TB-Profiler result

Run: ERR10112875
Summary

Run ID: ERR10112875

Sample name:

Date: 2024-10-04T15:42:43.702610

Number of reads: 4989029

Percentage reads mapped: 99.64

Median coverage: 146.0

Strain: lineage2.2.1.1;lineage4.3.2.1

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 0.22
lineage2 East-Asian RD105 0.77
lineage4.3.2 Euro-American (LAM) None 0.24
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.77
lineage4.3.2.1 Euro-American (LAM) RD761 0.22
lineage2.2 East-Asian (Beijing) RD105;RD207 0.77
lineage4 Euro-American None 0.24
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.78
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Gln10Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid folC p.Arg49Trp 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
rpoB 761155 p.Ser450Leu missense_variant 0.25 rifampicin Assoc w R
rpoB 761161 p.Leu452Pro missense_variant 0.79 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.16 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.21 isoniazid Assoc w R High-level resistance
pncA 2289213 p.Gln10Pro missense_variant 0.17 pyrazinamide Assoc w R
folC 2747454 p.Arg49Trp missense_variant 0.26 para-aminosalicylic_acid 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
gyrB 5520 p.Pro94Leu missense_variant 0.19 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7222 c.1983C>T synonymous_variant 0.19 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.79 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.72 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.23 isoniazid
ethionamide
ccsA 620625 p.Ile245Met missense_variant 0.79 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.78 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.75 ethionamide Uncertain significance
rpoB 761505 p.Ser567Ala missense_variant 0.21 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.84 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.23 rifampicin Not assoc w R
rpoC 766740 p.Val1124Gly missense_variant 0.16 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 0.68 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.72 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.71 bedaquiline
clofazimine
rpsL 781301 c.-259C>T upstream_gene_variant 0.74 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.77 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 0.73 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.19 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.8 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 0.77 pyrazinamide Not assoc w R
Rv1979c 2223014 p.Tyr51Asn missense_variant 0.72 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2714846 p.Val163Ile missense_variant 0.79 kanamycin Not assoc w R
amikacin Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.27 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.77 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 0.79 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.25 pyrazinamide 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 0.75 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.76 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.75 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 0.77 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.75 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.27 streptomycin Not assoc w R