TB-Profiler result

Run: ERR4814071
Summary

Run ID: ERR4814071

Sample name:

Date: 2024-04-15T11:39:53.859437

Number of reads: 2598241

Percentage reads mapped: 99.49

Median coverage: 93.0

Strain: lineage4.3.4.1;lineage4.4.1

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 0.8
lineage4.3.4.1 Euro-American (LAM) RD174 0.83
lineage4.4.1 Euro-American (S-type) None 0.18
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.79
lineage4.4 Euro-American None 0.19
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 5075 c.-164delG upstream_gene_variant 0.23 levofloxacin
moxifloxacin
gyrB 6028 c.789C>T synonymous_variant 0.85 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8639 c.1338G>A synonymous_variant 0.79 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 759608 c.-199C>T upstream_gene_variant 0.81 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.68 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 801066 c.258G>A synonymous_variant 0.81 linezolid Not assoc w R - Interim
sigE 1364434 p.Arg8Trp missense_variant 0.86 pyrazinamide Not assoc w R
embR 1417997 c.-650G>A upstream_gene_variant 0.13 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
ndh 2102990 p.Val18Ala missense_variant 0.16 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223297 c.-133G>C upstream_gene_variant 0.24 clofazimine Uncertain significance
bedaquiline Uncertain significance
ahpC 2726323 p.Pro44Arg missense_variant 0.82 isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.85 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448598 p.Ile32Thr missense_variant 0.77 ethionamide Uncertain significance
Rv3083 3448608 c.105G>A synonymous_variant 0.25 ethionamide Not assoc w R - Interim
Rv3236c 3612009 p.Ala370Thr missense_variant 0.84 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878270 p.Leu80Val missense_variant 0.79 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.88 pyrazinamide Not assoc w R
panD 4043996 p.Ala96Thr missense_variant 0.18 pyrazinamide Uncertain significance
ubiA 4268982 c.852G>A synonymous_variant 0.79 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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.73 streptomycin Not assoc w R