TB-Profiler result

Run: SRR11567801
Summary

Run ID: SRR11567801

Sample name:

Date: 2024-03-25T19:07:09.135846

Number of reads: 10887794

Percentage reads mapped: 99.52

Median coverage: 288.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.99
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Thr275Pro Uncertain significance Mutation from literature
ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol embB p.Gln497Lys Assoc w R
pyrazinamide pncA p.Pro54Arg Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Gly88Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Gly88Ala Assoc w R - Interim
p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.693_694dupGA 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
gyrA 7564 p.Gly88Ala missense_variant 0.99 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Ala missense_variant 1.0 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)
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155289 p.Thr275Pro missense_variant 0.99 isoniazid Uncertain significance Mutation from literature
pncA 2289081 p.Pro54Arg missense_variant 0.99 pyrazinamide Assoc w R
ahpC 2726145 c.-48G>A upstream_gene_variant 0.98 isoniazid Uncertain significance Mutation from literature
embB 4248002 p.Gln497Lys missense_variant 0.99 ethambutol Assoc w R
ethA 4326779 c.693_694dupGA frameshift_variant 0.17 ethionamide 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
dnaA 1093 p.Ile365Val missense_variant 0.11 isoniazid Uncertain significance
dnaA 1277 p.Thr426Ile missense_variant 0.82 isoniazid Uncertain significance
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 7892 c.591G>A synonymous_variant 0.99 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 576386 c.1040dupC frameshift_variant 0.98 ethionamide Uncertain significance
isoniazid Uncertain significance
ccsA 620029 c.139C>T synonymous_variant 0.99 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rpoB 761496 p.Tyr564His missense_variant 0.97 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 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
Rv1258c 1406101 p.Pro414Ser missense_variant 0.99 streptomycin Uncertain significance
isoniazid Not assoc w R
pyrazinamide Not assoc w R - Interim
Rv1258c 1407363 c.-23C>T upstream_gene_variant 0.99 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834165 c.624A>G synonymous_variant 1.0 pyrazinamide
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
PPE35 2170568 p.Ile15Met missense_variant 0.99 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
eis 2715076 p.Ala86Val missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2752c 3066155 c.36dupC frameshift_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625112 p.Ala501Val missense_variant 0.99 bedaquiline
rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269299 p.Ile179Leu missense_variant 0.98 ethambutol Uncertain significance
ethA 4326066 p.Arg470Cys missense_variant 0.99 ethionamide
ethA 4326899 p.Pro192Arg missense_variant 0.19 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 1.0 capreomycin
amikacin
kanamycin