TB-Profiler result

Run: ERR11775955
Summary

Run ID: ERR11775955

Sample name:

Date: 2024-05-22T16:23:30.511669

Number of reads: 8133458

Percentage reads mapped: 99.59

Median coverage: 262.0

Strain: lineage2.2.1;lineage4.2.1.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.76
lineage4.2 Euro-American None 0.23
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.76
lineage2.2 East-Asian (Beijing) RD105;RD207 0.77
lineage4 Euro-American None 0.25
lineage4.2.1.1 Euro-American (TUR) None 0.22
lineage4.2.1 Euro-American (TUR) None 0.26
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
pyrazinamide
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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 0.86 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.8 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.74 isoniazid Assoc w R 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 4969 c.-271G>T upstream_gene_variant 0.74 levofloxacin
moxifloxacin
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 0.77 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.72 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.25 ethionamide
isoniazid
ccsA 620625 p.Ile245Met missense_variant 0.7 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.83 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.81 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.81 rifampicin Not assoc w R
rpoC 764058 p.Ala230Val missense_variant 0.78 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 0.79 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.78 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 777451 p.Val344Leu missense_variant 0.25 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpR5 779100 c.111T>C synonymous_variant 0.22 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.71 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.27 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.73 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254582 c.-48A>C upstream_gene_variant 0.25 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.75 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
atpE 1460876 c.-169G>A upstream_gene_variant 0.15 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 streptomycin
kanamycin
capreomycin
amikacin
inhA 1673401 c.-801G>A upstream_gene_variant 0.28 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.77 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
bacA 2063685 c.1044G>A synonymous_variant 0.22 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.78 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.88 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.17 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2747437 p.Met54Ile missense_variant 0.75 para-aminosalicylic_acid
Rv2752c 3067157 c.-966G>T upstream_gene_variant 0.28 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086742 c.-78A>C upstream_gene_variant 0.26 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.74 pyrazinamide Not assoc w R - Interim
lpqB 3623652 p.Pro420Leu missense_variant 0.27 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.79 bedaquiline Uncertain significance
rifampicin 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 0.73 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.8 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 0.78 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.74 streptomycin Not assoc w R
gid 4407934 p.Leu90Arg missense_variant 0.76 streptomycin Uncertain significance
gid 4408213 c.-11C>T upstream_gene_variant 0.25 streptomycin Uncertain significance