TB-Profiler result

Run: SRR6930932
Summary

Run ID: SRR6930932

Sample name:

Date: 2024-10-03T18:58:19.749833

Number of reads: 2364609

Percentage reads mapped: 99.6

Median coverage: 112.0

Strain: 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
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 1.0
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.Gly234Glu Uncertain significance Mutation from literature
ethambutol embB p.Gln497Pro Uncertain significance Mutation from literature
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin rrs n.514A>C 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 0.98 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin Assoc w R
katG 2155411 p.Gly234Glu missense_variant 1.0 isoniazid Uncertain significance Mutation from literature
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide Assoc w R
embB 4248003 p.Gln497Pro missense_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4249583 p.Asp1024Asn missense_variant 1.0 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
rpoC 764817 p.Val483Ala missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 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 1253742 p.Leu265Phe missense_variant 0.68 levofloxacin Uncertain significance
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2169071 c.1463_1541delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNA frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2477c 2783267 p.Asp259Gly missense_variant 1.0 kanamycin
levofloxacin Uncertain significance
moxifloxacin
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin
ald 3087095 c.276C>T synonymous_variant 1.0 cycloserine
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
Rv3236c 3612047 p.Ala357Val missense_variant 1.0 pyrazinamide Uncertain significance
fbiB 3640915 c.-620C>T upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
clpC1 4040021 c.684A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338586 c.-78_-66delAGAGCTCGGAGCT upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin