TB-Profiler result

Run: SRR998662
Summary

Run ID: SRR998662

Sample name:

Date: 2024-10-04T23:51:21.295786

Number of reads: 536562

Percentage reads mapped: 98.92

Median coverage: 12.0

Strain: lineage4.1.3;lineage6.3.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 0.22
lineage4.6.2 Euro-American RD726 0.29
lineage4.1 Euro-American None 0.12
lineage6.3 West-Africa 2 RD702 0.27
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.39
lineage6.3.1 West-Africa 2 RD702 0.1
lineage6 West-Africa 2 RD702 0.06
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 6446 p.Ala403Ser missense_variant 0.38 levofloxacin Not assoc w R
moxifloxacin 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 9143 c.1842T>C synonymous_variant 0.44 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
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
katG 2155503 c.609C>T synonymous_variant 0.26 isoniazid Not assoc w R
PPE35 2169715 p.Gly300Ser missense_variant 0.5 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
lpqB 3624660 p.Ala84Gly missense_variant 0.42 rifampicin Uncertain significance
bedaquiline Uncertain significance
aftB 4267272 p.Lys522Arg missense_variant 0.42 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 0.95 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