TB-Profiler result

Run: SRR6131528
Summary

Run ID: SRR6131528

Sample name:

Date: 2024-04-15T08:17:17.375689

Number of reads: 13891623

Percentage reads mapped: 45.63

Median coverage: 12.0

Strain: lineage4.1.1.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.93
lineage4.1.1.3 Euro-American (X-type) RD193 0.46
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.52
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 7362 p.Glu21Gln 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
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 762899 c.3093G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762911 p.Ile1035Met missense_variant 0.26 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 0.37 rifampicin
rpoB 762942 c.3136_3138delATCinsGG frameshift_variant&missense_variant 0.36 rifampicin
rpoC 762947 c.-423C>G upstream_gene_variant 0.28 rifampicin
rpoC 762971 c.-399G>C upstream_gene_variant 0.32 rifampicin
rpoB 762977 c.3171C>T synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 762989 c.3183G>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 0.42 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.13 streptomycin
kanamycin
capreomycin
amikacin
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223682 c.-518C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R