TB-Profiler result

Run: SRR1169026
Summary

Run ID: SRR1169026

Sample name:

Date: 2024-04-15T07:40:43.403298

Number of reads: 3312779

Percentage reads mapped: 99.6

Median coverage: 70.0

Strain: lineage2.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: Other

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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 0.55
lineage2 East-Asian RD105 0.43
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.42
lineage2.2 East-Asian (Beijing) RD105;RD207 0.47
lineage4 Euro-American None 0.6
lineage4.3.3 Euro-American (LAM) RD115 0.54
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.115delC 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 4408087 c.115delC frameshift_variant 0.44 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 8040 p.Gly247Ser missense_variant 0.49 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 0.4 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.33 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.49 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.39 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.53 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.52 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.67 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.42 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 0.39 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.47 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.48 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 0.42 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303095 c.165G>A synonymous_variant 0.49 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
sigE 1364706 c.294G>A synonymous_variant 0.57 pyrazinamide Not assoc w R - Interim
Rv1258c 1406089 p.Ala418Ser missense_variant 0.47 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide
Rv1258c 1406760 c.580_581insC frameshift_variant 0.33 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 0.56 pyrazinamide Not assoc w R - Interim
rpsA 1834836 p.Met432Thr missense_variant 0.44 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 0.49 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.55 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.36 pyrazinamide Not assoc w R
Rv1979c 2222112 c.1052dupT frameshift_variant 0.54 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2290080 c.-839T>A upstream_gene_variant 0.53 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 0.65 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.42 para-aminosalicylic_acid
Rv2477c 2783650 c.393C>T synonymous_variant 0.51 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2752c 3066133 p.Ala20Val missense_variant 0.52 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.52 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.51 pyrazinamide Not assoc w R - Interim
lpqB 3624078 p.Gly278Glu missense_variant 0.61 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.5 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.41 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.52 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.39 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.52 ethambutol Not assoc w R
ethA 4327406 p.Leu23Arg missense_variant 0.34 ethionamide 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 0.27 streptomycin Not assoc w R
gid 4407797 p.Ser136Pro missense_variant 0.49 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.45 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.62 streptomycin Not assoc w R