TB-Profiler result

Run: ERR3273160
Summary

Run ID: ERR3273160

Sample name:

Date: 2024-04-16T07:05:09.601757

Number of reads: 2329177

Percentage reads mapped: 99.4

Median coverage: 69.0

Strain: lineage2.2.2;lineage4.4.1.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.67
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.65
lineage2.2 East-Asian (Beijing) RD105;RD207 0.65
lineage4.4.1 Euro-American (S-type) None 0.29
lineage4 Euro-American None 0.33
lineage4.4.1.1 Euro-American None 0.3
lineage4.4 Euro-American None 0.31
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 embB p.Gln497Arg Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
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 0.62 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.59 kanamycin Assoc w R
capreomycin Assoc w R
amikacin Assoc w R
katG 2155167 p.Ser315Thr missense_variant 0.57 isoniazid Assoc w R High-level resistance
embB 4248003 p.Gln497Arg missense_variant 0.62 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.67 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.71 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.65 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.61 rifampicin Not assoc w R
rpoC 765678 p.Arg770Leu missense_variant 0.59 rifampicin
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 0.62 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.62 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.64 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
rrs 1471798 n.-48G>A upstream_gene_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.69 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.94 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 0.31 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.66 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.72 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.32 pyrazinamide Not assoc w R
Rv1979c 2223269 c.-105G>A upstream_gene_variant 0.68 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3064663 p.Lys510Arg missense_variant 0.26 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.95 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.29 ethionamide Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 0.27 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.62 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.94 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627848 c.-499C>G upstream_gene_variant 0.6 bedaquiline
rifampicin
embC 4238963 c.-900C>T upstream_gene_variant 0.27 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.65 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.78 ethambutol Not assoc w R
ubiA 4269153 c.681C>A synonymous_variant 0.6 ethambutol 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 0.89 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.52 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.63 streptomycin Not assoc w R