TB-Profiler result

Run: ERR5897097
Summary

Run ID: ERR5897097

Sample name:

Date: 2024-10-05T03:22:07.151744

Number of reads: 7897892

Percentage reads mapped: 99.39

Median coverage: 238.0

Strain: lineage3;lineage4.6.2.1

Spoligotype:

Drug-resistance: MDR-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 0.12
lineage4.6 Euro-American None 0.89
lineage4.6.2 Euro-American RD726 0.87
lineage4 Euro-American None 0.88
lineage4.6.2.1 Euro-American RD726 0.89
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Arg Assoc w R
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)
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
streptomycin gid c.351delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
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
rpoB 761140 p.His445Arg missense_variant 0.89 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.12 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.14 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.1 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)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288883 p.Leu120Arg missense_variant 0.12 pyrazinamide Assoc w R
embB 4247429 p.Met306Leu missense_variant 0.29 ethambutol Assoc w R
embB 4247429 p.Met306Val missense_variant 0.71 ethambutol Assoc w R
gid 4407851 c.351delG frameshift_variant 0.84 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
dnaA 324 c.324C>G synonymous_variant 0.86 isoniazid Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7581 p.Asp94Ser missense_variant 0.84 levofloxacin
moxifloxacin
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
Rv0565c 657081 c.390G>A synonymous_variant 0.12 ethionamide Not assoc w R - Interim
nusG 734810 p.Glu186Ala missense_variant 0.11 rifampicin Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.11 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.11 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.15 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 0.12 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 778298 c.183G>A synonymous_variant 0.91 bedaquiline Not assoc w R - Interim
clofazimine 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 0.13 linezolid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
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
tlyA 1918272 c.333C>T synonymous_variant 0.12 capreomycin Not assoc w R - Interim
bacA 2063187 c.1542C>T synonymous_variant 0.89 kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.12 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.16 pyrazinamide Not assoc w R
Rv1979c 2221882 p.Leu428Gln missense_variant 0.82 bedaquiline
clofazimine
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.14 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.12 pyrazinamide
eis 2714606 p.Ala243Ser missense_variant 0.89 kanamycin
amikacin
ahpC 2726105 c.-88G>A upstream_gene_variant 0.17 isoniazid Not assoc w R
ahpC 2726600 c.408T>C synonymous_variant 0.8 isoniazid
Rv2680 2996208 p.Ala35Asp missense_variant 0.87 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.15 cycloserine
fbiD 3338919 c.-199C>G upstream_gene_variant 0.86 pretomanid
delamanid
clofazimine
alr 3841473 c.-53G>A upstream_gene_variant 0.13 cycloserine
rpoA 3878654 c.-147A>G upstream_gene_variant 0.83 rifampicin Uncertain significance
glpK 4138622 c.1134C>T synonymous_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242883 c.3021C>T synonymous_variant 0.91 ethambutol Not assoc w R - Interim
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 0.15 streptomycin Not assoc w R
gid 4407790 p.Ala138Val missense_variant 0.14 streptomycin Uncertain significance