TB-Profiler result

Run: SRR3732704
Summary

Run ID: SRR3732704

Sample name:

Date: 2024-10-04T13:37:59.147428

Number of reads: 4170259

Percentage reads mapped: 99.59

Median coverage: 81.0

Strain: lineage4.1.2.1;lineage4.6.2.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.66
lineage4.6.2 Euro-American RD726 0.58
lineage4.1 Euro-American None 0.4
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.58
lineage4.1.2 Euro-American None 0.42
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.47
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
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 7361 c.60C>T synonymous_variant 0.39 levofloxacin
moxifloxacin
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.46 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.43 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.28 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.33 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.4 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 778298 c.183G>A synonymous_variant 0.59 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 0.99 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 0.66 kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
PPE35 2168569 p.Thr682Pro missense_variant 0.44 pyrazinamide
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.5 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.33 isoniazid
Rv2680 2996208 p.Ala35Asp missense_variant 0.59 capreomycin Uncertain significance
thyX 3067474 p.Pro158Ala missense_variant 0.55 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.4 cycloserine
Rv3083 3448567 p.His22Asp missense_variant 0.7 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.35 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626161 c.453C>T synonymous_variant 0.41 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrA 3627756 c.-407A>T upstream_gene_variant 0.49 rifampicin
bedaquiline
clpC1 4038408 p.Pro766Leu missense_variant 0.43 pyrazinamide Uncertain significance
clpC1 4038857 c.1848C>A synonymous_variant 0.29 pyrazinamide
embC 4239298 c.-565C>T upstream_gene_variant 0.48 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.31 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 0.59 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 0.62 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.62 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