TB-Profiler result

Run: SRR25827381
Summary

Run ID: SRR25827381

Sample name:

Date: 2024-04-14T23:07:32.064312

Number of reads: 6823291

Percentage reads mapped: 99.02

Median coverage: 236.0

Strain: lineage3;lineage4.3.4.2

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 0.85
lineage4.3 Euro-American (LAM) None 0.15
lineage4 Euro-American None 0.14
lineage4.3.4 Euro-American (LAM) RD174 0.13
lineage4.3.4.2 Euro-American (LAM) RD174 0.14
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
p.Thr275Ala Uncertain significance Mutation from literature
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
pyrazinamide pncA c.395delG Assoc w R
p.Gly97Asp Assoc w R
streptomycin rrs n.906A>G Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
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 7582 p.Asp94Gly missense_variant 0.88 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.83 streptomycin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
katG 2155289 p.Thr275Ala missense_variant 0.86 isoniazid Uncertain significance Mutation from literature
pncA 2288846 c.395delG frameshift_variant 0.81 pyrazinamide Assoc w R
pncA 2288952 p.Gly97Asp missense_variant 0.17 pyrazinamide Assoc w R
eis 2715342 c.-10G>A upstream_gene_variant 0.86 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
embA 4243221 c.-12C>T upstream_gene_variant 0.16 ethambutol Uncertain significance Mutation from literature
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
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
fgd1 491742 c.960T>C synonymous_variant 0.85 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.84 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.8 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.8 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.85 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 765862 p.Phe831Leu missense_variant 0.83 rifampicin Uncertain significance
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
mmpR5 778996 p.Val3Ile missense_variant 0.14 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.88 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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 2154724 p.Arg463Leu missense_variant 0.82 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.87 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 0.81 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.85 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.87 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.84 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
Rv2477c 2782957 c.1086A>G synonymous_variant 0.17 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2752c 3065293 p.Val300Ala missense_variant 0.11 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
thyA 3073687 p.Ala262Val missense_variant 0.83 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.16 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623174 c.1737G>C synonymous_variant 0.85 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841473 c.-53G>A upstream_gene_variant 0.87 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.16 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.83 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.81 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 4239763 c.-100C>T upstream_gene_variant 0.14 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.86 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.23 ethambutol
embB 4247429 c.916_918delATGinsGA frameshift_variant&missense_variant 0.84 ethambutol
aftB 4267492 p.Ala449Thr missense_variant 0.83 ethambutol Uncertain significance
ethA 4327076 p.Phe133Ser missense_variant 0.84 ethionamide 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
gid 4407588 c.615A>G synonymous_variant 0.87 streptomycin Not assoc w R
gid 4408114 p.Gly30Asp missense_variant 0.88 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.12 streptomycin Not assoc w R