TB-Profiler result

Run: SRR29093639
Summary

Run ID: SRR29093639

Sample name:

Date: 2025-03-08T06:46:06.970159

Number of reads: 2222898

Percentage reads mapped: 99.53

Median coverage: 73.0

Strain: lineage4.9.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.9.1 Euro-American (H37Rv-like) None 0.98
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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 rpoB p.Ser450Leu Assoc w R
p.Arg552Cys Uncertain significance Mutation from literature: Frequently occurs together with other RRDR resistance mutations - potentially a compensatory mutation. doi: 10.1056/NEJMc1413930
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Gln Assoc w R - Interim
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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 0.98 rifampicin Assoc w R
rpoB 761460 p.Arg552Cys missense_variant 1.0 rifampicin Uncertain significance Mutation from literature: Frequently occurs together with other RRDR resistance mutations - potentially a compensatory mutation. doi: 10.1056/NEJMc1413930
rpsL 781687 p.Lys43Arg missense_variant 0.17 streptomycin Assoc w R
rpsL 781821 p.Lys88Gln missense_variant 0.79 streptomycin Assoc w R - Interim
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.81 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.16 ethambutol 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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8978 c.1677C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289138 p.Leu35Arg missense_variant 0.95 pyrazinamide Not assoc w R - Interim
fbiD 3339385 p.Asp90Asn missense_variant 0.97 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
embB 4247028 p.Leu172Arg missense_variant 0.2 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R