TB-Profiler result

Run: SRR5710016
Summary

Run ID: SRR5710016

Sample name:

Date: 2024-10-05T05:09:14.992089

Number of reads: 6250751

Percentage reads mapped: 99.59

Median coverage: 176.0

Strain: lineage2.2.1.1

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 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Arg Assoc w R
p.Glu460Gly Uncertain significance Mutation from literature
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)
p.Gly40Trp Uncertain significance Mutation from literature
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Lys Assoc w R
pyrazinamide pncA c.-1082_314del Assoc w R
streptomycin rrs n.907A>C Uncertain significance Mutation from literature
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.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
cycloserine alr p.Leu113Arg Mutation from literature
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
ethA c.481_482delAT Assoc w R
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 0.43 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 7582 p.Asp94Gly missense_variant 0.53 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761140 p.His445Arg missense_variant 0.99 rifampicin Assoc w R
rpoB 761185 p.Glu460Gly missense_variant 0.98 rifampicin Uncertain significance Mutation from literature
rrs 1472752 n.907A>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance Mutation from literature
inhA 1673423 c.-779G>T upstream_gene_variant 0.45 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)
inhA 1674319 p.Gly40Trp missense_variant 0.5 isoniazid Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288927 c.-1082_314del frameshift_variant&start_lost 0.99 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.51 kanamycin Assoc w R
alr 3841083 p.Leu113Arg missense_variant 0.47 cycloserine Mutation from literature
embB 4248002 p.Gln497Lys missense_variant 0.99 ethambutol Assoc w R
ethA 4326991 c.481_482delAT frameshift_variant 1.0 ethionamide 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 9086 c.1785C>T synonymous_variant 0.99 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.99 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 761821 p.Ser672Phe missense_variant 0.45 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766365 p.Ala999Gly missense_variant 0.54 rifampicin
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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 1.0 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781301 c.-259C>T upstream_gene_variant 0.98 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254131 p.Glu135Ala missense_variant 0.41 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.99 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 1.0 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 1.0 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 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 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2714846 p.Val163Ile missense_variant 0.99 kanamycin Not assoc w R
amikacin Not assoc w R
thyX 3067947 c.-2C>T upstream_gene_variant 0.99 para-aminosalicylic_acid
thyA 3073970 c.501delC frameshift_variant 0.99 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 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 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840259 p.Tyr388Asp missense_variant 0.45 cycloserine
alr 3841356 p.Ser22Leu missense_variant 0.33 cycloserine
alr 3841527 c.-107C>A upstream_gene_variant 0.98 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.99 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269317 p.Ser173Ala missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269714 p.Leu40Phe missense_variant 0.99 ethambutol Uncertain significance
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 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.99 streptomycin Not assoc w R