TB-Profiler result

Run: ERR4811870
Summary

Run ID: ERR4811870

Sample name:

Date: 2024-10-04T01:52:07.435521

Number of reads: 2656725

Percentage reads mapped: 99.8

Median coverage: 85.0

Strain: lineage4.3.4.2;lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.71
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.27
lineage4.3.4 Euro-American (LAM) RD174 0.75
lineage4.3.4.2 Euro-American (LAM) RD174 0.7
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
dnaA 371 p.Pro124Leu missense_variant 0.28 isoniazid Not assoc w R
gyrB 5009 c.-231G>A upstream_gene_variant 0.74 levofloxacin
moxifloxacin
gyrB 6140 p.Val301Leu missense_variant 0.79 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6208 c.969G>A synonymous_variant 0.72 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.73 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.73 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620455 p.Ala189Thr missense_variant 0.67 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.76 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
atpE 1460992 c.-53A>C upstream_gene_variant 0.29 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.65 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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
kasA 2518247 p.Ala45Ser missense_variant 0.71 isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.74 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.71 cycloserine
ald 3087026 p.Asp69Glu missense_variant 0.31 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.74 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.73 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.69 cycloserine
alr 3840764 c.657G>C synonymous_variant 0.39 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.79 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 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 0.73 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.72 streptomycin Not assoc w R