TB-Profiler result

Run: SRR1049738
Summary

Run ID: SRR1049738

Sample name:

Date: 2024-04-15T22:08:11.816576

Number of reads: 4264552

Percentage reads mapped: 98.82

Median coverage: 98.0

Strain: lineage4.1.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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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 0.25
lineage4.1 Euro-American None 0.79
lineage4.1.2 Euro-American None 0.78
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.77
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.24
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asn Assoc w R
p.His445Tyr Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
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
rpoB 761139 p.His445Asn missense_variant 0.26 rifampicin Assoc w R
rpoB 761139 p.His445Tyr missense_variant 0.74 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.19 isoniazid Assoc w R High-level resistance
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 434 p.His145Arg missense_variant 0.19 isoniazid Uncertain significance
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 0.32 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 491591 p.Lys270Met missense_variant 0.83 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.82 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.8 ethionamide Uncertain significance
Rv0565c 657449 p.Gly8Ser missense_variant 0.16 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.69 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.29 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.78 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 0.7 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
embR 1417942 c.-595G>T upstream_gene_variant 0.24 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.19 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.21 isoniazid Not assoc w R
PPE35 2169398 c.1214dupG frameshift_variant 0.21 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.79 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.17 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.26 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.26 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.33 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
glpK 4139015 c.741G>T synonymous_variant 0.24 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
embC 4239298 c.-565C>T upstream_gene_variant 0.84 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.79 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 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.25 streptomycin Not assoc w R