TB-Profiler result

Run: ERR2512786
Summary

Run ID: ERR2512786

Sample name:

Date: 2024-04-15T01:44:48.497723

Number of reads: 4393258

Percentage reads mapped: 99.67

Median coverage: 147.0

Strain: lineage4.1.2.1;lineage4.7

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.5
lineage4.1.2 Euro-American None 0.45
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.46
lineage4.7 Euro-American (mainly T) None 0.52
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
isoniazid
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
embB 4247431 p.Met306Ile missense_variant 0.49 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 1505 p.Arg502His missense_variant 0.53 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 0.49 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8571 p.Leu424Val missense_variant 0.52 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 0.49 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.49 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.52 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.49 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.42 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.39 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 0.47 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781800 c.241C>T synonymous_variant 0.51 streptomycin Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.49 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1673472 c.-730C>T upstream_gene_variant 0.5 ethionamide Uncertain significance
isoniazid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.38 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2169413 c.1200T>C synonymous_variant 0.46 pyrazinamide
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 0.47 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.48 cycloserine
lpqB 3623383 p.Ala510Thr missense_variant 0.47 bedaquiline
rifampicin Uncertain significance
lpqB 3624090 p.Ala274Val missense_variant 0.51 bedaquiline
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.51 bedaquiline Uncertain significance
rifampicin Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.39 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.41 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 0.46 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.45 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 0.42 capreomycin
amikacin
kanamycin