TB-Profiler result

Run: SRR25827715
Summary

Run ID: SRR25827715

Sample name:

Date: 2024-04-15T13:26:07.836138

Number of reads: 9336849

Percentage reads mapped: 98.79

Median coverage: 307.0

Strain: lineage3;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
lineage3 East-African-Indian RD750 0.62
lineage4 Euro-American None 0.39
lineage4.8 Euro-American (mainly T) RD219 0.37
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 gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.62 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
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 0.6 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.59 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.68 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576453 p.Val369Gly missense_variant 0.23 ethionamide
isoniazid
Rv0565c 657081 c.390G>A synonymous_variant 0.61 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.7 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.62 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.61 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 0.67 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.61 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 1474001 n.344C>T non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.52 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2103245 c.-203G>A upstream_gene_variant 0.6 ethionamide
delamanid
isoniazid
katG 2154724 p.Arg463Leu missense_variant 0.61 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.65 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
Rv1979c 2223491 c.-327C>A upstream_gene_variant 0.37 clofazimine Not assoc w R
bedaquiline Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.68 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.63 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.64 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.6 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
ald 3086788 c.-32T>C upstream_gene_variant 0.61 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.65 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840652 p.Val257Leu missense_variant 0.57 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.68 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.66 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 4242075 p.Arg738Gln missense_variant 0.6 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245835 p.Leu868Arg missense_variant 0.17 ethambutol
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 0.74 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.6 streptomycin Not assoc w R
gid 4408273 c.-72delG upstream_gene_variant 0.43 streptomycin