TB-Profiler result

Run: ERR9027230
Summary

Run ID: ERR9027230

Sample name:

Date: 2024-04-15T07:17:08.056560

Number of reads: 1121232

Percentage reads mapped: 97.35

Median coverage: 39.0

Strain: lineage4.1.2.1;lineage4.3.3

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 0.47
lineage4.1.2 Euro-American None 0.49
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.55
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.48
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide pncA c.390_391dupGG Assoc w R
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA p.Leu74Pro Uncertain significance Mutation from literature
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 0.5 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.22 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.47 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
tlyA 1918160 p.Leu74Pro missense_variant 0.39 capreomycin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288850 c.390_391dupGG frameshift_variant 0.6 pyrazinamide Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.43 ethambutol 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 698 p.Arg233Gln missense_variant 0.55 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 8040 p.Gly247Ser missense_variant 0.71 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 0.28 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575423 p.Arg26Cys missense_variant 0.59 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.3 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.45 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.42 rifampicin Not assoc w R
rpoC 764931 p.Ala521Asp missense_variant 0.38 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.29 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.68 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1303095 c.165G>A synonymous_variant 0.47 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1304962 p.Trp678Gly missense_variant 0.36 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.27 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 2156196 c.-85C>T upstream_gene_variant 0.62 isoniazid 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 0.61 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.43 isoniazid
eis 2715340 c.-8C>T upstream_gene_variant 0.48 amikacin Uncertain significance
kanamycin Uncertain significance
ribD 2986827 c.-12G>A upstream_gene_variant 0.55 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.49 para-aminosalicylic_acid
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
clpC1 4038287 c.2418C>T synonymous_variant 0.42 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.51 pyrazinamide Not assoc w R - Interim
embC 4239298 c.-565_-564delCCinsTA upstream_gene_variant 0.4 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.44 ethambutol Not assoc w R
whiB6 4338594 c.-73T>G upstream_gene_variant 0.49 capreomycin
amikacin
kanamycin
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 4407790 p.Ala138Val missense_variant 0.55 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.61 streptomycin Not assoc w R