Run ID: SRR28351648
Sample name:
Date: 2024-05-22T13:20:29.350917
Number of reads: 18848233
Percentage reads mapped: 99.83
Median coverage: 618.0
Strain: lineage2.2.1;lineage4.2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.16 |
lineage4.2 | Euro-American | None | 0.85 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.16 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.16 |
lineage4 | Euro-American | None | 0.84 |
lineage4.2.1 | Euro-American (TUR) | None | 0.84 |
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.Trp328Cys | Uncertain significance | Mutation from literature | |
p.Ser315Thr | Assoc w R | High-level resistance | ||
ahpC | c.-74G>A | Uncertain significance | Mutation from literature | |
ethambutol | embB | p.Ser297Ala | Uncertain significance | Mutation from literature |
pyrazinamide | ||||
streptomycin | rpsL | p.Lys88Arg | Assoc w R | |
rrs | n.514A>C | Assoc w R | ||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | eis | c.-12C>T | Assoc w R | |
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.87 | rifampicin | Assoc w R | |
rpsL | 781822 | p.Lys88Arg | missense_variant | 0.84 | streptomycin | Assoc w R | |
rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 0.15 | streptomycin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.83 | 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 | 2155128 | p.Trp328Cys | missense_variant | 0.13 | isoniazid | Uncertain significance | Mutation from literature |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.88 | isoniazid | Assoc w R | High-level resistance |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 0.86 | kanamycin | Assoc w R | |
ahpC | 2726119 | c.-74G>A | upstream_gene_variant | 0.16 | isoniazid | Uncertain significance | Mutation from literature |
embB | 4247402 | p.Ser297Ala | missense_variant | 0.88 | 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 | 0.84 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.14 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.15 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 619969 | p.Val27Ile | missense_variant | 0.83 | capreomycin | Not assoc w R - Interim |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.12 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.15 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.87 | rifampicin | Uncertain significance |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.13 | 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 | 776100 | p.Thr794Ile | missense_variant | 0.16 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.14 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.14 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800204 | c.-605T>C | upstream_gene_variant | 0.84 | linezolid | |
Rv1129c | 1254056 | p.Asp160Ala | missense_variant | 0.15 | moxifloxacin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.15 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.17 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.16 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.99 | 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 | 0.85 | 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 | 0.84 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.15 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.17 | pyrazinamide | Not assoc w R |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 0.84 | 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 | 0.85 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.14 | pyrazinamide | Not assoc w R - Interim |
lpqB | 3623222 | c.1689A>G | synonymous_variant | 0.85 | 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 | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.15 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiA | 3640407 | c.-136G>T | upstream_gene_variant | 0.17 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | ||||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.13 | ethambutol | Not assoc w R |
embB | 4249594 | c.3081G>A | synonymous_variant | 0.83 | ethambutol | Not assoc w R - Interim |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.16 | ethambutol | Not assoc w R |
ethA | 4326632 | p.His281Pro | missense_variant | 0.84 | ethionamide | Uncertain significance |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 0.84 | ethionamide | |
whiB6 | 4338290 | c.231dupA | frameshift_variant | 0.15 | 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 | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.19 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.16 | streptomycin | Not assoc w R |