TB-Profiler result

Run: ERR495195
Summary

Run ID: ERR495195

Sample name:

Date: 2024-10-03T18:08:35.750492

Number of reads: 2755428

Percentage reads mapped: 99.42

Median coverage: 52.0

Strain: lineage2.2.1.1;lineage4.3.2.1

Spoligotype:

Drug-resistance: Other

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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 0.81
lineage2 East-Asian RD105 0.1
lineage4.3.2 Euro-American (LAM) None 0.82
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.1
lineage4.3.2.1 Euro-American (LAM) RD761 0.85
lineage2.2 East-Asian (Beijing) RD105;RD207 0.08
lineage4 Euro-American None 0.91
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.11
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.-32487_*7308del Assoc w R
kanamycin
cycloserine
ethionamide ethA c.-25934_*15779del 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
tlyA 1885452 c.-32487_*7308del transcript_ablation 0.9 capreomycin Assoc w R
ethA 4310224 c.-25934_*15779del transcript_ablation 0.96 ethionamide 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 5520 p.Pro94Leu missense_variant 0.84 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7222 c.1983C>T synonymous_variant 0.62 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 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
Rv0565c 657142 p.Arg110His missense_variant 0.17 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.2 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.88 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.18 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.21 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.17 bedaquiline
clofazimine
rpsL 781301 c.-259C>T upstream_gene_variant 0.22 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.84 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
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
PPE35 2167926 p.Leu896Ser missense_variant 0.2 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ribD 2960912 c.-25926_*1550del transcript_ablation 0.96 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.79 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3446632 c.-1871_*21046del transcript_ablation 0.91 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.15 pyrazinamide Not assoc w R - Interim
lpqB 3624351 p.Ala187Val missense_variant 0.9 rifampicin Uncertain significance
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.87 pyrazinamide 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 0.12 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.23 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.14 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
gid 4407588 c.615A>G synonymous_variant 0.24 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.96 streptomycin Not assoc w R