TB-Profiler result

Run: SRR29017429
Summary

Run ID: SRR29017429

Sample name:

Date: 2025-03-06T08:51:18.770890

Number of reads: 1852616

Percentage reads mapped: 99.72

Median coverage: 58.0

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) None 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.His445Asn Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature: doi: 10.1128/AAC.03285-14
embB p.Met306Val Assoc w R
pyrazinamide pncA p.Thr135Pro Assoc w R
c.349dupC Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 c.198delG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.198delG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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 761139 p.His445Asn missense_variant 1.0 rifampicin Assoc w R
mmpR5 779181 c.198delG frameshift_variant 0.99 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
pncA 2288839 p.Thr135Pro missense_variant 0.19 pyrazinamide Assoc w R
pncA 2288892 c.349dupC frameshift_variant 0.66 pyrazinamide Assoc w R
embA 4243221 c.-12C>T upstream_gene_variant 0.98 ethambutol Uncertain significance Mutation from literature: doi: 10.1128/AAC.03285-14
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol 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
gyrB 6166 c.927C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13636 c.-78A>G upstream_gene_variant 1.0 isoniazid Uncertain significance
rpoB 761832 p.Thr676Pro missense_variant 1.0 rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.22 ethambutol Uncertain significance
ubiA 4269171 c.663C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
gid 4408063 p.Arg47Gln missense_variant 1.0 streptomycin Uncertain significance