TB-Profiler result

Run: ERR1035046
Summary

Run ID: ERR1035046

Sample name:

Date: 2024-04-15T08:46:52.497208

Number of reads: 7620364

Percentage reads mapped: 99.46

Median coverage: 160.0

Strain: lineage3;lineage4.7

Spoligotype:

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.55
lineage4.7 Euro-American (mainly T) None 0.45
lineage4 Euro-American None 0.45
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.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. 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.Met306Ile Assoc w R
pyrazinamide pncA p.Gly97Asp Assoc w R
streptomycin
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 inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
ethA p.Thr342Lys Uncertain significance Mutation from literature
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 0.45 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 761155 p.Ser450Leu missense_variant 0.45 rifampicin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.45 isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
katG 2155167 p.Ser315Thr missense_variant 0.48 isoniazid Assoc w R High-level resistance
pncA 2288952 p.Gly97Asp missense_variant 0.43 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.57 ethambutol Assoc w R
ethA 4326449 p.Thr342Lys missense_variant 0.49 ethionamide 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.56 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8056 p.Arg252Leu missense_variant 0.58 levofloxacin Not assoc w R - Interim
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 0.56 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13887 c.-329T>C upstream_gene_variant 0.49 isoniazid
fgd1 491742 c.960T>C synonymous_variant 0.52 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 656114 p.Ser453Ala missense_variant 0.62 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.6 ethionamide Not assoc w R - Interim
Rv0565c 657497 c.-27G>A upstream_gene_variant 0.46 ethionamide Uncertain significance
hadA 732145 c.216C>T synonymous_variant 0.53 isoniazid Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.52 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.56 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.51 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.38 rifampicin Uncertain significance
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 0.49 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.53 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
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.45 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.58 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 0.57 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.57 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 0.57 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.58 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.6 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.57 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
thyA 3074424 c.48G>T synonymous_variant 0.58 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.5 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.57 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.55 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.54 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 4138654 c.1102C>T synonymous_variant 0.61 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
embC 4242075 p.Arg738Gln missense_variant 0.47 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.98 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.43 ethambutol Not assoc w R
ethA 4328212 c.-740delC upstream_gene_variant 0.5 ethionamide
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 0.59 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.58 streptomycin Not assoc w R
gid 4407704 p.Ala167Pro missense_variant 0.42 streptomycin Uncertain significance