TB-Profiler result

Run: SRR5341343
Summary

Run ID: SRR5341343

Sample name:

Date: 2024-03-25T22:02:42.315104

Number of reads: 2453981

Percentage reads mapped: 99.18

Median coverage: 70.0

Strain: lineage3;lineage4.6.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.54
lineage4.6 Euro-American None 0.47
lineage4.6.2 Euro-American RD726 0.5
lineage4 Euro-American None 0.45
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
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 gid c.351delG 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
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
inhA 1673425 c.-777C>T upstream_gene_variant 0.62 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
gid 4407851 c.351delG frameshift_variant 0.45 streptomycin Assoc w R
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
dnaA 324 c.324C>G synonymous_variant 0.43 isoniazid Not assoc w R - Interim
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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.54 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 656959 p.His171Pro missense_variant 0.46 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.4 ethionamide Not assoc w R - Interim
nusG 733947 c.-307G>T upstream_gene_variant 0.48 rifampicin
rpoB 759746 c.-61C>T upstream_gene_variant 0.66 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.56 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.51 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 0.53 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778298 c.183G>A 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.4 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471648 n.-198A>C upstream_gene_variant 0.46 streptomycin
kanamycin
capreomycin
amikacin
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 2063187 c.1542C>T synonymous_variant 0.4 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.44 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.64 pyrazinamide 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
pncA 2289047 c.195C>T synonymous_variant 0.43 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.56 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.49 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.49 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ribD 2986797 c.-42C>A upstream_gene_variant 0.43 para-aminosalicylic_acid
Rv2680 2996208 p.Ala35Asp missense_variant 0.34 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.61 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.48 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640606 p.Leu22Val missense_variant 0.66 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
alr 3841473 c.-53G>A upstream_gene_variant 0.54 cycloserine
rpoA 3878654 c.-147A>G upstream_gene_variant 0.4 rifampicin Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.49 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.42 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.5 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242883 c.3021C>T synonymous_variant 0.35 ethambutol Not assoc w R - Interim
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 0.44 streptomycin Not assoc w R