TB-Profiler result

Run: SRR25827506
Summary

Run ID: SRR25827506

Sample name:

Date: 2024-10-05T01:20:43.704379

Number of reads: 9683261

Percentage reads mapped: 98.61

Median coverage: 322.0

Strain: lineage3;lineage4.8

Spoligotype:

Drug-resistance: MDR-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 0.5
lineage4 Euro-American None 0.5
lineage4.8 Euro-American (mainly T) RD219 0.49
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.Met306Val Assoc w R
pyrazinamide pncA p.Cys14* Assoc w R
streptomycin rrs n.906A>G Uncertain significance Mutation from literature
gid c.351delG Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 0.54 rifampicin Assoc w R
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.55 isoniazid Assoc w R High-level resistance
pncA 2289200 p.Cys14* stop_gained 0.43 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.57 ethambutol Assoc w R
gid 4407851 c.351delG frameshift_variant 0.54 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.53 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.51 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.52 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.51 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.53 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.55 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.48 rifampicin Not assoc w R
rpoC 766488 p.Pro1040Arg missense_variant 0.51 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 0.5 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 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.58 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.56 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 0.48 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.49 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223491 c.-327C>A upstream_gene_variant 0.47 bedaquiline Uncertain significance
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.5 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.5 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.43 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.53 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
ald 3086788 c.-32T>C upstream_gene_variant 0.54 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.51 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878637 c.-130G>C upstream_gene_variant 0.27 rifampicin
panD 4044703 c.-422C>G upstream_gene_variant 0.52 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.46 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.51 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
embC 4242075 p.Arg738Gln missense_variant 0.53 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245835 p.Leu868Arg missense_variant 0.16 ethambutol
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 0.5 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.48 streptomycin Not assoc w R
gid 4408273 c.-72delG upstream_gene_variant 0.5 streptomycin