TB-Profiler result

Run: SRR6936661
Summary

Run ID: SRR6936661

Sample name:

Date: 2024-05-20T09:10:18.261481

Number of reads: 441716

Percentage reads mapped: 99.62

Median coverage: 26.5

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.76
lineage2.2 East-Asian (Beijing) RD105;RD207 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
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fbiC c.1001delC Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA c.471delC Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1303929 c.1001delC frameshift_variant 0.45 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3641011 c.471delC frameshift_variant 0.26 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-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 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
gyrA 7929 c.630delC frameshift_variant 0.4 moxifloxacin
levofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 760139 c.336delC frameshift_variant 0.38 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 1.0 rifampicin Not assoc w R
rpoC 767149 c.3782delG frameshift_variant 0.46 rifampicin
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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.97 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 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 1.0 isoniazid Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
levofloxacin Not assoc w R
fbiC 1304671 p.Val581Leu missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
sigE 1364706 c.294G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
amikacin
streptomycin
capreomycin
rrl 1475203 n.1551delC non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1475203 n.1551delC non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917637 c.-302delC upstream_gene_variant 0.36 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102249 c.794delC frameshift_variant 0.43 ethionamide Uncertain significance
isoniazid Uncertain significance
delamanid Uncertain significance
ndh 2102292 c.750delC frameshift_variant 0.2 ethionamide Uncertain significance
isoniazid Uncertain significance
delamanid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170209 c.403delG frameshift_variant 0.82 pyrazinamide Uncertain significance
Rv1979c 2222826 c.338dupT frameshift_variant 0.33 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
folC 2746630 c.968delG frameshift_variant 0.25 para-aminosalicylic_acid
folC 2746842 c.756delC frameshift_variant 0.29 para-aminosalicylic_acid
thyX 3067446 c.499delG frameshift_variant 0.24 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568995 c.-317_-316insG upstream_gene_variant 0.18 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625962 c.651delC frameshift_variant 0.22 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3627582 c.-970delG upstream_gene_variant 0.61 rifampicin
bedaquiline
ddn 3986612 c.-231delG upstream_gene_variant 0.32 pretomanid
delamanid
panD 4043867 p.Gly139* stop_gained 1.0 pyrazinamide Uncertain significance
embC 4242622 c.2762delG frameshift_variant 0.52 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243791 c.562delC frameshift_variant 0.52 ethambutol Uncertain significance
embB 4249646 c.3136delG frameshift_variant 0.33 ethambutol
aftB 4267647 p.Asp397Gly missense_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 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.97 streptomycin Not assoc w R