Run ID: SRR28498452
Sample name:
Date: 2024-05-22T14:31:24.278322
Number of reads: 2486284
Percentage reads mapped: 99.33
Median coverage: 73.0
Strain: lineage4.2.1
Spoligotype:
Drug-resistance: XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.2 | Euro-American | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.2.1 | Euro-American (TUR) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. 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.Ser297Ala | Uncertain significance | Mutation from literature |
pyrazinamide | pncA | p.Phe58Ser | Assoc w R - Interim | |
streptomycin | rpsL | p.Lys88Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrB | p.Asp461His | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
gyrA | p.Asp94Ala | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |
ofloxacin | ||||
levofloxacin | gyrB | p.Asp461His | Assoc w R - Interim | |
gyrA | p.Asp94Ala | Assoc w R | ||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1484G>T | Assoc w R | |
capreomycin | rrs | n.1484G>T | Assoc w R | |
tlyA | c.692dupC | Assoc w R | ||
kanamycin | rrs | n.1484G>T | Assoc w R | |
eis | c.-12C>T | Assoc w R | ||
cycloserine | alr | p.Phe4Leu | Mutation from literature | |
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid | rplC | p.Cys154Arg | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrB | 6620 | p.Asp461His | missense_variant | 1.0 | moxifloxacin | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
levofloxacin | Assoc w R - Interim | ||||||
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
levofloxacin | Assoc w R | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781822 | p.Lys88Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
rplC | 801268 | p.Cys154Arg | missense_variant | 1.0 | linezolid | Assoc w R | |
rrs | 1473329 | n.1484G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Assoc w R | |
amikacin | Assoc w R | ||||||
kanamycin | Assoc w R | ||||||
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 1.0 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
tlyA | 1918629 | c.692dupC | frameshift_variant | 1.0 | capreomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289069 | p.Phe58Ser | missense_variant | 1.0 | pyrazinamide | Assoc w R - Interim | |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 1.0 | kanamycin | Assoc w R | |
alr | 3841409 | p.Phe4Leu | missense_variant | 0.99 | cycloserine | Mutation from literature | |
embB | 4247402 | p.Ser297Ala | missense_variant | 1.0 | ethambutol | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491247 | c.465C>T | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
ccsA | 619969 | p.Val27Ile | missense_variant | 1.0 | capreomycin | Not assoc w R - Interim |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
rpoC | 764817 | p.Val483Gly | 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 | 800204 | c.-605T>C | upstream_gene_variant | 1.0 | linezolid | |
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 |
bacA | 2063685 | c.1044G>A | synonymous_variant | 1.0 | streptomycin | Not assoc w R - Interim |
kanamycin | Not assoc w R - Interim | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
bacA | 2063911 | p.Ile273Thr | missense_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
ald | 3086742 | c.-78A>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
lpqB | 3623222 | c.1689A>G | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
rifampicin | Not assoc w R - Interim | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4249594 | c.3081G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
ethA | 4326632 | p.His281Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
ethA | 4328376 | c.-903G>C | 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 |