TB-Profiler result

Run: SRR28394141
Summary

Run ID: SRR28394141

Sample name:

Date: 2024-10-03T19:22:23.751302

Number of reads: 1679877

Percentage reads mapped: 99.62

Median coverage: 49.0

Strain: lineage2.2.1;lineage4

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.71
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.69
lineage2.2 East-Asian (Beijing) RD105;RD207 0.71
lineage4 Euro-American None 0.29
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
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
inhA 1673423 c.-779G>T upstream_gene_variant 0.35 ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer 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 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.72 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.79 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.73 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.68 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.68 ethionamide Uncertain significance
rpoB 761889 p.Val695Leu missense_variant 0.33 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.8 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 0.78 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.68 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.67 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 0.57 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 0.7 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 0.66 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 0.8 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.57 pyrazinamide Not assoc w R
Rv1979c 2221911 c.1254G>A synonymous_variant 0.76 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv1979c 2222852 p.Ala105Thr missense_variant 0.71 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.29 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289463 c.-222C>G upstream_gene_variant 0.81 pyrazinamide
Rv2681 2997755 c.1017G>C synonymous_variant 0.72 capreomycin Not assoc w R - Interim
Rv2752c 3065517 c.675C>T synonymous_variant 0.25 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.79 cycloserine
Rv3083 3448439 c.-64delA upstream_gene_variant 0.41 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.74 pyrazinamide Not assoc w R - Interim
lpqB 3624869 c.42C>T synonymous_variant 0.58 rifampicin
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 0.82 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.7 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044017 p.Ala89Thr missense_variant 0.71 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.78 ethambutol Not assoc w R
embB 4248403 c.1890G>A synonymous_variant 0.7 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.73 ethambutol Not assoc w R
ethA 4328317 c.-844C>T upstream_gene_variant 0.28 ethionamide
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 0.63 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.7 streptomycin Not assoc w R