TB-Profiler result

Run: SRR19428558
Summary

Run ID: SRR19428558

Sample name:

Date: 2024-10-05T11:46:49.057469

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 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 576077 c.730C>T synonymous_variant 0.42 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
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 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.33 bedaquiline
clofazimine
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 levofloxacin
moxifloxacin
isoniazid
rifampicin
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
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 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
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 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.62 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.42 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
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 rifampicin Not assoc w R
bedaquiline Uncertain significance
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 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
whiB6 4338846 c.-325T>G upstream_gene_variant 0.24 kanamycin
capreomycin
amikacin