TB-Profiler result

Run: SRR28351537
Summary

Run ID: SRR28351537

Sample name:

Date: 2024-10-05T00:03:01.027135

Number of reads: 10595023

Percentage reads mapped: 99.68

Median coverage: 311.0

Strain: lineage4.1.1.2

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
lineage4.1.1.2 Euro-American (X-type) None 0.95
lineage4.1 Euro-American None 1.0
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) 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.1312_1314delAAC Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
c.1312_1314delAAC Mutation from literature
isoniazid
ethambutol embB p.Met306Leu Assoc w R
pyrazinamide pncA c.505delG Assoc w R
p.Pro54Thr Assoc w R - Interim
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
capreomycin
kanamycin
cycloserine
ethionamide
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 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 761114 c.1312_1314delAAC conservative_inframe_deletion 1.0 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rifampicin Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.76 streptomycin Assoc w R
pncA 2288736 c.505delG frameshift_variant 0.79 pyrazinamide Assoc w R
pncA 2289082 p.Pro54Thr missense_variant 0.18 pyrazinamide Assoc w R - Interim
embB 4247429 p.Met306Leu missense_variant 0.8 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 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
Rv0010c 13637 c.-79C>T upstream_gene_variant 0.77 isoniazid Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
mmaA3 738135 c.15A>G synonymous_variant 1.0 isoniazid
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 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 1.0 linezolid
embR 1416803 c.544delA frameshift_variant 1.0 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854268 p.Ile221Met missense_variant 1.0 linezolid Uncertain significance
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 2155780 p.Gly111Asp missense_variant 1.0 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449787 c.1284C>T synonymous_variant 0.99 ethionamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626305 c.309C>T synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
glpK 4139251 p.Gly169Arg missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin
rifampicin Uncertain significance
ethambutol
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 4246930 p.Gln139His missense_variant 1.0 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.99 ethambutol Not assoc w R
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