Run ID: SRR28646082
Sample name:
Date: 2024-05-22T09:05:49.009247
Number of reads: 3200554
Percentage reads mapped: 99.25
Median coverage: 84.0
Strain: lineage4.1.2.1;lineage4.8
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 0.49 |
lineage4.1.2 | Euro-American | None | 0.5 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 0.54 |
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.49 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
rpoC | p.Gly332Arg | Uncertain significance | Mutation from literature | |
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.Met306Ile | Assoc w R | |
pyrazinamide | pncA | p.Ala146Val | Assoc w R | |
streptomycin | gid | p.Gln125* | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
ethA | c.1391dupA | Assoc w R | ||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.56 | rifampicin | Assoc w R | |
rpoC | 764363 | p.Gly332Arg | missense_variant | 0.58 | rifampicin | Uncertain significance | Mutation from literature |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.41 | 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) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.63 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288805 | p.Ala146Val | missense_variant | 0.48 | pyrazinamide | Assoc w R | |
embB | 4247431 | p.Met306Ile | missense_variant | 0.54 | ethambutol | Assoc w R | |
ethA | 4326082 | c.1391dupA | frameshift_variant | 0.47 | ethionamide | Assoc w R | |
gid | 4407830 | p.Gln125* | stop_gained | 0.57 | streptomycin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 371 | p.Pro124Leu | missense_variant | 0.6 | isoniazid | Not assoc w R |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.45 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.55 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13543 | p.Trp6Arg | missense_variant | 0.44 | isoniazid | Uncertain significance |
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.44 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
mshA | 575679 | p.Asn111Ser | missense_variant | 0.56 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.39 | ethionamide | Uncertain significance |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.44 | rifampicin | Not assoc w R |
rpoC | 765008 | p.Leu547Val | missense_variant | 0.48 | rifampicin | Uncertain significance |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.58 | rifampicin | Not assoc w R |
rpoC | 766085 | p.Pro906Ala | missense_variant | 0.52 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 777820 | c.661C>T | synonymous_variant | 0.54 | clofazimine | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
atpE | 1460992 | c.-53A>C | upstream_gene_variant | 0.48 | bedaquiline | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.51 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.5 | linezolid | Not assoc w R |
tlyA | 1917588 | c.-352C>T | upstream_gene_variant | 0.54 | capreomycin | |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
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 | 0.56 | isoniazid | |
eis | 2715432 | c.-100C>T | upstream_gene_variant | 0.54 | amikacin | |
kanamycin | ||||||
Rv2680 | 2996136 | p.Ser11Asn | missense_variant | 0.19 | capreomycin | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.49 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.4 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
alr | 3840764 | c.657G>C | synonymous_variant | 0.43 | cycloserine | |
rpoA | 3878432 | c.76C>T | synonymous_variant | 0.46 | rifampicin | Not assoc w R - Interim |
embC | 4239298 | c.-565C>T | upstream_gene_variant | 0.5 | 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 | 0.45 | 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 | 0.52 | capreomycin | |
amikacin | ||||||
kanamycin |