TB-Profiler result

Run: SRR5341243
Summary

Run ID: SRR5341243

Sample name:

Date: 2024-04-16T03:44:52.580238

Number of reads: 1617730

Percentage reads mapped: 99.38

Median coverage: 42.0

Strain: lineage1.2.2.2;lineage2.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.19
lineage2 East-Asian RD105 0.78
lineage1.2.2.2 Indo-Oceanic RD239 0.17
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.78
lineage2.2 East-Asian (Beijing) RD105;RD207 0.79
lineage1 Indo-Oceanic RD239 0.1
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 pncA p.His82Arg Assoc w R
streptomycin
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)
ofloxacin
levofloxacin gyrA p.Ala90Val 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 7570 p.Ala90Val missense_variant 0.19 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
pncA 2288997 p.His82Arg missense_variant 0.26 pyrazinamide 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 8685 p.Ile462Val missense_variant 0.7 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 0.95 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.81 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.79 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.83 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.72 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.87 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.91 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 0.98 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.97 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.83 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.31 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.3 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.79 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
tlyA 1918645 p.Asn236Asp missense_variant 0.26 capreomycin Uncertain significance
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
PPE35 2168742 p.Gly624Asp missense_variant 0.21 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.58 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.56 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.27 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726051 c.-142G>A upstream_gene_variant 0.28 isoniazid
thyX 3067467 p.Ala160Val missense_variant 0.91 para-aminosalicylic_acid
thyX 3068145 c.-200C>A upstream_gene_variant 0.66 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.68 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.76 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040719 c.-15A>G upstream_gene_variant 0.25 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.27 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4138630 p.Asp376Asn missense_variant 0.84 ethambutol
moxifloxacin Uncertain significance
streptomycin
levofloxacin Uncertain significance
rifampicin
isoniazid
glpK 4139183 c.570_572dupGGG disruptive_inframe_insertion 0.87 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid 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 0.66 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.2 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.7 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.23 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.13 ethambutol Not assoc w R
whiB6 4338203 p.Arg107Cys missense_variant 0.25 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.79 streptomycin Not assoc w R