TB-Profiler result

Run: SRR13837904
Summary

Run ID: SRR13837904

Sample name:

Date: 2024-04-15T14:54:03.743868

Number of reads: 1471899

Percentage reads mapped: 97.19

Median coverage: 50.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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
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
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 7877 p.His192Gln missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mshA 576146 p.Val267Leu missense_variant 1.0 ethionamide
isoniazid
hadA 732095 p.Pro56Thr missense_variant 1.0 isoniazid
rpoB 759869 c.63C>T synonymous_variant 1.0 rifampicin
rpoC 763782 p.Ser138* stop_gained 0.98 rifampicin
rpoC 764568 p.Lys400Thr missense_variant 0.94 rifampicin
mmpL5 777073 p.Lys470Glu missense_variant 1.0 clofazimine
bedaquiline
mmpL5 777311 c.1170C>T synonymous_variant 1.0 clofazimine
bedaquiline
mmpL5 778981 c.-501C>A upstream_gene_variant 1.0 clofazimine
bedaquiline
rplC 801436 p.Ser210Arg missense_variant 1.0 linezolid
fbiC 1303686 c.756C>G synonymous_variant 1.0 clofazimine
pretomanid
delamanid
rrs 1472605 n.760G>C non_coding_transcript_exon_variant 0.94 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674376 p.Pro59Ser missense_variant 1.0 ethionamide
isoniazid
tlyA 1917844 c.-96C>A upstream_gene_variant 1.0 capreomycin
tlyA 1918260 p.His107Gln missense_variant 1.0 capreomycin
bacA 2064394 p.Thr112Arg missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
katG 2154461 p.Ala551Pro missense_variant 1.0 isoniazid
Rv1979c 2222535 c.630C>G synonymous_variant 1.0 clofazimine
bedaquiline
kasA 2518608 p.Met165Thr missense_variant 1.0 isoniazid
eis 2714211 c.1122G>A synonymous_variant 1.0 amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ahpC 2726250 p.Gly20Arg missense_variant 1.0 isoniazid
Rv2752c 3066461 c.-270C>T upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066855 c.-664T>G upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
whiB7 3568939 c.-260T>C upstream_gene_variant 1.0 streptomycin
amikacin
kanamycin
Rv3236c 3612518 p.Tyr200Ser missense_variant 1.0 pyrazinamide
fbiB 3641684 p.Ser50Arg missense_variant 1.0 clofazimine
pretomanid
delamanid
glpK 4139507 p.Lys83Asn missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240263 p.Val134Ala missense_variant 1.0 ethambutol
embC 4240920 p.Leu353Pro missense_variant 1.0 ethambutol
embC 4241504 p.Val548Met missense_variant 1.0 ethambutol Uncertain significance
embB 4248000 p.Asp496Val missense_variant 1.0 ethambutol
aftB 4268715 p.Leu41Pro missense_variant 1.0 ethambutol
ethR 4327704 p.Lys52Asn missense_variant 1.0 ethionamide