TB-Profiler result

Run: SRR3647352
Summary

Run ID: SRR3647352

Sample name:

Date: 2024-10-05T03:44:48.928338

Number of reads: 7811905

Percentage reads mapped: 98.77

Median coverage: 217.0

Strain: La1.2;lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 0.91
lineage4.9 Euro-American (H37Rv-like) None 0.9
La1.2 M.bovis None 0.07
La1 M.bovis None 0.1
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid mmaA3 p.Gly98Asp Mutation from literature
ethambutol
pyrazinamide pncA p.His57Asp Assoc w R
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
mmaA3 737857 p.Gly98Asp missense_variant 0.11 isoniazid Mutation from literature
pncA 2289073 p.His57Asp missense_variant 0.14 pyrazinamide 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 467 p.His156Arg missense_variant 0.11 isoniazid Not assoc w R
gyrB 6446 p.Ala403Ser missense_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8741 c.1440C>T synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13197 p.Thr121Ser missense_variant 0.12 isoniazid Not assoc w R
Rv0010c 13228 c.330delG frameshift_variant 0.1 isoniazid Uncertain significance
Rv0010c 13460 c.99T>C synonymous_variant 0.15 isoniazid Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.12 ethionamide
mmpL5 775639 p.Ile948Val missense_variant 0.12 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.15 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpR5 779254 p.Arg89Trp missense_variant 0.87 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 0.11 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.1 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254582 c.-48A>G upstream_gene_variant 0.11 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.14 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
sigE 1364961 c.549A>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
embR 1417554 c.-207C>G upstream_gene_variant 0.11 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.14 linezolid Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.14 isoniazid Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.14 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.14 cycloserine
Rv3083 3448745 p.Ile81Ser missense_variant 0.1 ethionamide Uncertain significance
Rv3083 3448783 p.Val94Ile missense_variant 0.12 ethionamide Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 0.13 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.15 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038403 c.2302T>C synonymous_variant 0.11 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 0.14 ethambutol Not assoc w R
embC 4242970 c.3108C>T synonymous_variant 0.12 ethambutol Not assoc w R
embB 4247173 c.660G>A synonymous_variant 0.12 ethambutol Not assoc w R - Interim
aftB 4267858 p.Ile327Val missense_variant 0.12 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 0.13 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R