TB-Profiler result

Run: SRR28393388
Summary

Run ID: SRR28393388

Sample name:

Date: 2024-05-22T16:46:37.319537

Number of reads: 3403202

Percentage reads mapped: 99.5

Median coverage: 98.0

Strain: lineage4.3.4.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4.3.4.1 Euro-American (LAM) RD174 1.0
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 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.Asp435Val Assoc w R
isoniazid ahpC c.-54C>T Uncertain significance Mutation from literature
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Met306Leu Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA p.Val163Ala Assoc w R - Interim
streptomycin gid c.111dupA Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.743delA Assoc w R
kanamycin
cycloserine
ethionamide ethA p.Tyr147* Assoc w R
c.67delC Assoc w R
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 761110 p.Asp435Val missense_variant 1.0 rifampicin Assoc w R
tlyA 1918681 c.743delA frameshift_variant 0.54 capreomycin Assoc w R
pncA 2288754 p.Val163Ala missense_variant 1.0 pyrazinamide Assoc w R - Interim
ahpC 2726139 c.-54C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
embA 4243221 c.-12C>T upstream_gene_variant 0.49 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.17 ethambutol Assoc w R
ethA 4327033 p.Tyr147* stop_gained 0.55 ethionamide Assoc w R
ethA 4327406 c.67delC frameshift_variant 0.52 ethionamide Assoc w R
gid 4408091 c.111dupA frameshift_variant 1.0 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 0.99 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
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 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
rpsL 781466 c.-94A>T upstream_gene_variant 1.0 streptomycin Uncertain significance
Rv1129c 1254264 p.Val91Phe missense_variant 0.46 moxifloxacin
levofloxacin
rifampicin
isoniazid
sigE 1364434 p.Arg8Trp missense_variant 0.97 pyrazinamide Not assoc w R
sigE 1365000 c.588G>A synonymous_variant 0.47 pyrazinamide Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472923 n.1078G>A non_coding_transcript_exon_variant 0.52 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 2154235 p.Val626Glu missense_variant 1.0 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3064811 p.Thr461Pro missense_variant 0.57 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640316 c.-227A>C upstream_gene_variant 0.51 clofazimine
pretomanid
delamanid
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242736 p.Ile958Met missense_variant 0.66 ethambutol
whiB6 4338473 c.49A>C synonymous_variant 0.5 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
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 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R