TB-Profiler result

Run: ERR2510598
Summary

Run ID: ERR2510598

Sample name:

Date: 2024-10-05T13:51:05.638959

Number of reads: 1018185

Percentage reads mapped: 99.49

Median coverage: 23.0

Strain: lineage3;lineage4.6

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 0.16
lineage4.6 Euro-American None 0.8
lineage4 Euro-American None 0.84
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 embA c.-12C>T Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
pyrazinamide
streptomycin rrs n.514A>C Assoc w R
gid c.471delG Assoc w R
c.404dupT 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 1.0 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.88 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embA 4243221 c.-12C>T upstream_gene_variant 0.82 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.21 ethambutol Assoc w R
gid 4407731 c.471delG frameshift_variant 0.21 streptomycin Assoc w R
gid 4407798 c.404dupT frameshift_variant 0.83 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13677 c.-119G>T upstream_gene_variant 0.89 isoniazid Uncertain significance
ccsA 620577 c.687C>A synonymous_variant 0.29 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
rpoC 763644 p.Met92Thr missense_variant 0.75 rifampicin Uncertain significance
rpoC 764832 p.Glu488Gly missense_variant 0.77 rifampicin Uncertain significance
rpoC 766597 c.3228C>G synonymous_variant 0.75 rifampicin Not assoc w R - Interim
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 1253754 p.Thr261Pro missense_variant 0.45 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.24 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
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 2154724 p.Arg463Leu missense_variant 0.35 isoniazid Not assoc w R
PPE35 2168080 p.Thr845Ala missense_variant 0.89 pyrazinamide Uncertain significance
PPE35 2170198 p.Ala139Thr missense_variant 0.83 pyrazinamide Uncertain significance
PPE35 2170792 c.-180T>C upstream_gene_variant 0.76 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2746993 c.606C>T synonymous_variant 0.88 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.22 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
Rv3236c 3613057 c.60G>T synonymous_variant 0.82 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.16 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
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 1.0 kanamycin
capreomycin
amikacin