TB-Profiler result

Run: SRR6824707
Summary

Run ID: SRR6824707

Sample name:

Date: 2024-10-05T11:54:40.119823

Number of reads: 14657793

Percentage reads mapped: 98.89

Median coverage: 444.0

Strain: lineage2.2.1;lineage4.5

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.75
lineage2 East-Asian RD105 0.24
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.25
lineage2.2 East-Asian (Beijing) RD105;RD207 0.25
lineage4 Euro-American None 0.75
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.Ser315Asn Assoc w R High-level resistance
ethambutol
pyrazinamide pncA c.540dupC Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 0.26 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.25 streptomycin Assoc w R
katG 2155168 p.Ser315Asn missense_variant 0.2 isoniazid Assoc w R High-level resistance
pncA 2288701 c.540dupC frameshift_variant 0.2 pyrazinamide 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 7832 c.531G>T synonymous_variant 0.73 levofloxacin
moxifloxacin
gyrA 7892 c.591G>A synonymous_variant 0.71 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8834 c.1533C>T synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.27 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.24 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.76 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.29 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.24 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.24 ethionamide Uncertain significance
mmaA3 737305 p.Gly282Asp missense_variant 0.22 isoniazid
rpoB 762086 c.2280G>A synonymous_variant 0.79 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.27 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.25 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.27 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 778961 c.-481C>A upstream_gene_variant 0.23 bedaquiline
clofazimine
mmpS5 779615 c.-710C>G upstream_gene_variant 0.22 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.21 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.28 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.27 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 2154724 p.Arg463Leu missense_variant 0.22 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.2 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.72 pyrazinamide 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
Rv1979c 2223601 c.-437C>T upstream_gene_variant 0.24 bedaquiline
clofazimine
ald 3086788 c.-32T>C upstream_gene_variant 0.26 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.23 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.24 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 0.84 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.82 pyrazinamide Not assoc w R
embC 4241577 p.Thr572Met missense_variant 0.33 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.42 ethambutol Not assoc w R
embB 4247507 p.Trp332Arg missense_variant 0.33 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.2 ethambutol Not assoc w R
aftB 4268386 c.451T>C synonymous_variant 0.25 ethambutol
ethA 4327307 p.Asp56Ala missense_variant 0.76 ethionamide Uncertain significance
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 4407588 c.615A>G synonymous_variant 0.23 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.25 streptomycin Not assoc w R