TB-Profiler result

Run: SRR19409781
Summary

Run ID: SRR19409781

Sample name:

Date: 2024-04-16T01:07:54.148585

Number of reads: 1399021

Percentage reads mapped: 99.6

Median coverage: 70.0

Strain: lineage1.1.2;lineage3.1.1;lineage4

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 0.74
lineage1.1.2 Indo-Oceanic RD239 0.13
lineage3.1.1 East-African-Indian RD750 0.63
lineage1.1 Indo-Oceanic RD239 0.1
lineage4 Euro-American None 0.1
lineage3.1 East-African-Indian RD750 0.61
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 0.33 isoniazid Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.15 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.12 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
gyrA 8452 p.Ala384Val missense_variant 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.12 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 13298 p.Ile87Met missense_variant 0.11 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.89 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.71 ethionamide Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 0.15 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.56 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.73 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.97 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.16 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 0.88 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 0.87 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406349 p.Ile331Ser missense_variant 0.45 streptomycin
isoniazid
pyrazinamide
embR 1417554 c.-207C>G upstream_gene_variant 0.1 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.17 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 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 0.89 isoniazid Not assoc w R
katG 2155557 c.555C>T synonymous_variant 0.18 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.78 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.14 pyrazinamide Uncertain significance
PPE35 2170461 p.Gly51Glu missense_variant 0.6 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.15 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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 0.5 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.84 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.87 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.74 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 2996912 c.174C>T synonymous_variant 0.14 capreomycin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.93 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.17 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840636 p.Pro262Gln missense_variant 0.19 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.75 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.1 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4138622 c.1134C>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
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4139201 c.555C>T synonymous_variant 0.19 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240671 p.Thr270Ile missense_variant 0.15 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.64 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.85 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243813 p.Arg194Gln missense_variant 0.13 ethambutol Uncertain significance
embA 4243848 p.Val206Met missense_variant 0.14 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.14 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.12 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.12 ethambutol Not assoc w R
ethA 4327629 c.-156C>T upstream_gene_variant 0.11 ethionamide
ethA 4328329 c.-856C>G upstream_gene_variant 0.12 ethionamide
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 0.11 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.97 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.13 streptomycin Not assoc w R