TB-Profiler result

Run: ERR11080995
Summary

Run ID: ERR11080995

Sample name:

Date: 2024-04-16T11:36:54.759192

Number of reads: 2126671

Percentage reads mapped: 99.64

Median coverage: 56.0

Strain: lineage4.2.1.1;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 0.63
lineage4.2 Euro-American None 0.41
lineage4 Euro-American None 1.0
lineage4.2.1.1 Euro-American (TUR) None 0.38
lineage4.2.1 Euro-American (TUR) None 0.36
lineage4.3.3 Euro-American (LAM) RD115 0.6
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Leu Assoc w R
isoniazid inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>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.Gly406Ala Assoc w R
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA p.Val44Gly Assoc w R - Interim
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>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.His445Leu missense_variant 0.46 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.32 streptomycin Assoc w R
inhA 1673423 c.-779G>T upstream_gene_variant 0.46 ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.41 isoniazid Assoc w R High-level resistance
pncA 2289111 p.Val44Gly missense_variant 0.45 pyrazinamide Assoc w R - Interim
embB 4247730 p.Gly406Ala missense_variant 0.37 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.39 ethambutol Uncertain significance Mutation from literature
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 7058 p.Ile607Val missense_variant 0.65 levofloxacin Uncertain significance
moxifloxacin 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 0.45 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
ccsA 620511 c.621C>T synonymous_variant 0.44 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.64 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 777451 p.Val344Leu missense_variant 0.34 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.43 linezolid
Rv1129c 1254582 c.-48A>C upstream_gene_variant 0.34 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303095 c.165G>A synonymous_variant 0.62 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.6 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 2063685 c.1044G>A synonymous_variant 0.36 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2103023 p.Pro7Leu missense_variant 0.37 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
katG 2156196 c.-85C>T upstream_gene_variant 0.52 isoniazid Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.27 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 2518919 p.Gly269Ser missense_variant 0.66 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.65 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.58 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.4 cycloserine
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 0.48 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.53 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4268566 p.Ser91Ala missense_variant 0.55 ethambutol Uncertain significance
ethA 4327377 p.Ala33Pro missense_variant 0.37 ethionamide 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 1.0 capreomycin
amikacin
kanamycin
gid 4407598 p.Val202Glu missense_variant 0.4 streptomycin
gid 4408156 p.Leu16Arg missense_variant 0.57 streptomycin Not assoc w R
gid 4408213 c.-11C>T upstream_gene_variant 0.41 streptomycin Uncertain significance