TB-Profiler result

Run: SAMEA2533704
Summary

Run ID: SAMEA2533704

Sample name:

Date: 2024-03-26T16:28:52.100284

Number of reads: 3764874

Percentage reads mapped: 99.5

Median coverage: 125.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 1.0
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Gln Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Ala451Gly Assoc w R - Interim
isoniazid katG c.1414_1440dupCTAGTTTCGACCGCATGGGCGGCGGCG Mutation from literature
ethambutol embA c.-29_-28delCT Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.355_356delGC 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 761154 p.Ser450Gln missense_variant 1.0 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761158 p.Ala451Gly missense_variant 1.0 rifampicin Assoc w R - Interim
rpsL 781687 p.Lys43Arg missense_variant 0.55 streptomycin Assoc w R
katG 2154671 c.1414_1440dupCTAGTTTCGACCGCATGGGCGGCGGCG conservative_inframe_insertion 1.0 isoniazid Mutation from literature
embA 4243203 c.-29_-28delCT upstream_gene_variant 0.58 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.41 ethambutol Assoc w R
gid 4407846 c.355_356delGC frameshift_variant 0.31 streptomycin 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
dnaA 1163 p.Thr388Ile missense_variant 0.38 isoniazid Uncertain significance
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 491591 p.Lys270Met missense_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.99 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765882 p.Ser838Cys missense_variant 0.24 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 1.0 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781768 p.Glu70Ala missense_variant 1.0 streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1833742 p.Glu67Asp missense_variant 1.0 pyrazinamide Uncertain significance
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
ahpC 2726141 c.-52C>A upstream_gene_variant 1.0 isoniazid Uncertain significance
pepQ 2859371 p.Lys350Gln missense_variant 1.0 clofazimine
bedaquiline
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.26 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.15 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641013 c.471C>T synonymous_variant 1.0 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
embC 4239298 c.-565C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269116 p.Arg240Cys missense_variant 0.49 ethambutol Uncertain significance
ubiA 4269162 p.Leu224Phe missense_variant 0.45 ethambutol 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