TB-Profiler result

Run: ERR144612
Summary

Run ID: ERR144612

Sample name:

Date: 2024-04-15T06:25:29.741548

Number of reads: 6854082

Percentage reads mapped: 99.61

Median coverage: 151.0

Strain: lineage4.1.2;lineage4.3.4.1;lineage4.8

Spoligotype:

Drug-resistance: RR-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 0.48
lineage4.1 Euro-American None 0.24
lineage4.1.2 Euro-American None 0.06
lineage4.3.4.1 Euro-American (LAM) RD174 0.47
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.31
lineage4.3.4 Euro-American (LAM) RD174 0.48
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
isoniazid
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
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 1474 p.Asp492Asn missense_variant 0.29 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 0.66 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.75 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13717 c.-159T>G upstream_gene_variant 0.17 isoniazid
mshA 575679 p.Asn111Ser missense_variant 0.13 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.31 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.21 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.32 rifampicin Not assoc w R
rpoC 763783 c.414G>A synonymous_variant 0.49 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.48 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.19 rifampicin Not assoc w R
rpoC 765325 c.1956C>T synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 765435 p.His689Arg missense_variant 0.15 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 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
rplC 800219 c.-590T>C upstream_gene_variant 0.14 linezolid
sigE 1364434 p.Arg8Trp missense_variant 0.36 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.1 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.27 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.7 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2064647 p.Thr28Pro missense_variant 0.27 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
PPE35 2168147 c.2464_2466delCCAinsTG frameshift_variant&missense_variant 0.49 pyrazinamide Uncertain significance
Rv1979c 2223123 c.42G>A synonymous_variant 0.46 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2746540 c.1059G>A synonymous_variant 0.47 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.26 capreomycin
Rv2681 2996821 p.Gly28Ala missense_variant 0.46 capreomycin Uncertain significance
thyX 3067487 p.Lys153Asn missense_variant 0.5 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.47 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.78 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.45 pyrazinamide Not assoc w R
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.36 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.66 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3642576 p.Val348Ile missense_variant 0.13 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.57 pyrazinamide Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.28 pyrazinamide Not assoc w R
panD 4045058 c.-777G>A upstream_gene_variant 0.36 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.2 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.16 ethambutol Not assoc w R
ethR 4326910 c.-639G>A upstream_gene_variant 0.14 ethionamide
whiB6 4338550 c.-29A>T upstream_gene_variant 0.49 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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 0.66 capreomycin
amikacin
kanamycin
whiB6 4338735 c.-214C>G upstream_gene_variant 0.42 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.42 streptomycin Not assoc w R