TB-Profiler result

Run: SRR18715462
Summary

Run ID: SRR18715462

Sample name:

Date: 2024-04-16T10:59:31.233779

Number of reads: 2996684

Percentage reads mapped: 99.53

Median coverage: 90.0

Strain: lineage2.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.62
lineage2 East-Asian RD105 0.37
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.36
lineage2.2 East-Asian (Beijing) RD105;RD207 0.37
lineage4 Euro-American None 0.62
lineage4.3.3 Euro-American (LAM) RD115 0.59
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
rpoC p.Gly332Arg Uncertain significance Mutation from literature
p.Asp485Asn Uncertain significance Mutation from literature
isoniazid katG p.Ile335Val Uncertain significance Mutation from literature
p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gly406Asp Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpoC 764363 p.Gly332Arg missense_variant 0.14 rifampicin Uncertain significance Mutation from literature
rpoC 764822 p.Asp485Asn missense_variant 0.4 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.39 streptomycin Assoc w R
katG 2155109 p.Ile335Val missense_variant 0.34 isoniazid Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4247730 p.Gly406Asp missense_variant 0.64 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.32 ethambutol 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 8040 p.Gly247Ser missense_variant 0.6 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
fgd1 491742 c.960T>C synonymous_variant 0.46 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.42 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.42 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.43 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.68 rifampicin Not assoc w R
rpoC 766488 p.Pro1040Arg missense_variant 0.62 rifampicin Uncertain significance
rpoC 766667 p.Ser1100Ala missense_variant 0.68 rifampicin Uncertain significance
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 0.45 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.38 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.29 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302917 c.-14_-13insA upstream_gene_variant 0.42 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.32 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.28 pyrazinamide Not assoc w R - Interim
rpsA 1834776 p.Ala412Val missense_variant 0.38 pyrazinamide Uncertain significance
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 0.27 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.41 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.65 isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.5 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339490 p.Leu125Ile missense_variant 0.61 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.31 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 0.43 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640879 c.337C>T synonymous_variant 0.32 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
alr 3840953 c.468C>T synonymous_variant 0.62 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.56 pyrazinamide 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 0.41 ethambutol Not assoc w R
embA 4243598 c.366G>A synonymous_variant 0.38 ethambutol Not assoc w R - Interim
embA 4244823 p.Val531Leu missense_variant 0.56 ethambutol Uncertain significance
embB 4247872 c.1359C>T synonymous_variant 0.37 ethambutol Not assoc w R - Interim
embB 4248316 c.1803C>T synonymous_variant 0.7 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.33 ethambutol Not assoc w R
ethA 4326474 p.Pro334Ala missense_variant 0.33 ethionamide Uncertain significance
whiB6 4338326 p.Ala66Thr missense_variant 0.32 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 0.37 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.33 streptomycin Not assoc w R
gid 4408009 p.Val65Ala missense_variant 0.68 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.72 streptomycin Not assoc w R