TB-Profiler result

Run: SRR25827730
Summary

Run ID: SRR25827730

Sample name:

Date: 2024-04-14T23:07:43.510891

Number of reads: 18256685

Percentage reads mapped: 99.28

Median coverage: 619.0

Strain: lineage2.2.1.1;lineage4.3.3

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 0.77
lineage2 East-Asian RD105 0.22
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.23
lineage2.2 East-Asian (Beijing) RD105;RD207 0.23
lineage4 Euro-American None 0.78
lineage4.3.3 Euro-American (LAM) RD115 0.78
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.23
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 embB p.Met306Val Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 0.2 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.2 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.21 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.17 ethambutol 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 8040 p.Gly247Ser missense_variant 0.73 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 491742 c.960T>C synonymous_variant 0.25 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.22 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.21 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.23 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.23 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.26 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.24 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.72 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 0.24 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.24 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.22 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 0.24 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.17 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 0.25 pyrazinamide Not assoc w R - Interim
rpsA 1834836 p.Met432Thr missense_variant 0.75 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 0.25 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.23 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 2518919 p.Gly269Ser missense_variant 0.76 isoniazid
eis 2714846 p.Val163Ile missense_variant 0.22 amikacin Not assoc w R
kanamycin Not assoc w R
Rv2477c 2784211 c.-169A>C upstream_gene_variant 0.25 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2784613 c.-571T>C upstream_gene_variant 0.71 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
thyA 3073868 p.Thr202Ala missense_variant 0.72 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22 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 0.22 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640230 c.-313T>G upstream_gene_variant 0.22 clofazimine
pretomanid
delamanid
clpC1 4038287 c.2418C>T synonymous_variant 0.79 pyrazinamide Not assoc w R
glpK 4139365 p.Arg131Ser missense_variant 0.75 ethambutol Uncertain significance
moxifloxacin
streptomycin Uncertain significance
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4139485 p.Thr91Ala missense_variant 0.76 ethambutol Uncertain significance
moxifloxacin
streptomycin Uncertain significance
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.22 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.15 ethambutol
embB 4247880 p.Val456Ala missense_variant 0.2 ethambutol Uncertain significance
embB 4248115 c.1602C>T synonymous_variant 0.22 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.23 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 4338599 c.-78A>C upstream_gene_variant 0.78 capreomycin
amikacin Uncertain significance
kanamycin
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.23 streptomycin Not assoc w R
gid 4407720 c.483C>G synonymous_variant 0.8 streptomycin Not assoc w R - Interim
gid 4407927 p.Glu92Asp missense_variant 0.21 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.8 streptomycin Not assoc w R