TB-Profiler result

Run: SRR28868527
Summary

Run ID: SRR28868527

Sample name:

Date: 2025-02-11T11:51:26.746198

Number of reads: 2053326

Percentage reads mapped: 98.62

Median coverage: 72.0

Strain: lineage4.4.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.4 Euro-American None 0.61
lineage4.4.2 Euro-American None 0.6
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 8147 p.Asn282Lys missense_variant 0.39 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 490748 c.-35G>A upstream_gene_variant 0.46 pretomanid
delamanid
clofazimine
rpoB 760640 c.834C>T synonymous_variant 0.59 rifampicin Not assoc w R - Interim
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
rplC 800155 c.-654A>C upstream_gene_variant 0.2 linezolid
fbiC 1304501 p.Ala524Gly missense_variant 0.49 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fbiC 1305357 c.2427C>G synonymous_variant 0.43 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
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
tlyA 1918439 p.Leu167Arg missense_variant 0.21 capreomycin
bacA 2064706 p.Pro8Leu missense_variant 0.63 kanamycin Uncertain significance
capreomycin
streptomycin Uncertain significance
amikacin Uncertain significance
PPE35 2168742 p.Gly624Asp missense_variant 0.31 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3066099 p.Met31Ile missense_variant 0.69 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.56 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625321 c.1293A>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
alr 3841534 c.-114C>T upstream_gene_variant 0.46 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 0.77 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.69 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.63 ethambutol Not assoc w R
ethA 4327376 p.Ala33Gly missense_variant 0.41 ethionamide Uncertain significance
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