TB-Profiler result

Run: SRR28394209
Summary

Run ID: SRR28394209

Sample name:

Date: 2024-05-22T18:57:37.592618

Number of reads: 3267859

Percentage reads mapped: 99.62

Median coverage: 92.0

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 0.95
lineage4.3.4.1 Euro-American (LAM) RD174 0.95
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.95
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)
ahpC c.-74G>A Uncertain significance Mutation from literature
ethambutol embB p.Ser347Ile Uncertain significance Mutation from literature
pyrazinamide pncA p.Tyr103* Assoc w R
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 0.92 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 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)
pncA 2288933 p.Tyr103* stop_gained 0.89 pyrazinamide Assoc w R
ahpC 2726119 c.-74G>A upstream_gene_variant 0.91 isoniazid Uncertain significance Mutation from literature
embB 4247553 p.Ser347Ile missense_variant 0.96 ethambutol Uncertain significance Mutation from literature
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764918 p.Val517Leu missense_variant 0.93 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.89 rifampicin Not assoc w R
rpoC 765590 p.Arg741Ser missense_variant 0.95 rifampicin Uncertain significance
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
sigE 1364434 p.Arg8Trp missense_variant 0.94 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1833612 p.Ala24Gly missense_variant 0.99 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.95 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154158 p.Ser652Pro missense_variant 0.92 isoniazid Uncertain significance
Rv1979c 2223123 c.42G>A synonymous_variant 0.92 clofazimine Not assoc w R - Interim
bedaquiline 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
thyA 3073868 p.Thr202Ala missense_variant 0.96 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.95 cycloserine
ald 3087412 p.Asp198Gly missense_variant 0.94 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.98 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.97 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.94 pyrazinamide 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 0.98 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.98 capreomycin
amikacin
kanamycin
gid 4407679 p.Arg175Pro missense_variant 0.96 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.97 streptomycin Not assoc w R