TB-Profiler result

Run: SRR25340778
Summary

Run ID: SRR25340778

Sample name:

Date: 2024-04-15T13:22:44.380432

Number of reads: 6146934

Percentage reads mapped: 99.44

Median coverage: 163.0

Strain: lineage3.1.2;lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.65
lineage3.1.2 East-African-Indian RD750 0.71
lineage4 Euro-American None 0.38
lineage4.8 Euro-American (mainly T) RD219 0.33
lineage3.1 East-African-Indian RD750 0.62
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
dnaA 302 p.Ala101Asp missense_variant 0.27 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 0.71 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.65 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 490935 c.153C>T synonymous_variant 0.3 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.7 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.67 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.67 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.65 rifampicin Not assoc w R
rpoB 763031 c.3225T>C 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
mmpL5 776100 p.Thr794Ile missense_variant 0.67 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.74 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364847 c.435G>T synonymous_variant 0.63 pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.35 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.62 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918104 c.165G>A synonymous_variant 0.64 capreomycin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.69 isoniazid Not assoc w R
katG 2155697 p.Ala139Thr missense_variant 0.63 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.74 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.71 pyrazinamide 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 2223491 c.-327C>A upstream_gene_variant 0.43 clofazimine Not assoc w R
bedaquiline Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.76 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.78 pyrazinamide
kasA 2517923 c.-192C>T upstream_gene_variant 0.43 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.72 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.58 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2680 2996043 c.-62A>C upstream_gene_variant 0.19 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.68 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.6 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.59 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.65 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240966 c.1104G>A synonymous_variant 0.42 ethambutol Not assoc w R - Interim
embC 4242075 p.Arg738Gln missense_variant 0.51 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338472 p.Arg17Lys missense_variant 0.62 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 0.62 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.66 streptomycin Not assoc w R