TB-Profiler result

Run: SRR25827789
Summary

Run ID: SRR25827789

Sample name:

Date: 2024-04-15T13:26:08.669056

Number of reads: 22410499

Percentage reads mapped: 98.24

Median coverage: 325.0

Strain: lineage2.2.1;lineage4.1.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.09
lineage4.1 Euro-American None 0.76
lineage4.1.2 Euro-American None 0.78
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.79
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.09
lineage2.2 East-Asian (Beijing) RD105;RD207 0.12
lineage4 Euro-American None 0.78
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.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin
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 0.22 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.2 isoniazid Assoc w R High-level resistance
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
dnaA 1348 c.1348C>T synonymous_variant 0.74 isoniazid Not assoc w R - Interim
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 0.72 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.23 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575679 p.Asn111Ser missense_variant 0.8 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.23 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.79 ethionamide Uncertain significance
Rv0565c 657507 c.-37C>A upstream_gene_variant 0.77 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.74 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.2 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.77 rifampicin Not assoc w R
rpoC 766466 p.Glu1033Lys missense_variant 0.15 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.25 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 0.78 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.2 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
katG 2154724 p.Arg463Leu missense_variant 0.24 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.19 pyrazinamide Not assoc w R
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 0.75 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.12 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.81 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 0.77 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.2 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.19 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.17 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.17 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.2 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.16 ethambutol Not assoc w R - Interim
embB 4247028 p.Leu172Arg missense_variant 0.19 ethambutol
embB 4247039 p.Phe176Val missense_variant 0.17 ethambutol
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 4407588 c.615A>G synonymous_variant 0.2 streptomycin Not assoc w R
gid 4408368 c.-166A>G upstream_gene_variant 0.77 streptomycin