TB-Profiler result

Run: SRR7516376
Summary

Run ID: SRR7516376

Sample name:

Date: 2025-02-11T20:07:22.779094

Number of reads: 1786400

Percentage reads mapped: 99.56

Median coverage: 53.0

Strain: lineage2.2.1;lineage4.8

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 0.36
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.33
lineage2.2 East-Asian (Beijing) RD105;RD207 0.39
lineage4 Euro-American None 0.63
lineage4.8 Euro-American (mainly T) RD219 0.6
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
p.Tyr334His Uncertain significance Mutation from literature
pyrazinamide pncA p.His71Arg Assoc w R
p.His51Gln Assoc w R
streptomycin rpsL p.Lys88Arg Assoc w R
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>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
gyrA 7582 p.Asp94Gly missense_variant 0.35 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761095 p.Leu430Pro missense_variant 0.76 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.31 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.35 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.31 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289030 p.His71Arg missense_variant 0.37 pyrazinamide Assoc w R
pncA 2289089 p.His51Gln missense_variant 0.57 pyrazinamide Assoc w R
embA 4243221 c.-12C>T upstream_gene_variant 0.43 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.59 ethambutol Assoc w R
embB 4247513 p.Tyr334His missense_variant 0.4 ethambutol Uncertain significance Mutation from literature
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 6518 p.Val427Met missense_variant 0.51 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.33 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.26 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.28 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.34 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.33 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.33 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.29 ethionamide Uncertain significance
nusG 733930 c.-324C>A upstream_gene_variant 0.64 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.43 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.31 rifampicin Uncertain significance
rpoC 766645 p.Glu1092Asp missense_variant 0.36 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 0.42 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.39 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.36 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.3 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1416476 p.Tyr291Cys missense_variant 0.68 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.71 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.28 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.46 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 0.39 isoniazid Not assoc w R
katG 2156618 c.-507C>G upstream_gene_variant 0.35 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.52 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.45 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
kasA 2518912 c.798G>C synonymous_variant 0.7 isoniazid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.54 capreomycin
ald 3087532 p.Ala238Asp missense_variant 0.42 cycloserine
Rv3236c 3612229 c.888C>T synonymous_variant 0.28 pyrazinamide Not assoc w R - Interim
Rv3236c 3612813 p.Thr102Ala missense_variant 0.44 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.29 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.39 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.4 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.37 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 0.19 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.43 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.33 streptomycin Not assoc w R