TB-Profiler result

Run: SRR28393630
Summary

Run ID: SRR28393630

Sample name:

Date: 2024-10-03T19:24:54.693027

Number of reads: 2432374

Percentage reads mapped: 99.63

Median coverage: 68.5

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 1.0
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American None 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 c.1297_1299dupTTC Assoc w R
c.1297_1299dupTTC Mutation from literature
isoniazid inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG c.1081dupG Assoc w R High-level resistance
c.47delC Assoc w R High-level resistance
ahpC c.-52C>T Uncertain significance Mutation from literature
ethambutol
pyrazinamide pncA c.406delG Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>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
rpoB 761102 c.1297_1299dupTTC conservative_inframe_insertion 1.0 rifampicin Assoc w R
rifampicin Mutation from literature
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 1673423 c.-779G>T upstream_gene_variant 1.0 ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155030 c.1081dupG frameshift_variant 0.14 isoniazid Assoc w R High-level resistance
katG 2156064 c.47delC frameshift_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288835 c.406delG frameshift_variant 1.0 pyrazinamide Assoc w R
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid Uncertain significance 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 1452 p.Met484Ile 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 1.0 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781276 c.-284A>C upstream_gene_variant 1.0 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834212 p.Ala224Gly missense_variant 1.0 pyrazinamide Uncertain significance
tsnR 1853456 c.-150C>T upstream_gene_variant 0.13 linezolid
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.19 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.19 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.16 capreomycin
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
glpK 4139083 p.Arg225Trp missense_variant 0.35 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
glpK 4139183 c.572dupG frameshift_variant 0.18 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
glpK 4139605 p.Pro51Thr missense_variant 0.2 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4239298 c.-565C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4247412 p.Asp300Gly missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269100 p.Gly245Val missense_variant 0.14 ethambutol
ubiA 4269340 p.Gly165Val missense_variant 1.0 ethambutol Uncertain significance
ethA 4326801 c.670_672dupAAG conservative_inframe_insertion 0.98 ethionamide Uncertain significance
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 4338600 c.-79T>G upstream_gene_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338602 c.-81A>T upstream_gene_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407902 p.Leu101Phe missense_variant 1.0 streptomycin Uncertain significance