TB-Profiler result

Run: ERR4799200
Summary

Run ID: ERR4799200

Sample name:

Date: 2024-10-04T12:54:35.124827

Number of reads: 4533954

Percentage reads mapped: 99.64

Median coverage: 131.0

Strain: lineage4.6.2.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.98
lineage4.6.2 Euro-American RD726 0.99
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.98
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
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrB p.Ala504Val Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Ala504Val Assoc w R - Interim
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
gyrB 6750 p.Ala504Val 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)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R 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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777311 c.1170C>G synonymous_variant 0.98 bedaquiline
clofazimine
mmpL5 778298 c.183G>A synonymous_variant 0.97 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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 2063187 c.1542C>T synonymous_variant 0.97 kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.96 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2996208 p.Ala35Asp missense_variant 0.98 capreomycin Uncertain significance
thyX 3067474 p.Pro158Ala missense_variant 0.98 para-aminosalicylic_acid
ald 3087733 p.Val305Ala missense_variant 0.98 cycloserine
Rv3083 3448567 p.His22Asp missense_variant 0.99 ethionamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
embA 4243230 c.-3C>T upstream_gene_variant 0.99 ethambutol Uncertain significance
aftB 4267272 p.Lys522Arg missense_variant 0.96 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 0.99 ethionamide Not assoc w R - Interim
ethA 4326885 p.Ser197Pro missense_variant 0.97 ethionamide Uncertain significance
ethR 4328004 c.456G>A synonymous_variant 0.98 ethionamide Not assoc w R - Interim
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