TB-Profiler result

Run: ERR4798816
Summary

Run ID: ERR4798816

Sample name:

Date: 2024-04-15T18:49:52.213623

Number of reads: 4303002

Percentage reads mapped: 99.65

Median coverage: 125.0

Strain: lineage2.2.1;lineage3;lineage4.1.1.3;lineage4.9

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
lineage3 East-African-Indian RD750 0.22
lineage2 East-Asian RD105 0.45
lineage4.1 Euro-American None 0.09
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.46
lineage4.1.1.3 Euro-American (X-type) RD193 0.11
lineage2.2 East-Asian (Beijing) RD105;RD207 0.43
lineage4 Euro-American None 0.34
lineage4.1.1 Euro-American (X-type) None 0.11
lineage4.9 Euro-American (H37Rv-like) None 0.2
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
embB p.Gly406Ser Assoc w R
pyrazinamide pncA c.391dupG 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)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly 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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 0.43 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.46 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.45 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.4 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.3 capreomycin Assoc w R
kanamycin Assoc w R
amikacin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.44 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 0.52 isoniazid Assoc w R High-level resistance
pncA 2288850 c.391dupG frameshift_variant 0.46 pyrazinamide Assoc w R
embA 4243217 c.-16C>T upstream_gene_variant 0.38 ethambutol Uncertain significance Mutation from literature
embB 4247729 p.Gly406Ser missense_variant 0.44 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 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.79 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.78 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.55 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.46 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.72 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.49 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.24 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.19 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.65 rifampicin Not assoc w R
rpoC 764723 p.Phe452Leu missense_variant 0.44 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 0.77 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.79 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.47 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.38 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 0.85 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.11 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.62 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303326 c.396C>T synonymous_variant 0.38 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.4 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.43 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.79 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 0.68 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.77 pyrazinamide Not assoc w R
PPE35 2168686 p.Thr643Ala missense_variant 0.12 pyrazinamide Uncertain significance
Rv1979c 2222357 p.Thr270Ala missense_variant 0.48 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.9 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.25 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.29 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.22 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.19 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.85 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.47 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.85 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.44 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841473 c.-53G>A upstream_gene_variant 0.26 cycloserine
clpC1 4039799 c.906C>T synonymous_variant 0.17 pyrazinamide
panD 4044858 c.-577T>C upstream_gene_variant 0.2 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.24 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.21 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.23 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.81 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.11 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.35 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.48 ethambutol Not assoc w R
whiB6 4338333 c.188dupC frameshift_variant 0.45 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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 0.85 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.66 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.47 streptomycin Not assoc w R