TB-Profiler result

Run: ERR2510340
Summary

Run ID: ERR2510340

Sample name:

Date: 2024-10-05T03:05:07.722889

Number of reads: 1798884

Percentage reads mapped: 99.68

Median coverage: 61.0

Strain: lineage3;lineage4.9

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 0.83
lineage4 Euro-American None 0.17
lineage4.9 Euro-American (H37Rv-like) None 0.15
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.Met306Val Assoc w R
pyrazinamide pncA p.Pro54Leu Assoc w R
streptomycin rpsL p.Lys43Arg 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
rpoB 761155 p.Ser450Leu missense_variant 0.24 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.17 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.17 isoniazid Assoc w R High-level resistance
pncA 2289081 p.Pro54Leu missense_variant 0.17 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.14 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
gyrB 6463 c.1224C>T synonymous_variant 0.9 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.92 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.83 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.82 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 576400 c.1053C>T synonymous_variant 0.18 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.76 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.88 rifampicin Not assoc w R
rpoB 761461 p.Arg552Leu missense_variant 0.18 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.91 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.89 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 0.84 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 1254562 c.-28T>C upstream_gene_variant 0.8 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 0.85 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 0.95 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.83 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
pncA 2289365 c.-125delC upstream_gene_variant 0.81 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.79 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.89 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2477c 2783502 c.541T>C synonymous_variant 0.19 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.94 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.79 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3642877 p.Lys448Arg missense_variant 0.74 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rpoA 3877536 c.972C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.88 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.79 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
glpK 4139246 c.510C>T synonymous_variant 0.81 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.9 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.87 ethambutol Not assoc w R
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 0.88 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.73 streptomycin Not assoc w R