TB-Profiler result

Run: ERR10748344
Summary

Run ID: ERR10748344

Sample name:

Date: 2024-10-04T01:35:04.630207

Number of reads: 1011431

Percentage reads mapped: 99.87

Median coverage: 41.0

Strain: lineage2.2.1;lineage4.7

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.21
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.17
lineage2.2 East-Asian (Beijing) RD105;RD207 0.22
lineage4.7 Euro-American (mainly T) None 0.76
lineage4 Euro-American None 0.82
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)
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 0.25 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.24 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)
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
gyrB 6798 p.Gly520Ala missense_variant 0.72 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.24 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.19 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.32 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575578 c.231G>C synonymous_variant 0.7 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.22 isoniazid Not assoc w R
ethionamide Not assoc w R
mmaA3 738234 c.-85C>T upstream_gene_variant 0.85 isoniazid
rpoC 763555 c.186C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 765462 p.Asn698Thr missense_variant 0.2 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.21 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.24 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 778979 c.-74G>T upstream_gene_variant 0.23 bedaquiline Not assoc w R - Interim
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.32 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.25 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.24 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.74 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.29 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.35 pyrazinamide Not assoc w R
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 0.16 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.19 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.31 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.19 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.79 ethambutol Not assoc w R
aftB 4267992 p.Thr282Met missense_variant 0.8 ethambutol Uncertain significance
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 0.23 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.2 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.25 streptomycin Not assoc w R