TB-Profiler result

Run: SRR20969615
Summary

Run ID: SRR20969615

Sample name:

Date: 2024-10-04T03:25:03.623230

Number of reads: 9864089

Percentage reads mapped: 99.62

Median coverage: 237.0

Strain: lineage2.2.1.1;lineage4.4.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.84
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.83
lineage2.2 East-Asian (Beijing) RD105;RD207 0.83
lineage4 Euro-American None 0.17
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.85
lineage4.4 Euro-American None 0.17
lineage4.4.2 Euro-American None 0.16
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Tyr Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Tyr 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 7581 p.Asp94Tyr missense_variant 0.84 levofloxacin Assoc w R
moxifloxacin Assoc w R 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
dnaA 365 p.Thr122Ile missense_variant 0.14 isoniazid 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8351 p.Asp350Glu missense_variant 0.14 levofloxacin
moxifloxacin
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 0.83 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.82 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.86 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.82 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.85 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.81 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.18 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 0.84 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.81 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.82 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 0.83 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 0.86 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673970 c.-232C>T upstream_gene_variant 0.17 isoniazid Uncertain significance
ethionamide
rpsA 1834177 c.636A>C synonymous_variant 0.82 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 0.82 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.8 pyrazinamide Not assoc w R
PPE35 2170865 c.-253G>A upstream_gene_variant 0.16 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2714762 c.571C>T synonymous_variant 0.8 kanamycin
amikacin
eis 2714846 p.Val163Ile missense_variant 0.8 kanamycin Not assoc w R
amikacin Not assoc w R
Rv2477c 2784034 c.9G>A synonymous_variant 0.82 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2680 2996097 c.-8A>C upstream_gene_variant 0.11 capreomycin
Rv2752c 3066099 p.Met31Ile missense_variant 0.14 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.23 ethionamide
whiB7 3568629 c.47_50dupCGGT frameshift_variant 0.14 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.87 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 0.87 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044052 p.His77Arg missense_variant 0.88 pyrazinamide
embC 4238963 c.-900C>T upstream_gene_variant 0.23 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.86 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 0.21 ethambutol Not assoc w R
embB 4247249 p.Gly246Arg missense_variant 0.14 ethambutol Uncertain significance
embB 4248115 c.1602C>T synonymous_variant 0.84 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.8 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.14 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.15 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 0.85 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.86 streptomycin Not assoc w R