TB-Profiler result

Run: ERR279473
Summary

Run ID: ERR279473

Sample name:

Date: 2024-10-05T13:53:22.310623

Number of reads: 1655312

Percentage reads mapped: 99.44

Median coverage: 30.0

Strain: lineage4.1.2.1

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 0.94
lineage4.1.2 Euro-American None 0.94
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.94
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
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.-38083_*8634del Assoc w R
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
tlyA 1879856 c.-38083_*8634del transcript_ablation 0.91 capreomycin 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.87 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
mshA 575645 c.299_*46632del frameshift_variant&stop_lost&splice_region_variant 0.92 isoniazid Uncertain significance
ethionamide Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.94 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.91 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.89 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.93 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254582 c.-48A>C upstream_gene_variant 0.87 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833674 p.Lys45Glu missense_variant 0.79 pyrazinamide Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2166382 c.1081_*1266del stop_lost&conservative_inframe_deletion&splice_region_variant 0.91 pyrazinamide
PPE35 2167927 c.1187_2685del frameshift_variant 0.92 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.97 isoniazid
Rv2680 2960617 c.-35487_*11600del transcript_ablation 0.94 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.35 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.91 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.97 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627756 c.-407A>T upstream_gene_variant 0.67 rifampicin
bedaquiline
panD 4044725 c.-444C>T upstream_gene_variant 0.9 pyrazinamide
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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407973 p.Val77Gly missense_variant 1.0 streptomycin Uncertain significance