TB-Profiler result

Run: ERR4800302
Summary

Run ID: ERR4800302

Sample name:

Date: 2024-04-14T23:48:42.754239

Number of reads: 2644315

Percentage reads mapped: 99.57

Median coverage: 72.0

Strain: lineage3;lineage4.4.1.1

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 0.77
lineage4.4.1 Euro-American (S-type) None 0.27
lineage4 Euro-American None 0.25
lineage4.4.1.1 Euro-American None 0.23
lineage4.4 Euro-American None 0.26
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide pncA c.149delT Assoc w R
streptomycin gid c.351delG Assoc w R
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)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.19 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
rpoB 761155 p.Ser450Leu missense_variant 0.25 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.15 isoniazid Assoc w R High-level resistance
pncA 2289092 c.149delT frameshift_variant 0.34 pyrazinamide Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.34 ethambutol Assoc w R
gid 4407851 c.351delG frameshift_variant 0.27 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.83 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.8 ethionamide Not assoc w R - Interim
hadA 732233 p.Lys102Glu missense_variant 0.83 isoniazid Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.62 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.77 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.81 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 0.81 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 1254562 c.-28T>C upstream_gene_variant 0.74 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254572 c.-38T>A upstream_gene_variant 0.28 moxifloxacin
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
bacA 2063946 c.783C>T synonymous_variant 0.79 streptomycin
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ndh 2102990 p.Val18Ala missense_variant 0.17 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.75 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.72 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.28 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 0.71 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.69 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.77 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.74 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
Rv2681 2997730 p.Ala331Val missense_variant 0.65 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.28 ethionamide Not assoc w R - Interim
Rv3083 3448684 p.Thr61Ala missense_variant 0.73 ethionamide Uncertain significance
Rv3083 3449922 c.1419G>A synonymous_variant 0.68 ethionamide Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 0.2 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
ddn 3986977 p.Pro45Leu missense_variant 0.23 delamanid Uncertain significance
pretomanid
clpC1 4039667 p.Gln346His missense_variant 0.73 pyrazinamide Uncertain significance
clpC1 4040126 c.579C>T synonymous_variant 0.63 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.76 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.78 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 4238963 c.-900C>T upstream_gene_variant 0.19 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.72 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.98 ethambutol Not assoc w R
embC 4243129 c.3267G>A synonymous_variant 0.3 ethambutol Not assoc w R - Interim
embA 4244050 p.Asp273Gly missense_variant 0.73 ethambutol 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 0.99 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.76 streptomycin Not assoc w R