TB-Profiler result

Run: SRR28393316
Summary

Run ID: SRR28393316

Sample name:

Date: 2024-10-03T17:03:50.153472

Number of reads: 3486105

Percentage reads mapped: 99.79

Median coverage: 98.0

Strain: lineage4

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 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 rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Gly Uncertain significance Mutation from literature
ahpC c.-52C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Ala134Val Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.94delT Assoc w R
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 1.0 rifampicin Assoc w R
katG 2155169 p.Ser315Gly missense_variant 0.98 isoniazid Uncertain significance Mutation from literature
pncA 2288841 p.Ala134Val missense_variant 1.0 pyrazinamide Assoc w R
ahpC 2726141 c.-52C>T upstream_gene_variant 0.99 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.98 ethambutol Assoc w R
ethA 4327379 c.94delT frameshift_variant 0.96 ethionamide 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 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
rpoB 761889 p.Val695Leu missense_variant 0.99 rifampicin Uncertain significance
rpoC 766488 p.Pro1040Gln missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776440 p.Asp681Asn missense_variant 0.98 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 0.99 linezolid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 kanamycin
capreomycin
streptomycin
amikacin
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
PPE35 2168981 c.1632A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
PPE35 2168985 p.Thr543Met missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168987 p.Thr542Ala missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168990 c.1623T>G synonymous_variant 1.0 pyrazinamide
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3065074 p.Ser373Tyr missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3065517 c.675C>T synonymous_variant 0.98 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
Rv3083 3449563 p.Gly354Ser missense_variant 1.0 ethionamide Uncertain significance
rpoA 3878635 c.-128C>T upstream_gene_variant 0.23 rifampicin
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243217 c.-16C>A upstream_gene_variant 1.0 ethambutol Uncertain significance
ethA 4328317 c.-844C>T upstream_gene_variant 0.99 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407995 p.Ser70Arg missense_variant 0.99 streptomycin Uncertain significance