TB-Profiler result

Run: SRR28888044
Summary

Run ID: SRR28888044

Sample name:

Date: 2024-10-03T19:26:30.139447

Number of reads: 5768811

Percentage reads mapped: 99.88

Median coverage: 344.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: XDR-TB

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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 1.0
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Arg 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
pyrazinamide pncA p.Gly108Arg Assoc w R
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Ala504Thr Uncertain significance Mutation from literature
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 gyrB p.Ala504Thr Uncertain significance Mutation from literature
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 alr p.Met343Thr Mutation from literature
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine mmpR5 c.421dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.421dupG 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
gyrB 6749 p.Ala504Thr missense_variant 1.0 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrA 7570 p.Ala90Val missense_variant 1.0 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)
rpoB 761140 p.His445Arg missense_variant 1.0 rifampicin Assoc w R
mmpR5 779407 c.421dupG frameshift_variant 1.0 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 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 2288920 p.Gly108Arg missense_variant 1.0 pyrazinamide Assoc w R
alr 3840393 p.Met343Thr missense_variant 0.99 cycloserine Mutation from literature
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
dnaA 698 p.Arg233Gln missense_variant 1.0 isoniazid 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 8040 p.Gly247Ser 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
mmaA3 737814 c.335_336insA frameshift_variant 1.0 isoniazid
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766203 p.Gly945Asp missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpR5 779056 p.Met23Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 0.99 streptomycin Not assoc w R
fbiC 1303095 c.165G>A synonymous_variant 0.99 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304962 p.Trp678Gly missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 1.0 pyrazinamide Not assoc w R - Interim
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
katG 2156196 c.-85C>T upstream_gene_variant 1.0 isoniazid 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
kasA 2518919 p.Gly269Ser missense_variant 1.0 isoniazid
folC 2746340 p.Ala420Val missense_variant 1.0 para-aminosalicylic_acid
ribD 2986827 c.-12G>A upstream_gene_variant 1.0 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.99 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640801 p.His87Tyr missense_variant 1.0 pretomanid
delamanid
clofazimine
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243190 c.-43delGinsCC upstream_gene_variant 1.0 ethambutol Uncertain significance
ubiA 4269159 c.675G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
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 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R