TB-Profiler result

Run: ERR4816451
Summary

Run ID: ERR4816451

Sample name:

Date: 2024-10-05T03:15:42.477292

Number of reads: 1868822

Percentage reads mapped: 99.82

Median coverage: 43.0

Strain: lineage3;lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.2
lineage4 Euro-American None 0.81
lineage4.9 Euro-American (H37Rv-like) None 0.86
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 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.19 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.23 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.15 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 619952 p.Ala21Val missense_variant 0.33 kanamycin
capreomycin
amikacin
mmpL5 775639 p.Ile948Val missense_variant 0.31 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 0.37 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.23 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.25 pyrazinamide Not assoc w R
ahpC 2726105 c.-88G>A upstream_gene_variant 0.21 isoniazid Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.37 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841473 c.-53G>A upstream_gene_variant 0.23 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.29 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 0.18 ethambutol Not assoc w R
embA 4245881 p.Asp883Glu missense_variant 0.16 ethambutol Uncertain significance
aftB 4267142 c.1695C>A synonymous_variant 0.21 ethambutol Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 0.17 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.19 kanamycin
capreomycin
amikacin