TB-Profiler result

Run: SRR19428558
Summary

Run ID: SRR19428558

Sample name:

Date: 2024-04-14T19:48:15.184830

Number of reads: 400039

Percentage reads mapped: 99.57

Median coverage: 17.0

Strain: lineage2.2.1;lineage3.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.34
lineage3 East-African-Indian RD750 0.21
lineage2 East-Asian RD105 0.11
lineage3.1.1 East-African-Indian RD750 0.16
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.09
lineage2.2 East-Asian (Beijing) RD105;RD207 0.16
lineage4.2.2.2 Euro-American (Ural) None 0.3
lineage3.1 East-African-Indian RD750 0.23
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
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
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 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
fgd1 491742 c.960T>C synonymous_variant 0.56 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576077 c.730C>T synonymous_variant 0.42 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
Rv0565c 657425 p.Gly16Ser missense_variant 0.73 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.6 rifampicin Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.62 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.33 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.45 linezolid
Rv1129c 1253806 c.729C>T synonymous_variant 0.9 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.54 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.76 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.54 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.62 pyrazinamide Not assoc w R
PPE35 2170461 p.Gly51Glu missense_variant 0.33 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
Rv2477c 2782498 c.1545C>T synonymous_variant 0.62 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.42 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.39 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.33 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.33 ethambutol 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
whiB6 4338846 c.-325T>G upstream_gene_variant 0.24 capreomycin
amikacin
kanamycin