TB-Profiler result

Run: ERR369620
Summary

Run ID: ERR369620

Sample name:

Date: 2024-10-04T17:43:24.730230

Number of reads: 4685599

Percentage reads mapped: 99.68

Median coverage: 105.0

Strain: lineage4.2.2;lineage4.6.2.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.46
lineage4.6 Euro-American None 0.53
lineage4.6.2 Euro-American RD726 0.54
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.5
lineage4.2 Euro-American None 0.47
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
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
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>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
inhA 1673425 c.-777C>T upstream_gene_variant 0.59 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 2155167 p.Ser315Thr missense_variant 0.46 isoniazid Assoc w R High-level resistance
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
mshA 576077 c.730C>T synonymous_variant 0.44 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
rpoC 763447 c.78C>T synonymous_variant 0.45 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 778298 c.183G>A synonymous_variant 0.52 bedaquiline Not assoc w R - Interim
clofazimine 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 0.39 linezolid
Rv1129c 1254624 c.-90G>T upstream_gene_variant 0.44 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
inhA 1674167 c.-35T>C upstream_gene_variant 0.19 isoniazid
ethionamide
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 2063187 c.1542C>T synonymous_variant 0.47 kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
bacA 2063685 c.1044G>A synonymous_variant 0.45 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.52 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2155389 c.723C>G synonymous_variant 0.53 isoniazid Not assoc w R
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.52 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2996208 p.Ala35Asp missense_variant 0.53 capreomycin Uncertain significance
Rv2752c 3066276 c.-85G>A upstream_gene_variant 0.42 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.44 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyX 3067474 p.Pro158Ala missense_variant 0.5 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.45 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.51 cycloserine
Rv3083 3448567 p.His22Asp missense_variant 0.55 ethionamide Uncertain significance
Rv3236c 3612469 c.648A>G synonymous_variant 0.53 pyrazinamide Not assoc w R - Interim
Rv3236c 3612571 c.546C>T synonymous_variant 0.55 pyrazinamide Not assoc w R
Rv3236c 3612910 p.Leu69Phe missense_variant 0.44 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.39 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242550 c.2688C>G synonymous_variant 0.43 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 0.48 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 0.54 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.6 ethionamide 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 4407794 p.Arg137Trp missense_variant 0.53 streptomycin Uncertain significance
gid 4408464 c.-262G>T upstream_gene_variant 0.47 streptomycin