TB-Profiler result

Run: SRR12420677
Summary

Run ID: SRR12420677

Sample name:

Date: 2024-04-15T22:27:08.875237

Number of reads: 3447635

Percentage reads mapped: 98.62

Median coverage: 81.0

Strain: lineage2.2.1;lineage4.3.4.1

Spoligotype:

Drug-resistance: HR-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 0.75
lineage2 East-Asian RD105 0.19
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.19
lineage2.2 East-Asian (Beijing) RD105;RD207 0.18
lineage4.3.4.1 Euro-American (LAM) RD174 0.81
lineage4 Euro-American None 0.78
lineage4.3.4 Euro-American (LAM) RD174 0.8
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 0.33 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.23 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
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
gyrA 9659 c.2358C>G synonymous_variant 0.91 levofloxacin
moxifloxacin
fgd1 491742 c.960T>C synonymous_variant 0.2 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.3 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.4 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.37 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.36 ethionamide Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.75 rifampicin Not assoc w R
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 0.21 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.16 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.27 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364434 p.Arg8Trp missense_variant 0.87 pyrazinamide Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.24 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.29 pyrazinamide Not assoc w R - Interim
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 2154279 c.1833C>T synonymous_variant 0.88 isoniazid Not assoc w R - Interim
PPE35 2168434 p.Gly727Trp missense_variant 0.81 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.96 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2290039 c.-798C>A upstream_gene_variant 0.3 pyrazinamide
thyA 3073868 p.Thr202Ala missense_variant 0.83 para-aminosalicylic_acid
thyA 3073948 p.Pro175Gln missense_variant 0.18 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448937 p.Tyr145Cys missense_variant 0.79 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.83 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.23 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.26 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640346 c.-197G>A upstream_gene_variant 0.2 clofazimine
pretomanid
delamanid
fbiA 3640377 c.-166G>A upstream_gene_variant 0.17 clofazimine
pretomanid
delamanid
clpC1 4038287 c.2418C>T synonymous_variant 0.71 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 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 0.17 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.11 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.71 streptomycin Not assoc w R