TB-Profiler result

Run: SRR17856659
Summary

Run ID: SRR17856659

Sample name:

Date: 2024-10-04T04:13:42.209034

Number of reads: 5560314

Percentage reads mapped: 99.57

Median coverage: 167.0

Strain: lineage3

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin gid c.259_283delCAGGTAGTTCTCCTAGAACCGCTAC Assoc w R
p.Gly73Glu Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.25 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 0.13 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.18 isoniazid Assoc w R High-level resistance
pncA 2289252 c.-11A>G upstream_gene_variant 0.18 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.13 ethambutol Assoc w R
gid 4407919 c.259_283delCAGGTAGTTCTCCTAGAACCGCTAC frameshift_variant 0.75 streptomycin Assoc w R
gid 4407985 p.Gly73Glu missense_variant 0.75 streptomycin 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 902 p.Val301Ala missense_variant 0.11 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13897 c.-339C>T upstream_gene_variant 0.8 isoniazid
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657336 c.133_134dupCG frameshift_variant 0.19 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764616 p.Asn416Thr missense_variant 0.14 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303331 p.Arg134Leu missense_variant 0.16 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embR 1417517 c.-170T>G upstream_gene_variant 0.24 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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
katG 2154692 p.Ser474Ala missense_variant 0.18 isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155685 p.Lys143Glu missense_variant 0.84 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2169041 c.1572G>A synonymous_variant 0.23 pyrazinamide Not assoc w R - Interim
PPE35 2169044 c.1569G>C synonymous_variant 0.38 pyrazinamide Not assoc w R - Interim
PPE35 2169047 p.Ile522Val missense_variant 0.37 pyrazinamide Uncertain significance
PPE35 2169053 c.1560T>C synonymous_variant 0.61 pyrazinamide Not assoc w R
PPE35 2169056 c.1557A>G synonymous_variant 0.35 pyrazinamide Not assoc w R - Interim
PPE35 2169059 c.1554G>A synonymous_variant 0.25 pyrazinamide
PPE35 2169063 p.Met517Thr missense_variant 0.62 pyrazinamide
PPE35 2169065 p.Ala516Ile missense_variant 0.25 pyrazinamide
PPE35 2169068 c.1545G>T synonymous_variant 0.25 pyrazinamide
PPE35 2169071 c.1542A>G synonymous_variant 0.34 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.84 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 1.0 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2752c 3064784 p.Ser470Pro missense_variant 0.86 levofloxacin Uncertain significance
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086787 c.-33A>C upstream_gene_variant 0.37 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3642877 p.Lys448Arg missense_variant 0.19 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
panD 4044703 c.-422C>G upstream_gene_variant 0.81 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4139246 c.510C>T synonymous_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240009 c.147G>A synonymous_variant 0.83 ethambutol Not assoc w R - Interim
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326848 p.Pro209Leu missense_variant 0.18 ethionamide
whiB6 4338358 p.Ala55Asp missense_variant 0.83 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R