TB-Profiler result

Run: SRR14801488
Summary

Run ID: SRR14801488

Sample name:

Date: 2024-04-15T12:37:44.244852

Number of reads: 1716530

Percentage reads mapped: 99.66

Median coverage: 49.0

Strain: lineage2.2.1;lineage4.8

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 0.37
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.4
lineage2.2 East-Asian (Beijing) RD105;RD207 0.43
lineage4 Euro-American None 0.58
lineage4.8 Euro-American (mainly T) RD219 0.63
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.87delC Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.140delT Assoc w R
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
ethA 4327333 c.140delT frameshift_variant 0.47 ethionamide Assoc w R
gid 4408115 c.87delC frameshift_variant 0.61 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 0.42 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.46 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
mshA 575907 p.Ala187Val missense_variant 0.44 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.42 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.59 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.39 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.27 ethionamide Uncertain significance
nusG 733988 c.-266G>T upstream_gene_variant 0.38 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.37 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 0.5 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.46 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.54 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 0.35 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 0.39 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.59 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.39 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.51 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 0.56 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.4 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.49 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
ahpC 2725921 c.-272A>T upstream_gene_variant 0.33 isoniazid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.63 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.4 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.31 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.41 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.39 bedaquiline Uncertain significance
rifampicin Not assoc w R
glpK 4138759 p.Leu333Ile missense_variant 0.5 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.45 ethambutol Not assoc w R
embA 4244904 p.Val558Leu missense_variant 0.38 ethambutol Uncertain significance
embB 4248933 p.Asn807Thr missense_variant 0.54 ethambutol Uncertain significance
ethR 4327084 c.-465G>A upstream_gene_variant 0.45 ethionamide
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 0.37 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.42 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.37 streptomycin Not assoc w R