TB-Profiler result

Run: SRR19392723
Summary

Run ID: SRR19392723

Sample name:

Date: 2024-04-16T03:34:07.720293

Number of reads: 960488

Percentage reads mapped: 99.54

Median coverage: 50.0

Strain: lineage1.1.2;lineage3.1.1;lineage4.6.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.7
lineage1.1.2 Indo-Oceanic RD239 0.05
lineage4.6 Euro-American None 0.05
lineage3.1.1 East-African-Indian RD750 0.23
lineage1.1 Indo-Oceanic RD239 0.07
lineage4 Euro-American None 0.15
lineage4.6.1.1 Euro-American RD724 0.12
lineage1 Indo-Oceanic RD239 0.08
lineage4.6.1 Euro-American (Uganda) RD724 0.06
lineage3.1 East-African-Indian RD750 0.34
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 1277 p.Thr426Ile missense_variant 0.14 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7539 p.Thr80Ala missense_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.15 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 13250 c.309G>A synonymous_variant 0.4 isoniazid Not assoc w R - Interim
Rv0010c 13605 c.-47G>T upstream_gene_variant 0.13 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.8 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 574900 c.-448G>C upstream_gene_variant 0.47 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575080 c.-268A>G upstream_gene_variant 0.13 ethionamide Uncertain significance
isoniazid Uncertain significance
ccsA 620625 p.Ile245Met missense_variant 0.18 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.73 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.19 ethionamide
hadA 732265 c.336G>A synonymous_variant 0.15 isoniazid Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 0.15 rifampicin Not assoc w R
rpoB 760948 p.Asn381Ser missense_variant 0.2 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 0.75 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.87 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 0.86 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 800357 c.-452C>A upstream_gene_variant 0.18 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.92 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.15 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.14 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.52 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.14 linezolid Not assoc w R
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 2154724 p.Arg463Leu missense_variant 0.7 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.69 pyrazinamide Not assoc w R
PPE35 2170461 p.Gly51Glu missense_variant 0.14 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
pncA 2289047 c.195C>T synonymous_variant 0.26 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.68 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.62 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.68 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
Rv2681 2997736 c.1009_1011delCCG conservative_inframe_deletion 0.32 capreomycin Uncertain significance
Rv2752c 3064632 c.1560C>T synonymous_variant 0.15 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 0.86 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.11 ethionamide Uncertain significance
Rv3236c 3612870 p.Ala83Ser missense_variant 0.41 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 0.88 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3642098 c.564G>A synonymous_variant 0.46 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
alr 3840636 p.Pro262Gln missense_variant 0.32 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.21 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.25 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 4241042 p.Asn394Asp missense_variant 0.12 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.24 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.71 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.21 ethambutol Not assoc w R
embA 4245883 p.Gly884Asp missense_variant 0.31 ethambutol 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 1.0 capreomycin
amikacin
kanamycin
whiB6 4338846 c.-325T>G upstream_gene_variant 0.19 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.84 streptomycin Not assoc w R