TB-Profiler result

Run: SRR6824414
Summary

Run ID: SRR6824414

Sample name:

Date: 2024-04-16T01:23:48.607439

Number of reads: 9940415

Percentage reads mapped: 98.9

Median coverage: 291.0

Strain: lineage3;lineage4.5

Spoligotype:

Drug-resistance: MDR-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 0.2
lineage4.5 Euro-American RD122 0.76
lineage4 Euro-American None 0.76
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
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)
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
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 761155 p.Ser450Leu missense_variant 0.18 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.17 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
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 1417 p.Val473Ile missense_variant 0.72 isoniazid Uncertain significance
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 7892 c.591G>A synonymous_variant 0.77 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 0.24 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 619751 c.-140G>A upstream_gene_variant 0.19 capreomycin
amikacin
kanamycin
ccsA 620029 c.139C>T synonymous_variant 0.77 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.28 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.2 rifampicin Not assoc w R
rpoB 760688 p.Phe294Leu missense_variant 0.78 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 0.19 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.21 rifampicin Not assoc w R
rpoC 765617 p.Glu750Lys missense_variant 0.17 rifampicin
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 0.22 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.24 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473610 n.-48C>T upstream_gene_variant 0.74 capreomycin
linezolid
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
katG 2154724 p.Arg463Leu missense_variant 0.19 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.26 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.79 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 0.16 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.25 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.26 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.26 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
ald 3086788 c.-32T>C upstream_gene_variant 0.26 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878575 c.-68C>T upstream_gene_variant 0.84 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.79 pyrazinamide Not assoc w R
clpC1 4040753 c.-49G>A upstream_gene_variant 0.14 pyrazinamide Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.21 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.22 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 0.21 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 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 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.27 streptomycin Not assoc w R
gid 4408027 p.Leu59Pro missense_variant 0.15 streptomycin