TB-Profiler result

Run: SRR11638839
Summary

Run ID: SRR11638839

Sample name:

Date: 2024-03-26T19:07:14.445304

Number of reads: 10828416

Percentage reads mapped: 89.31

Median coverage: 327.0

Strain: lineage3

Spoligotype:

Drug-resistance: 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 0.95
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
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 embB p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA c.390_391dupGG Assoc w R
p.Leu120Arg Assoc w R
streptomycin rrs n.514A>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA 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
ethA c.672dupG Assoc w R
clofazimine mmpR5 c.198delG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.198delG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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 7582 p.Asp94Gly missense_variant 0.4 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761109 p.Asp435Tyr missense_variant 0.54 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.44 rifampicin Assoc w R
mmpR5 779181 c.198delG frameshift_variant 0.55 clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rrs 1472359 n.514A>T non_coding_transcript_exon_variant 0.56 streptomycin Uncertain significance Mutation from literature
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.55 kanamycin Assoc w R
capreomycin Assoc w R
amikacin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.93 ethionamide Assoc w R Alias fabG1_c.-15C>T
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)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288850 c.390_391dupGG frameshift_variant 0.48 pyrazinamide Assoc w R
pncA 2288883 p.Leu120Arg missense_variant 0.48 pyrazinamide Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.34 ethambutol Uncertain significance Mutation from literature
ethA 4326801 c.672dupG frameshift_variant 0.47 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
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 8164 p.Ala288Asp missense_variant 0.57 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
nusG 734810 p.Glu186Ala missense_variant 0.48 rifampicin Uncertain significance
nusG 734869 p.Ser206Gly missense_variant 0.49 rifampicin Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.94 rifampicin Not assoc w R
rpoB 760062 p.Glu86Lys missense_variant 0.55 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 0.92 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.43 rifampicin Uncertain significance
rpoC 766582 c.3213C>A synonymous_variant 0.49 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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800302 c.-507A>G upstream_gene_variant 0.48 linezolid
rplC 800389 c.-420G>A upstream_gene_variant 0.44 linezolid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 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
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
tlyA 1918272 c.333C>T synonymous_variant 0.41 capreomycin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 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
pncA 2289047 c.195C>T synonymous_variant 0.41 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.94 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.96 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.94 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
Rv2752c 3065607 c.585C>T synonymous_variant 0.52 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087904 p.Pro362Leu missense_variant 0.53 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841473 c.-53G>A upstream_gene_variant 0.39 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.92 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.95 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
glpK 4139246 c.510C>T synonymous_variant 0.5 ethambutol Not assoc w R
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
embC 4242075 p.Arg738Gln missense_variant 0.92 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsCC frameshift_variant&missense_variant 0.63 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 0.5 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 1.0 streptomycin Not assoc w R
gid 4407790 p.Ala138Val missense_variant 0.41 streptomycin Uncertain significance