TB-Profiler result

Run: ERR11068799
Summary

Run ID: ERR11068799

Sample name:

Date: 2024-04-15T01:18:07.269852

Number of reads: 2556024

Percentage reads mapped: 99.46

Median coverage: 78.0

Strain: lineage4.1.2.1;lineage4.2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2.1 Euro-American None 0.87
lineage4.2.2 Euro-American (Ural) None 0.86
lineage4.1 Euro-American None 0.13
lineage4.1.2 Euro-American None 0.13
lineage4.2 Euro-American None 0.88
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.13
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 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)
p.Ile194Thr Uncertain significance Mutation from literature
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA c.474_475dupCC Assoc w R
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ile194Thr 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
rpoB 761155 p.Ser450Leu missense_variant 0.87 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.87 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.78 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
inhA 1674782 p.Ile194Thr missense_variant 0.89 isoniazid Uncertain significance Mutation from literature
ethionamide Uncertain significance Mutation from literature
pncA 2288766 c.474_475dupCC frameshift_variant 0.89 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.88 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
dnaA 1131 c.1131C>A synonymous_variant 0.9 isoniazid Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.99 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 0.14 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.16 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 576077 c.730C>T synonymous_variant 0.88 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
Rv0565c 656226 c.1245C>G synonymous_variant 0.81 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.11 ethionamide Uncertain significance
rpoC 764959 c.1590G>A synonymous_variant 0.16 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.15 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.98 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 800204 c.-605T>C upstream_gene_variant 0.87 linezolid
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
bacA 2063685 c.1044G>A synonymous_variant 0.84 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.86 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2102726 p.His106Arg missense_variant 0.74 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
Rv1979c 2223233 c.-69G>C upstream_gene_variant 0.2 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.41 capreomycin Uncertain significance
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.92 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.93 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877956 p.Glu184Asp missense_variant 0.85 rifampicin Uncertain significance
rpoA 3878572 c.-65G>C upstream_gene_variant 0.89 rifampicin Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.23 ethambutol Not assoc w R
embC 4239334 c.-529T>C upstream_gene_variant 0.81 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
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 1.0 capreomycin
amikacin
kanamycin
gid 4408009 p.Val65Ala missense_variant 0.91 streptomycin Uncertain significance