TB-Profiler result

Run: ERR2307411
Summary

Run ID: ERR2307411

Sample name:

Date: 2024-04-16T06:57:33.662951

Number of reads: 2322272

Percentage reads mapped: 99.57

Median coverage: 81.0

Strain: lineage2.2.1;lineage4

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 0.69
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.71
lineage2.2 East-Asian (Beijing) RD105;RD207 0.74
lineage4 Euro-American None 0.33
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.495delG Assoc w R
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 0.72 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.66 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.62 isoniazid Assoc w R High-level resistance
pncA 2289252 c.-11A>G upstream_gene_variant 0.73 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.62 ethambutol Assoc w R
ethA 4326978 c.495delG frameshift_variant 0.3 ethionamide 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
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 7892 c.591G>A synonymous_variant 0.31 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 0.77 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.7 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620619 c.729G>A synonymous_variant 0.22 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.76 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.74 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.69 ethionamide Uncertain significance
rpoB 759387 c.-420T>C upstream_gene_variant 0.32 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.64 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.74 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 0.76 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.73 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 778090 p.Gly131Arg missense_variant 0.28 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.67 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 0.64 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1304610 c.1680C>T synonymous_variant 0.33 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.67 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1416966 p.Ala128Pro missense_variant 0.33 ethambutol Uncertain significance
embR 1417403 c.-56G>A upstream_gene_variant 0.21 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474074 n.417C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.73 pyrazinamide Not assoc w R - Interim
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
katG 2154724 p.Arg463Leu missense_variant 0.7 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.75 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
ald 3086731 c.-89A>G upstream_gene_variant 0.75 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.77 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.76 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 0.7 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.32 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242835 c.2973C>T synonymous_variant 0.33 ethambutol Not assoc w R - Interim
embA 4243346 c.114A>G synonymous_variant 0.56 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.65 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.75 ethambutol Not assoc w R
ethA 4327310 p.Ser55Cys missense_variant 0.35 ethionamide Uncertain significance
whiB6 4338371 p.Thr51Pro missense_variant 0.78 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
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 0.61 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.66 streptomycin Not assoc w R