TB-Profiler result

Run: ERR4813498
Summary

Run ID: ERR4813498

Sample name:

Date: 2024-04-15T21:24:33.586972

Number of reads: 2505418

Percentage reads mapped: 98.78

Median coverage: 74.0

Strain: lineage2.2.1;lineage4.1.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.1
lineage4.1 Euro-American None 0.89
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.06
lineage2.2 East-Asian (Beijing) RD105;RD207 0.16
lineage4 Euro-American None 0.88
lineage4.1.1 Euro-American (X-type) None 0.89
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 rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.8delA 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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.17 streptomycin Assoc w R
ethA 4327465 c.8delA frameshift_variant 0.15 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 6052 p.Ile271Met missense_variant 0.83 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7005 p.Gly589Val missense_variant 0.18 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7221 p.Ser661Thr missense_variant 0.87 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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
fgd1 491742 c.960T>C synonymous_variant 0.22 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.85 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.12 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.94 rifampicin Not assoc w R
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 0.11 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.14 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.86 linezolid
Rv1129c 1254514 c.20delT frameshift_variant 0.12 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embR 1416699 p.Leu217Val missense_variant 0.89 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.15 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3066898 c.-707C>T upstream_gene_variant 0.86 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.93 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627511 c.-162C>G upstream_gene_variant 0.95 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4039958 c.747G>A synonymous_variant 0.16 pyrazinamide
embC 4242803 p.Val981Leu missense_variant 0.91 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.92 ethambutol Not assoc w R
ethA 4326116 p.Thr453Ile missense_variant 0.82 ethionamide Uncertain significance
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 4407588 c.615A>G synonymous_variant 0.11 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.13 streptomycin Not assoc w R