TB-Profiler result

Run: SAMEA104362086
Summary

Run ID: SAMEA104362086

Sample name:

Date: 2024-04-15T13:30:16.953979

Number of reads: 10010212

Percentage reads mapped: 99.61

Median coverage: 295.0

Strain: lineage2.2.1;lineage4.7

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.64
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.67
lineage2.2 East-Asian (Beijing) RD105;RD207 0.67
lineage4.7 Euro-American (mainly T) None 0.35
lineage4 Euro-American None 0.37
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.-16C>T Uncertain significance Mutation from literature
embB p.Gly406Ala Assoc w R
pyrazinamide pncA p.Thr142Ala Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
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 ethA p.Ser390Phe Assoc w R - Interim
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
gyrA 7570 p.Ala90Val missense_variant 0.77 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.64 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.62 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.68 amikacin Assoc w R
kanamycin Assoc w R
capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.67 isoniazid Assoc w R High-level resistance
pncA 2288818 p.Thr142Ala missense_variant 0.72 pyrazinamide Assoc w R
embA 4243217 c.-16C>T upstream_gene_variant 0.63 ethambutol Uncertain significance Mutation from literature
embB 4247730 p.Gly406Ala missense_variant 0.64 ethambutol Assoc w R
ethA 4326305 p.Ser390Phe missense_variant 0.67 ethionamide Assoc w R - Interim
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 0.76 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.68 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13627 c.-69A>G upstream_gene_variant 0.58 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.71 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.62 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.61 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.68 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.66 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.68 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.71 rifampicin Uncertain significance
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 0.64 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.65 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.58 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253966 p.Leu190Ser missense_variant 0.35 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.73 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303897 c.967C>T synonymous_variant 0.62 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.64 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.32 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.66 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.67 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 0.61 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.77 pyrazinamide Not assoc w R
PPE35 2169261 p.Leu451Arg missense_variant 0.73 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2747740 c.-142A>G upstream_gene_variant 0.32 para-aminosalicylic_acid
Rv2681 2997538 p.Asp267Gly missense_variant 0.56 capreomycin Uncertain significance
thyA 3074003 p.Gly157Ser missense_variant 0.37 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.75 cycloserine
ald 3087208 p.Leu130Pro missense_variant 0.6 cycloserine
Rv3236c 3612424 c.693G>A synonymous_variant 0.35 pyrazinamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.65 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.6 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.65 bedaquiline Uncertain significance
rifampicin 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 0.62 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.41 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.61 ethambutol Not assoc w R
whiB6 4338473 c.49A>C synonymous_variant 0.63 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 0.62 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.68 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.66 streptomycin Not assoc w R
gid 4408413 c.-211C>T upstream_gene_variant 0.67 streptomycin