TB-Profiler result

Run: ERR114465
Summary

Run ID: ERR114465

Sample name:

Date: 2024-04-16T11:54:08.394522

Number of reads: 3735770

Percentage reads mapped: 99.49

Median coverage: 85.0

Strain: lineage3.1.3;lineage4.8.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.83
lineage3.1.3 East-African-Indian RD750 0.84
lineage4 Euro-American None 0.2
lineage4.8 Euro-American (mainly T) RD219 0.17
lineage4.8.2 Euro-American (mainly T) RD219 0.14
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 rrs n.514A>C Assoc w R
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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.96 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 0.74 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8135 c.834C>T synonymous_variant 0.27 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 0.7 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.86 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.77 ethionamide Not assoc w R - Interim
nusG 734261 p.Thr3Asn missense_variant 0.79 rifampicin Not assoc w R
nusG 734658 c.405A>G synonymous_variant 0.22 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.84 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.79 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 0.82 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776891 p.Gln530His missense_variant 0.19 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.79 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406613 p.Glu243Ala missense_variant 0.79 streptomycin Uncertain significance
isoniazid Not assoc w R
pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834159 c.618G>A synonymous_variant 0.81 pyrazinamide Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.75 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.86 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.82 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.22 pyrazinamide Not assoc w R
PPE35 2168337 p.Leu759Ser missense_variant 0.19 pyrazinamide Uncertain significance
Rv1979c 2222732 c.432delT frameshift_variant 0.84 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289365 c.-125delC upstream_gene_variant 0.83 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.91 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.8 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
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.26 capreomycin
thyA 3074197 p.Pro92Leu missense_variant 0.81 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.85 cycloserine
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.14 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.8 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625836 p.Met260Val missense_variant 0.14 bedaquiline
rifampicin Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.19 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.89 pyrazinamide
embC 4242075 p.Arg738Gln missense_variant 0.85 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249195 c.2682C>A synonymous_variant 0.8 ethambutol Not assoc w R
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 0.79 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.83 streptomycin Not assoc w R
gid 4408175 p.Ala10Pro missense_variant 0.79 streptomycin Uncertain significance