TB-Profiler result

Run: SRR19115690
Summary

Run ID: SRR19115690

Sample name:

Date: 2024-04-15T00:49:06.303510

Number of reads: 11486770

Percentage reads mapped: 99.5

Median coverage: 319.0

Strain: lineage4.2.2.2;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
lineage4.2.2 Euro-American (Ural) None 0.44
lineage4.6 Euro-American None 0.54
lineage4.6.2 Euro-American RD726 0.46
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.53
lineage4.2 Euro-American None 0.48
lineage4 Euro-American None 1.0
lineage4.2.2.2 Euro-American (Ural) None 0.48
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 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 8688 p.Ala463Ser missense_variant 0.41 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
mshA 576077 c.730C>T synonymous_variant 0.44 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.26 ethionamide
isoniazid
Rv0565c 657425 p.Gly16Ser missense_variant 0.58 ethionamide Uncertain significance
rpoB 761489 c.1683G>A synonymous_variant 0.55 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778298 c.183G>A synonymous_variant 0.46 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.47 linezolid
Rv1258c 1406353 p.Pro330Ser missense_variant 0.47 streptomycin
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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 0.59 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
bacA 2063685 c.1044G>A synonymous_variant 0.43 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.51 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2996208 p.Ala35Asp missense_variant 0.65 capreomycin Uncertain significance
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.44 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.51 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.5 cycloserine
Rv3083 3448567 p.His22Asp missense_variant 0.51 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.46 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 0.52 ethambutol Not assoc w R
ethA 4326049 c.1425C>T synonymous_variant 0.49 ethionamide
ethA 4326739 c.735C>G synonymous_variant 0.48 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.48 ethionamide Not assoc w R - Interim
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