TB-Profiler result

Run: ERR5897084
Summary

Run ID: ERR5897084

Sample name:

Date: 2024-06-18T07:59:50.706536

Number of reads: 13804461

Percentage reads mapped: 99.5

Median coverage: 364.0

Strain: lineage3;lineage4.9

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.4
lineage4 Euro-American None 0.6
lineage4.9 Euro-American (H37Rv-like) 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 rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
c.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Leu Assoc w R
p.Met306Val Assoc w R
pyrazinamide pncA p.Leu120Arg Assoc w R
p.Pro54Leu Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.878G>A Assoc w R - Interim
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
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
gyrA 7570 p.Ala90Val missense_variant 0.65 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
gyrA 7582 p.Asp94Gly missense_variant 0.33 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.62 streptomycin Assoc w R
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 0.13 streptomycin Assoc w R - Interim
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.62 capreomycin Assoc w R
kanamycin Assoc w R
amikacin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.26 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
inhA 1674048 c.-154G>A upstream_gene_variant 0.65 ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288883 p.Leu120Arg missense_variant 0.31 pyrazinamide Assoc w R
pncA 2289081 p.Pro54Leu missense_variant 0.59 pyrazinamide Assoc w R
embB 4247429 p.Met306Leu missense_variant 0.45 ethambutol Assoc w R
embB 4247429 p.Met306Val missense_variant 0.52 ethambutol 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 0.34 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.4 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.39 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576400 c.1053C>T synonymous_variant 0.61 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.31 ethionamide Not assoc w R - Interim
nusG 734810 p.Glu186Ala missense_variant 0.31 rifampicin Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.41 rifampicin Not assoc w R
rpoB 759786 c.-21G>C upstream_gene_variant 0.11 rifampicin Uncertain significance
rpoB 761461 p.Arg552Leu missense_variant 0.65 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.4 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.43 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.28 rifampicin Uncertain significance
rpoC 766582 c.3213C>A synonymous_variant 0.28 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 776100 p.Thr794Ile missense_variant 0.4 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
rplC 800389 c.-420G>A upstream_gene_variant 0.27 linezolid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.36 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.42 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918272 c.333C>T synonymous_variant 0.3 capreomycin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.36 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.38 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.41 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.4 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.43 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.41 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2477c 2783502 c.541T>C synonymous_variant 0.58 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2784443 c.-401G>T upstream_gene_variant 0.67 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 0.4 cycloserine
ald 3086987 p.Gln56His missense_variant 0.59 cycloserine
ald 3087367 p.Ala183Val missense_variant 0.55 cycloserine
ald 3087604 p.Ala262Glu missense_variant 0.63 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.38 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841473 c.-53G>A upstream_gene_variant 0.4 cycloserine
rpoA 3877536 c.972C>T synonymous_variant 0.61 rifampicin Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.37 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.43 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.42 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.39 ethambutol Not assoc w R
ubiA 4269124 p.Ala237Val missense_variant 0.61 ethambutol Uncertain significance
whiB6 4338307 p.Ala72Gly missense_variant 0.65 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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 0.34 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.39 streptomycin Not assoc w R
gid 4407790 p.Ala138Val missense_variant 0.23 streptomycin Uncertain significance