TB-Profiler result

Run: SRR6785155
Summary

Run ID: SRR6785155

Sample name:

Date: 2024-10-05T13:15:03.883292

Number of reads: 2944100

Percentage reads mapped: 99.72

Median coverage: 41.0

Strain: lineage2.2.1;lineage4.3

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.36
lineage2 East-Asian RD105 0.58
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.55
lineage2.2 East-Asian (Beijing) RD105;RD207 0.53
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Pro51Leu Uncertain significance Mutation from literature
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
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
rpsL 781687 p.Lys43Arg missense_variant 0.72 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.51 isoniazid Assoc w R High-level resistance
thyX 3067961 c.-16C>T upstream_gene_variant 0.3 para-aminosalicylic_acid Mutation from literature
ethA 4327322 p.Pro51Leu missense_variant 0.44 ethionamide 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 0.98 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
fgd1 491742 c.960T>C synonymous_variant 0.71 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.65 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.54 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.62 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.71 ethionamide Uncertain significance
rpoB 761799 p.Arg665Trp missense_variant 0.36 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.6 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.3 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.79 rifampicin Not assoc w R
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 0.65 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.66 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.58 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253304 p.Asn411Tyr missense_variant 0.3 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
fbiC 1304671 p.Val581Leu missense_variant 0.67 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
sigE 1364497 p.Ser29Cys missense_variant 0.29 pyrazinamide
sigE 1364706 c.294G>A synonymous_variant 0.57 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.62 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.7 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 0.62 isoniazid 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
kasA 2518919 p.Gly269Ser missense_variant 0.35 isoniazid
Rv2752c 3067135 c.-944C>T upstream_gene_variant 0.33 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.34 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.47 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.55 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.55 pyrazinamide Not assoc w R
panD 4043867 p.Gly139* stop_gained 0.49 pyrazinamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.72 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.62 ethambutol Not assoc w R
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 4407588 c.615A>G synonymous_variant 0.72 streptomycin Not assoc w R
gid 4407720 c.483C>G synonymous_variant 0.26 streptomycin Not assoc w R - Interim
gid 4407913 p.Arg97His missense_variant 0.27 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.67 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.43 streptomycin Not assoc w R