TB-Profiler result

Run: SRR28351560
Summary

Run ID: SRR28351560

Sample name:

Date: 2024-05-22T11:08:21.766788

Number of reads: 19736580

Percentage reads mapped: 98.98

Median coverage: 617.0

Strain: lineage3;lineage4.1.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.53
lineage4.1 Euro-American None 0.47
lineage4.1.1.1 Euro-American (X-type) RD183 0.45
lineage4 Euro-American None 0.48
lineage4.1.1 Euro-American (X-type) None 0.48
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
gyrB 6998 p.Arg587Cys missense_variant 0.48 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 0.99 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
fgd1 491742 c.960T>C synonymous_variant 0.54 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.44 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.53 ethionamide Uncertain significance
rpoB 759571 c.-236C>G upstream_gene_variant 0.51 rifampicin
rpoB 759746 c.-61C>T upstream_gene_variant 0.53 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.5 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.47 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.49 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 0.51 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776219 c.2262C>G synonymous_variant 0.51 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.46 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.53 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
fabG1 1673368 c.-72A>G upstream_gene_variant 0.45 ethionamide
isoniazid
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 2064631 p.Cys33Tyr missense_variant 0.46 streptomycin
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.52 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.48 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
pncA 2289047 c.195C>T synonymous_variant 0.53 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.56 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.58 isoniazid Not assoc w R
ahpC 2726210 c.18T>C synonymous_variant 0.52 isoniazid Not assoc w R - Interim
Rv2477c 2782498 c.1545C>T synonymous_variant 0.43 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
pepQ 2860150 p.Ala90Val missense_variant 0.39 clofazimine Uncertain significance
bedaquiline
Rv2752c 3065276 c.915delC frameshift_variant 0.5 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448398 c.-106G>T upstream_gene_variant 0.51 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641447 p.Thr302Met missense_variant 0.45 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
alr 3841473 c.-53G>A upstream_gene_variant 0.43 cycloserine
rpoA 3877553 p.Glu319Lys missense_variant 0.54 rifampicin Not assoc w R
rpoA 3878601 c.-95delG upstream_gene_variant 0.31 rifampicin Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.56 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.61 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240897 c.1035C>G synonymous_variant 0.39 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.52 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.44 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.48 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 4338621 c.-100G>A upstream_gene_variant 0.51 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.54 streptomycin Not assoc w R