TB-Profiler result

Run: SRR25827450
Summary

Run ID: SRR25827450

Sample name:

Date: 2024-04-15T11:03:35.481749

Number of reads: 7495709

Percentage reads mapped: 98.88

Median coverage: 249.0

Strain: lineage3;lineage4.1.1.1

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.51
lineage4.1 Euro-American None 0.48
lineage4.1.1.1 Euro-American (X-type) RD183 0.45
lineage4 Euro-American None 0.51
lineage4.1.1 Euro-American (X-type) None 0.47
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
pyrazinamide pncA p.Thr142Met Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 0.58 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.42 isoniazid Assoc w R High-level resistance
pncA 2288817 p.Thr142Met missense_variant 0.43 pyrazinamide 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 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 0.59 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.52 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.47 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.5 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.53 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.56 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.49 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 0.52 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 800219 c.-590T>C upstream_gene_variant 0.4 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.5 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254582 c.-48A>C upstream_gene_variant 0.47 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
rrl 1476436 n.2779A>G non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
fabG1 1673368 c.-72A>G upstream_gene_variant 0.43 ethionamide
isoniazid
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.99 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.49 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.48 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 0.53 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.5 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.52 isoniazid Not assoc w R
ahpC 2726210 c.18T>C synonymous_variant 0.47 isoniazid Not assoc w R - Interim
Rv2477c 2782498 c.1545C>T synonymous_variant 0.5 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641447 p.Thr302Met missense_variant 0.5 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
rpoA 3877553 p.Glu319Lys missense_variant 0.44 rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.49 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.5 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 4240897 c.1035C>G synonymous_variant 0.53 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.57 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.43 ethambutol Not assoc w R
embA 4245835 p.Leu868Arg missense_variant 0.18 ethambutol
embB 4247015 p.Ser168Ala missense_variant 0.23 ethambutol
embB 4249408 c.2895G>A synonymous_variant 0.42 ethambutol Not assoc w R
aftB 4269096 c.-260C>G upstream_gene_variant 0.45 ethambutol
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 0.55 streptomycin Not assoc w R