Run ID: SRR998802
Sample name:
Date: 2024-10-04T00:58:51.703176
Number of reads: 3567260
Percentage reads mapped: 99.35
Median coverage: 81.0
Strain: lineage4.1.3;lineage5.1.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1.3 | Euro-American | None | 0.87 |
lineage4.1 | Euro-American | None | 0.89 |
lineage4 | Euro-American | None | 0.94 |
lineage5.1.1 | West-Africa 1 | RD711 | 0.06 |
lineage5 | West-Africa 1 | RD711 | 0.09 |
lineage5.1 | West-Africa 1 | RD711 | 0.1 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.His445Asp | 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) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | p.Ile133Thr | Assoc w R | |
streptomycin | gid | p.Leu79Ser | Uncertain significance | Mutation from literature |
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 | 761139 | p.His445Asp | missense_variant | 0.95 | rifampicin | Assoc w R | |
inhA | 1674048 | c.-154G>A | upstream_gene_variant | 0.92 | ethionamide | Assoc w R - Interim | Alias fabG1_p.Leu203Leu |
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) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.84 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288844 | p.Ile133Thr | missense_variant | 0.93 | pyrazinamide | Assoc w R | |
embB | 4247429 | p.Met306Val | missense_variant | 0.89 | ethambutol | Assoc w R | |
gid | 4407967 | p.Leu79Ser | missense_variant | 0.87 | streptomycin | Uncertain significance | Mutation from literature |
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 | 9143 | c.1842T>C | synonymous_variant | 0.14 | 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 | |||||
gyrA | 9557 | c.2256G>C | synonymous_variant | 0.97 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.13 | isoniazid | Not assoc w R |
mshA | 574557 | c.-791C>G | upstream_gene_variant | 0.94 | isoniazid | |
ethionamide | ||||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.87 | ethionamide | Uncertain significance |
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.15 | ethionamide | |
rpoC | 763904 | p.Ala179Ser | missense_variant | 0.11 | rifampicin | |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.91 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rpsL | 781421 | c.-139C>A | upstream_gene_variant | 0.94 | streptomycin | Uncertain significance |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.13 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 0.16 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
fbiC | 1304610 | c.1680C>T | synonymous_variant | 0.85 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
Rv1258c | 1406740 | p.His201Tyr | missense_variant | 0.21 | streptomycin | |
pyrazinamide | ||||||
isoniazid | ||||||
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.15 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
inhA | 1673338 | c.-864G>A | upstream_gene_variant | 0.14 | isoniazid | |
ethionamide | ||||||
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 |
ndh | 2101921 | c.1122G>A | synonymous_variant | 0.17 | isoniazid | Not assoc w R - Interim |
delamanid | Not assoc w R - Interim | |||||
ethionamide | Not assoc w R - Interim | |||||
ndh | 2103112 | c.-70G>T | upstream_gene_variant | 0.21 | isoniazid | Not assoc w R - Interim |
delamanid | Uncertain significance | |||||
ethionamide | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
eis | 2715511 | c.-179C>T | upstream_gene_variant | 0.88 | kanamycin | |
amikacin | ||||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.92 | cycloserine | |
ald | 3087084 | c.266delA | frameshift_variant | 0.14 | cycloserine | |
lpqB | 3623291 | c.1620C>A | synonymous_variant | 0.87 | rifampicin | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
lpqB | 3624350 | c.561G>T | synonymous_variant | 0.13 | rifampicin | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
lpqB | 3624660 | p.Ala84Gly | missense_variant | 0.76 | rifampicin | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
alr | 3840932 | c.489C>T | synonymous_variant | 0.12 | cycloserine | |
rpoA | 3878493 | c.15G>A | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
ddn | 3986987 | c.144G>T | synonymous_variant | 0.14 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
ddn | 3987180 | p.Asp113Asn | missense_variant | 0.15 | pretomanid | |
delamanid | Uncertain significance | |||||
clpC1 | 4040010 | p.Ala232Asp | missense_variant | 0.12 | pyrazinamide | Uncertain significance |
glpK | 4139131 | p.Glu209Lys | missense_variant | 0.13 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Uncertain significance | |||||
embC | 4240986 | p.Arg375Gln | missense_variant | 0.81 | ethambutol | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.87 | ethambutol | Not assoc w R |
embA | 4244220 | c.988C>T | synonymous_variant | 0.13 | ethambutol | Not assoc w R |
embA | 4244635 | p.Val468Ala | missense_variant | 0.12 | ethambutol | Not assoc w R - Interim |
embA | 4245147 | p.Pro639Ser | missense_variant | 0.13 | ethambutol | Not assoc w R - Interim |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.1 | ethambutol | Not assoc w R |
ethA | 4326928 | c.546C>T | synonymous_variant | 0.15 | ethionamide | Not assoc w R - Interim |
ethA | 4327103 | p.Gly124Asp | missense_variant | 0.11 | ethionamide | Uncertain significance |
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 | 4407588 | c.615A>G | synonymous_variant | 0.17 | streptomycin | Not assoc w R |