TB-Profiler result

Run: ERR234667
Summary

Run ID: ERR234667

Sample name:

Date: 2024-10-04T05:09:28.071734

Number of reads: 8309599

Percentage reads mapped: 99.66

Median coverage: 180.0

Strain: lineage4.3.3;lineage6.2.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.84
lineage6.2 West-Africa 2 RD702 0.1
lineage6.2.2 West-Africa 2 RD702 0.11
lineage4 Euro-American None 0.85
lineage4.3.3 Euro-American (LAM) RD115 0.85
lineage6 West-Africa 2 RD702 0.12
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 8040 p.Gly247Ser missense_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.11 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.14 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 656432 p.Gly347Ser missense_variant 0.13 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.11 ethionamide
rpoB 760969 p.Ser388Leu missense_variant 0.16 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.13 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.82 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.16 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
Rv1129c 1253973 p.Gly188Arg missense_variant 0.11 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.18 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303095 c.165G>A synonymous_variant 0.86 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
embR 1416633 p.Leu239Val missense_variant 0.15 ethambutol Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.12 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.13 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674434 p.Val78Ala missense_variant 0.13 isoniazid Not assoc w R
ethionamide Uncertain significance
rpsA 1834836 p.Met432Thr missense_variant 0.86 pyrazinamide Not assoc w R - Interim
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
bacA 2063121 c.1608A>T synonymous_variant 0.12 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.16 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.2 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.85 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.16 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.13 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.85 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.79 para-aminosalicylic_acid
Rv2477c 2783007 p.Arg346Cys missense_variant 0.19 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.85 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 0.17 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612800 p.Val106Ala missense_variant 0.12 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625813 c.801C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
alr 3840559 p.Arg288Ser missense_variant 0.11 cycloserine
alr 3840618 p.Asp268Gly missense_variant 0.11 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.86 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.84 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.11 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.11 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243541 c.309C>T synonymous_variant 0.11 ethambutol Not assoc w R - Interim
embA 4244220 c.988C>T synonymous_variant 0.14 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.13 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.12 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.11 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.11 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.12 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.15 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
gid 4407588 c.615A>G synonymous_variant 0.17 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.83 streptomycin Not assoc w R