TB-Profiler result

Run: ERR037547
Summary

Run ID: ERR037547

Sample name:

Date: 2024-04-14T11:39:36.971559

Number of reads: 19657066

Percentage reads mapped: 99.39

Median coverage: 342.0

Strain: lineage1.1.3.2;lineage4.3.4.1

Spoligotype:

Drug-resistance: Sensitive

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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 0.93
lineage1.1.3 Indo-Oceanic RD239 0.12
lineage1.1.3.2 Indo-Oceanic RD239 0.09
lineage1.1 Indo-Oceanic RD239 0.07
lineage4.3.4.1 Euro-American (LAM) RD174 0.9
lineage4 Euro-American None 0.9
lineage4.3.4 Euro-American (LAM) RD174 0.91
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
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
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 6112 p.Met291Ile missense_variant 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8188 p.Leu296Pro missense_variant 0.11 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 619695 c.-196G>A upstream_gene_variant 0.11 capreomycin
amikacin
kanamycin
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.1 ethionamide
rpoB 763031 c.3225T>C synonymous_variant 0.1 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.92 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 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801166 p.Gly120Ser missense_variant 0.11 linezolid Uncertain significance
sigE 1364434 p.Arg8Trp missense_variant 0.91 pyrazinamide Not assoc w R
sigE 1364802 c.390C>A synonymous_variant 0.92 pyrazinamide
embR 1417793 c.-446C>T upstream_gene_variant 0.13 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854045 p.Tyr147Cys missense_variant 0.1 linezolid Not assoc w R
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
PPE35 2167926 p.Leu896Ser missense_variant 0.13 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.13 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.13 clofazimine Not assoc w R
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
Rv2477c 2784613 c.-571T>C upstream_gene_variant 0.81 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
thyA 3073868 p.Thr202Ala missense_variant 0.93 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.91 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640614 c.72C>T synonymous_variant 0.93 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
clpC1 4038287 c.2418C>T synonymous_variant 0.88 pyrazinamide Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.12 pyrazinamide Not assoc w R - Interim
glpK 4138918 p.Thr280Ala missense_variant 0.91 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.14 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245329 c.2097A>G synonymous_variant 0.91 ethambutol Not assoc w R - Interim
ubiA 4269411 c.423T>C synonymous_variant 0.92 ethambutol Not assoc w R - Interim
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 4338603 c.-82C>T upstream_gene_variant 0.12 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 4407588 c.615A>G synonymous_variant 0.11 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.13 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 0.13 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.9 streptomycin Not assoc w R