TB-Profiler result

Run: SRR10809008
Summary

Run ID: SRR10809008

Sample name:

Date: 2024-04-15T22:09:13.233274

Number of reads: 5351942

Percentage reads mapped: 99.56

Median coverage: 170.0

Strain: lineage4.1.2.1;lineage4.3

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.54
lineage4.1 Euro-American None 0.48
lineage4.1.2 Euro-American None 0.45
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.44
lineage4 Euro-American None 1.0
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
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 0.53 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
gyrB 5983 p.Ser248Arg missense_variant 0.16 levofloxacin
moxifloxacin
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 491591 p.Lys270Met missense_variant 0.43 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575423 p.Arg26Cys missense_variant 0.47 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.4 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.32 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.48 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.58 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.38 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 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
rpsL 781848 p.Ile97Val missense_variant 0.58 streptomycin
Rv1129c 1254132 p.Glu135Lys missense_variant 0.54 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
fbiC 1304135 p.Gly402Asp missense_variant 0.46 clofazimine
pretomanid
delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834279 c.738C>T synonymous_variant 0.36 pyrazinamide Not assoc w R - Interim
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 2062821 c.1908C>A synonymous_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
PPE35 2168558 c.2055C>G synonymous_variant 0.51 pyrazinamide Not assoc w R - Interim
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 0.42 isoniazid
Rv2752c 3065970 c.222C>T synonymous_variant 0.62 ethambutol Not assoc w R - Interim
moxifloxacin
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 0.51 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.47 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.53 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.45 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 0.49 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 4408156 p.Leu16Arg missense_variant 0.52 streptomycin Not assoc w R