TB-Profiler result

Run: SRR29385502
Summary

Run ID: SRR29385502

Sample name:

Date: 2025-02-11T16:49:28.044353

Number of reads: 13576239

Percentage reads mapped: 99.61

Median coverage: 335.0

Strain: lineage2.2.1;lineage4.4.2

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
lineage2 East-Asian RD105 0.65
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.65
lineage2.2 East-Asian (Beijing) RD105;RD207 0.66
lineage4 Euro-American None 0.36
lineage4.4 Euro-American None 0.36
lineage4.4.2 Euro-American None 0.34
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asp Assoc w R
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly 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 7582 p.Asp94Gly missense_variant 0.38 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761139 p.His445Asp missense_variant 0.25 rifampicin 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 4957 c.-283G>A upstream_gene_variant 0.67 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 0.66 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.71 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.64 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.67 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.69 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.66 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 0.66 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.63 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 777171 p.His437Arg missense_variant 0.33 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 779202 c.-722G>A upstream_gene_variant 0.35 bedaquiline
clofazimine
mmpS5 779615 c.-710C>G upstream_gene_variant 0.66 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801361 p.Val185Ile missense_variant 0.34 linezolid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.65 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 0.6 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471679 n.-167C>T upstream_gene_variant 0.63 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.63 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 0.71 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.67 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
Rv2752c 3066099 p.Met31Ile missense_variant 0.4 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
Rv2752c 3066829 c.-638C>T upstream_gene_variant 0.66 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.61 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 0.61 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038824 c.1881C>T synonymous_variant 0.29 pyrazinamide Not assoc w R - Interim
panD 4044836 c.-555C>T upstream_gene_variant 0.37 pyrazinamide
embC 4238963 c.-900C>T upstream_gene_variant 0.31 ethambutol Not assoc w R
embC 4239700 c.-163A>G upstream_gene_variant 0.64 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.67 ethambutol Not assoc w R
embA 4244429 c.1197G>C synonymous_variant 0.69 ethambutol Not assoc w R - Interim
embA 4246508 c.3276G>A synonymous_variant 0.36 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.64 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.32 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.33 ethambutol Not assoc w R
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 0.65 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.69 streptomycin Not assoc w R