TB-Profiler result

Run: ERR4813672
Summary

Run ID: ERR4813672

Sample name:

Date: 2024-04-16T00:02:47.468414

Number of reads: 5905347

Percentage reads mapped: 99.69

Median coverage: 181.0

Strain: lineage2.2.1;lineage4.3.3;lineage4.4.1.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.13
lineage2 East-Asian RD105 0.65
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.68
lineage2.2 East-Asian (Beijing) RD105;RD207 0.67
lineage4.4.1 Euro-American (S-type) None 0.22
lineage4 Euro-American None 0.36
lineage4.4.1.1 Euro-American None 0.23
lineage4.3.3 Euro-American (LAM) RD115 0.13
lineage4.4 Euro-American None 0.23
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
p.Leu452Pro 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)
katG p.Asp94Gly Uncertain significance Mutation from literature
ahpC c.-81C>T Uncertain significance Mutation from literature
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
rpoB 761155 p.Ser450Leu missense_variant 0.14 rifampicin Assoc w R
rpoB 761161 p.Leu452Pro missense_variant 0.64 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.19 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
katG 2155831 p.Asp94Gly missense_variant 0.61 isoniazid Uncertain significance Mutation from literature
ahpC 2726112 c.-81C>T upstream_gene_variant 0.47 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
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 8116 p.Thr272Ile missense_variant 0.27 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.64 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.63 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.63 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.75 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.72 ethionamide Uncertain significance
rpoB 761032 p.Gln409Arg missense_variant 0.13 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.69 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.13 rifampicin Not assoc w R
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 0.63 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.65 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.61 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.69 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.56 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.57 pyrazinamide Not assoc w R - Interim
rpsA 1834683 p.Ala381Val missense_variant 0.13 pyrazinamide Uncertain significance
tsnR 1854169 c.564A>C synonymous_variant 0.61 linezolid Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917695 c.-245C>A upstream_gene_variant 0.15 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 0.24 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.69 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.65 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.2 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
kasA 2518919 p.Gly269Ser missense_variant 0.12 isoniazid
Rv2477c 2784248 c.-206C>G upstream_gene_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.72 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.12 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087755 c.936G>T synonymous_variant 0.74 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.22 ethionamide Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 0.2 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.73 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.62 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.11 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.28 ethambutol Not assoc w R
embC 4242182 p.Ala774Ser missense_variant 0.14 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.6 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.26 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.55 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 4407588 c.615A>G synonymous_variant 0.65 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.62 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.14 streptomycin Not assoc w R