TB-Profiler result

Run: SRR13837435
Summary

Run ID: SRR13837435

Sample name:

Date: 2024-04-15T12:34:42.283226

Number of reads: 881969

Percentage reads mapped: 99.06

Median coverage: 30.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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 fbiC c.170dupA Assoc w R - Interim Confers DLM-PMD cross-resistance
c.1116delC Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1303099 c.170dupA frameshift_variant 0.96 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiC 1304043 c.1116delC frameshift_variant 1.0 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
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 9490 p.Gly730Asp missense_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13883 c.-325T>A upstream_gene_variant 1.0 isoniazid
fgd1 491231 p.Phe150Tyr missense_variant 1.0 clofazimine
pretomanid
delamanid
Rv0565c 656020 p.Gly484Val missense_variant 1.0 ethionamide
rpoC 766128 p.Ala920Gly missense_variant 1.0 rifampicin
rpsL 781503 c.-57T>C upstream_gene_variant 1.0 streptomycin
rplC 800381 c.-428A>G upstream_gene_variant 1.0 linezolid Uncertain significance
sigE 1364655 p.Met81Ile missense_variant 1.0 pyrazinamide
Rv1258c 1406861 p.Ile160Met missense_variant 1.0 streptomycin
isoniazid
pyrazinamide
Rv1258c 1407463 c.-123G>C upstream_gene_variant 1.0 streptomycin
isoniazid
pyrazinamide
rrs 1472303 n.458G>A non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474235 n.578G>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475139 n.1482C>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476248 n.2591G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1476576 n.2919C>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
bacA 2063299 p.Trp477Leu missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
kasA 2518209 p.Thr32Arg missense_variant 1.0 isoniazid
folC 2746788 p.Ala271Pro missense_variant 1.0 para-aminosalicylic_acid
thyX 3067214 p.Ser244Arg missense_variant 1.0 para-aminosalicylic_acid
fbiD 3339396 c.279C>T synonymous_variant 1.0 clofazimine
pretomanid
delamanid
mtrA 3627293 p.Glu19Asp missense_variant 1.0 bedaquiline
rifampicin
rpoA 3878048 p.Ala154Ser missense_variant 1.0 rifampicin
panD 4044922 c.-641G>T upstream_gene_variant 1.0 pyrazinamide
glpK 4139628 p.Gln43Leu missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embB 4248368 p.Leu619Val missense_variant 1.0 ethambutol
ethA 4327082 p.Cys131Ser missense_variant 1.0 ethionamide
ethA 4327097 p.Leu126His missense_variant 1.0 ethionamide
gid 4407792 c.411G>C synonymous_variant 1.0 streptomycin