TB-Profiler result

Run: SRR29094067
Summary

Run ID: SRR29094067

Sample name:

Date: 2025-02-11T10:57:07.569173

Number of reads: 5024162

Percentage reads mapped: 99.08

Median coverage: 167.0

Strain: lineage2.2.2;lineage4.1.1.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.62
lineage4.1 Euro-American None 0.34
lineage4.1.1.3 Euro-American (X-type) RD193 0.36
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.65
lineage2.2 East-Asian (Beijing) RD105;RD207 0.63
lineage4 Euro-American None 0.35
lineage4.1.1 Euro-American (X-type) None 0.37
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro 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)
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA p.Ala381Pro Uncertain significance Mutation from literature
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761095 p.Leu430Pro missense_variant 0.72 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.65 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)
ethA 4326333 p.Ala381Pro missense_variant 0.66 ethionamide Uncertain significance Mutation from literature
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
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 491742 c.960T>C synonymous_variant 0.62 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.64 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.6 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.37 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.67 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.4 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.61 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.65 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781435 c.-125G>C upstream_gene_variant 0.3 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.37 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.59 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.63 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
katG 2154724 p.Arg463Leu missense_variant 0.73 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.69 pyrazinamide Not assoc w R
Rv1979c 2221939 p.Arg409Gln missense_variant 0.73 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.61 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040976 c.-272T>G upstream_gene_variant 0.6 pyrazinamide
glpK 4139947 c.-192C>A upstream_gene_variant 0.6 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.41 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.69 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.38 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.61 ethambutol Not assoc w R
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
whiB6 4338794 c.-273A>G upstream_gene_variant 0.68 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.65 streptomycin Not assoc w R
gid 4407798 c.405G>T synonymous_variant 0.36 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.68 streptomycin Not assoc w R