TB-Profiler result

Run: SRR6936634
Summary

Run ID: SRR6936634

Sample name:

Date: 2024-03-25T22:43:18.303541

Number of reads: 488110

Percentage reads mapped: 99.77

Median coverage: 28.0

Strain: lineage4

Spoligotype:

Drug-resistance: HR-TB

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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
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
c.702delG Assoc w R High-level resistance
ethambutol embB p.Gly406Cys Assoc w R
pyrazinamide
streptomycin gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fbiB c.402delC Assoc w R - Interim Confers DLM-PMD cross-resistance
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
katG 2155409 c.702delG frameshift_variant 0.38 isoniazid Assoc w R High-level resistance
fbiB 3641934 c.402delC frameshift_variant 0.23 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
embB 4247729 p.Gly406Cys missense_variant 1.0 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin Assoc w R
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 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8553 c.1255delG frameshift_variant 0.2 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620178 c.288G>C synonymous_variant 1.0 capreomycin
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rpoC 764818 c.1449G>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 767149 c.3782delG frameshift_variant 0.4 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254473 c.61delC frameshift_variant 0.18 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
fbiC 1304501 p.Ala524Gly missense_variant 0.97 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fbiC 1305357 c.2427C>G synonymous_variant 1.0 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853666 c.63delG frameshift_variant 0.69 linezolid Uncertain significance
tsnR 1853697 c.96delC frameshift_variant 0.41 linezolid Uncertain significance
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
ndh 2102292 c.750delC frameshift_variant 0.24 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
PPE35 2168742 p.Gly624Asp missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170209 c.403delG frameshift_variant 0.67 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2747734 c.-137delG upstream_gene_variant 0.18 para-aminosalicylic_acid
Rv2681 2996916 c.181delG frameshift_variant 0.32 capreomycin Uncertain significance
whiB7 3568918 c.-240delC upstream_gene_variant 0.48 streptomycin
amikacin
kanamycin
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038911 c.1793delC frameshift_variant 0.25 pyrazinamide
embC 4239437 c.-426T>C upstream_gene_variant 1.0 ethambutol Uncertain significance
embC 4241300 c.1440delC frameshift_variant 0.24 ethambutol
embC 4242622 c.2762delG frameshift_variant 0.5 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243185 c.-47delC upstream_gene_variant 0.33 ethambutol
embA 4243791 c.562delC frameshift_variant 0.39 ethambutol Uncertain significance
embA 4244566 c.1336delC frameshift_variant 0.35 ethambutol Uncertain significance
aftB 4267948 c.888delC frameshift_variant 0.44 ethambutol Uncertain significance
aftB 4268343 c.493delC frameshift_variant 0.29 ethambutol Uncertain significance
ethA 4327376 p.Ala33Gly missense_variant 1.0 ethionamide Uncertain significance
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