TB-Profiler result

Run: SRR19428577
Summary

Run ID: SRR19428577

Sample name:

Date: 2024-04-16T05:58:48.954823

Number of reads: 276926

Percentage reads mapped: 99.54

Median coverage: 12.0

Strain: lineage1.1.2;lineage3.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.17
lineage3.1.1 East-African-Indian RD750 0.56
lineage1.1 Indo-Oceanic RD239 0.31
lineage1 Indo-Oceanic RD239 0.19
lineage3.1 East-African-Indian RD750 0.5
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 0.38 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
fgd1 491742 c.960T>C synonymous_variant 0.87 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.7 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.78 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.8 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.46 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.46 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 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.91 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.27 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.9 pyrazinamide Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.44 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.5 pyrazinamide
Rv2752c 3064632 c.1560C>T synonymous_variant 0.5 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339741 c.624G>A synonymous_variant 0.32 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.58 pyrazinamide
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 4407588 c.615A>G synonymous_variant 0.83 streptomycin Not assoc w R