TB-Profiler result

Run: SRR25827407

Summary

Run ID: SRR25827407

Sample name:

Date: 2024-03-25T22:37:07.183112

Number of reads: 3316215

Percentage reads mapped: 96.17

Median coverage: 111.0

Strain: lineage2.2.1;lineage3

Spoligotype:

Drug-resistance: Pre-XDR-TB


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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.73
lineage2 East-Asian RD105 0.27
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.29
lineage2.2 East-Asian (Beijing) RD105;RD207 0.27
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
p.Gly406Ala Assoc w R
pyrazinamide pncA c.390_391dupGG Assoc w R
p.Leu27Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.351delG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Asn Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.78 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7581 p.Asp94Asn missense_variant 0.22 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.21 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288850 c.390_391dupGG frameshift_variant 0.74 pyrazinamide Assoc w R
pncA 2289162 p.Leu27Pro missense_variant 0.29 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.23 ethambutol Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.77 ethambutol Assoc w R
gid 4407851 c.351delG frameshift_variant 0.72 streptomycin 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
gyrB 5078 c.-162_-161insG upstream_gene_variant 0.3 levofloxacin
moxifloxacin
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 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.33 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.25 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.78 rifampicin Not assoc w R
rpoB 761465 c.1659G>A synonymous_variant 0.63 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 0.76 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764293 c.924G>C synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 764817 p.Val483Gly missense_variant 0.75 rifampicin Uncertain significance
rpoC 765383 p.Met672Leu missense_variant 0.14 rifampicin Uncertain significance
rpoC 766488 p.Pro1040Arg missense_variant 0.28 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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.26 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 1.0 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 0.23 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1673772 c.-430C>A upstream_gene_variant 0.19 ethionamide
isoniazid
inhA 1673778 c.-424C>G upstream_gene_variant 0.18 ethionamide
isoniazid
inhA 1673784 c.-418G>T upstream_gene_variant 0.2 ethionamide
isoniazid
inhA 1673787 c.-415G>C upstream_gene_variant 0.21 ethionamide
isoniazid
inhA 1673799 c.-403T>C upstream_gene_variant 0.21 ethionamide
isoniazid
inhA 1673802 c.-400A>G upstream_gene_variant 0.21 ethionamide
isoniazid
inhA 1673808 c.-394A>C upstream_gene_variant 0.19 ethionamide
isoniazid
fabG1 1673829 p.Asn130Lys missense_variant 0.16 ethionamide
isoniazid
fabG1 1673830 p.Lys131Arg missense_variant 0.16 ethionamide
isoniazid
inhA 1673838 c.-364T>C upstream_gene_variant 0.17 ethionamide
isoniazid
inhA 1673841 c.-361A>G upstream_gene_variant 0.16 ethionamide
isoniazid
fabG1 1673844 p.Met135Ile missense_variant 0.17 ethionamide
isoniazid
inhA 1673847 c.-355A>C upstream_gene_variant 0.17 ethionamide
isoniazid
inhA 1673853 c.-349A>C upstream_gene_variant 0.16 ethionamide
isoniazid
inhA 1673856 c.-346T>C upstream_gene_variant 0.15 ethionamide
isoniazid
inhA 1673865 c.-337C>G upstream_gene_variant 0.18 ethionamide
isoniazid
fabG1 1673870 p.Ser144Met missense_variant 0.17 ethionamide
isoniazid
inhA 1673877 c.-325C>G upstream_gene_variant 0.17 ethionamide
isoniazid
fabG1 1673905 p.Ser156Ala missense_variant 0.19 ethionamide
isoniazid
rpsA 1834177 c.636A>C synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.98 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 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 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
pncA 2289047 c.195C>T synonymous_variant 0.65 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.74 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.72 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.8 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3569220 c.-541C>T upstream_gene_variant 0.34 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.2 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 0.28 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.65 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.76 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.68 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243440 c.208C>T synonymous_variant 0.82 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.18 ethambutol Not assoc w R
embA 4245835 p.Leu868Arg missense_variant 0.17 ethambutol
ethA 4326676 p.Ser266Arg missense_variant 0.3 ethionamide Uncertain significance
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 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.37 streptomycin Not assoc w R