TB-Profiler result

Run: SAMEA5569971
Summary

Run ID: SAMEA5569971

Sample name:

Date: 2024-10-04T16:12:05.358697

Number of reads: 10193082

Percentage reads mapped: 99.75

Median coverage: 317.0

Strain: lineage4.3.4.1

Spoligotype:

Drug-resistance: MDR-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 0.96
lineage4.3.4.1 Euro-American (LAM) RD174 0.96
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.96
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Met434Ile Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Asp435Gly Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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.371dupT 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
rpoB 761108 p.Met434Ile missense_variant 0.93 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761110 p.Asp435Gly missense_variant 0.93 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
inhA 1673425 c.-777C>T upstream_gene_variant 0.95 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)
gid 4407831 c.371dupT frameshift_variant 0.96 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
gyrA 7362 p.Glu21Gln missense_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
hadA 731927 c.-3G>T upstream_gene_variant 0.95 isoniazid Uncertain significance
rpoB 761167 p.Pro454Leu missense_variant 0.95 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.97 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.97 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 0.98 streptomycin Not assoc w R
sigE 1364434 p.Arg8Trp missense_variant 0.95 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853603 c.-3C>T upstream_gene_variant 0.96 linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.93 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.96 capreomycin Not assoc w R
katG 2155787 p.Ala109Thr missense_variant 0.94 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.94 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726323 p.Pro44Arg missense_variant 0.96 isoniazid Uncertain significance
Rv2477c 2784613 c.-571T>C upstream_gene_variant 0.59 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyX 3067657 p.Arg97Trp missense_variant 0.97 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.96 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.97 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.95 pyrazinamide Not assoc w R
Rv3236c 3612896 p.Gly74Ala missense_variant 0.95 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.97 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.96 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.95 ethambutol Not assoc w R
embB 4248320 p.Gly603Arg missense_variant 0.89 ethambutol Uncertain significance
ubiA 4269721 p.Ala38Val missense_variant 0.96 ethambutol Uncertain significance
ethA 4327311 p.Ser55Ala missense_variant 0.96 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 0.97 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.97 kanamycin
capreomycin
amikacin
whiB6 4338761 c.-240C>T upstream_gene_variant 0.96 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.97 streptomycin Not assoc w R