TB-Profiler result

Run: SRR26399250
Summary

Run ID: SRR26399250

Sample name:

Date: 2024-10-05T10:48:58.466948

Number of reads: 1619434

Percentage reads mapped: 99.11

Median coverage: 44.0

Strain: lineage1.1.1;lineage2.2.1;lineage4.1.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.33
lineage4.1.2 Euro-American None 0.58
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.62
lineage1.1 Indo-Oceanic RD239 0.06
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.29
lineage2.2 East-Asian (Beijing) RD105;RD207 0.33
lineage4 Euro-American None 0.62
lineage1.1.1 Indo-Oceanic RD239 0.06
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 gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
gid 4408100 c.102delG frameshift_variant 0.66 streptomycin 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.23 isoniazid Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.28 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.44 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.78 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576602 p.Arg419Trp missense_variant 0.62 isoniazid
ethionamide
ccsA 620625 p.Ile245Met missense_variant 0.34 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.4 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.29 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.71 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.17 ethionamide
rpoB 760115 c.309C>T synonymous_variant 0.68 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.65 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.18 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.19 rifampicin Not assoc w R
rpoC 764061 p.Pro231Arg missense_variant 0.51 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.43 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 0.35 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.38 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 0.62 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 0.29 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.2 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673261 c.-941C>T upstream_gene_variant 0.68 isoniazid
ethionamide
inhA 1673406 c.-796C>G upstream_gene_variant 0.5 isoniazid Uncertain significance
ethionamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.31 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
bacA 2062922 p.Ile603Val missense_variant 0.15 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 0.17 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.48 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.56 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.13 bedaquiline Not assoc w R - Interim
clofazimine 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 2518076 c.-39C>T upstream_gene_variant 0.56 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.97 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.21 ethionamide Uncertain significance
Rv3236c 3613097 p.Leu7Pro missense_variant 0.54 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.18 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.23 pyrazinamide Not assoc w R - Interim
embC 4239298 c.-565C>T upstream_gene_variant 0.62 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.17 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.64 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.16 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.21 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.37 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.17 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 0.44 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.21 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.27 streptomycin Not assoc w R