TB-Profiler result

Run: ERR751393
Summary

Run ID: ERR751393

Sample name:

Date: 2024-04-15T16:41:47.651854

Number of reads: 4743716

Percentage reads mapped: 99.55

Median coverage: 98.0

Strain: lineage4.1.2.1;lineage4.3.4.2

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 0.42
lineage4.1 Euro-American None 0.57
lineage4.1.2 Euro-American None 0.52
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.56
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.45
lineage4.3.4.2 Euro-American (LAM) RD174 0.47
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 embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin
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 0.49 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.57 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile 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
gyrB 6140 p.Val301Leu missense_variant 0.47 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
Rv0010c 13490 p.Met23Ile missense_variant 0.55 isoniazid Uncertain significance
Rv0010c 13604 c.-46T>G upstream_gene_variant 0.59 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.46 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.5 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.46 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.54 rifampicin Not assoc w R
rpoB 760555 p.Glu250Gly missense_variant 0.63 rifampicin Not assoc w R - Interim
rpoC 764918 p.Val517Leu missense_variant 0.44 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.48 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.47 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 1302920 c.-11G>A upstream_gene_variant 0.56 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473868 n.211C>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833469 c.-73G>T upstream_gene_variant 0.46 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 0.55 isoniazid
folC 2746277 p.Asp441Gly missense_variant 0.51 para-aminosalicylic_acid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.21 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.51 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.46 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.55 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.41 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.49 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 0.58 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 4407970 p.Pro78Leu missense_variant 0.53 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.5 streptomycin Not assoc w R