoc w R | High-level resistance |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 434 | p.His145Arg | missense_variant | 0.27 | isoniazid | Uncertain significance |
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 | 8040 | p.Gly247Ser | missense_variant | 0.2 | 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 | 0.8 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
mshA | 575679 | p.Asn111Ser | missense_variant | 0.84 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.76 | ethionamide | Uncertain significance |
Rv0565c | 657449 | p.Gly8Ser | missense_variant | 0.27 | ethionamide | Uncertain significance |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.78 | rifampicin | Not assoc w R |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.21 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.76 | rifampicin | Not assoc w R |
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 | 0.7 | streptomycin | |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
embR | 1417942 | c.-595G>T | upstream_gene_variant | 0.2 | ethambutol | |
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 |
katG | 2156196 | c.-85C>T | upstream_gene_variant | 0.17 | isoniazid | Not assoc w R |
PPE35 | 2169398 | c.1214dupG | frameshift_variant | 0.19 | pyrazinamide | Uncertain significance |
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 | 0.75 | isoniazid | |
Rv2680 | 2996034 | c.-71G>A | upstream_gene_variant | 0.28 | capreomycin | Uncertain significance |
Rv2680 | 2996085 | c.-20G>A | upstream_gene_variant | 0.27 | capreomycin | Uncertain significance |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.21 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
clpC1 | 4038968 | c.1737G>A | synonymous_variant | 0.23 | pyrazinamide | Not assoc w R - Interim |
glpK | 4139015 | c.741G>T | synonymous_variant | 0.27 | 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 | |||||
glpK | 4139183 | c.572dupG | frameshift_variant | 0.18 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embC | 4239298 | c.-565C>T | upstream_gene_variant | 0.64 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.76 | ethambutol | Not assoc w R |
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 | 4408156 | p.Leu16Arg | missense_variant | 0.25 | streptomycin | Not assoc w R |