TB-Profiler result

Run: SRR13861245

Summary

Run ID: SRR13861245

Sample name:

Date: 2024-04-15T10:14:43.740554

Number of reads: 252213

Percentage reads mapped: 12.62

Median coverage: 8.0

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 ethA p.Ser424* Assoc w R
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
ethA 4326203 p.Ser424* stop_gained 1.0 ethionamide 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 1057 p.Val353Leu missense_variant 1.0 isoniazid Uncertain significance
gyrB 5532 c.295dupG frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
ccsA 619735 c.-156G>C upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
ccsA 620100 c.210G>T synonymous_variant 1.0 capreomycin
amikacin
kanamycin
Rv1258c 1407009 p.Ala111Asp missense_variant 1.0 streptomycin
isoniazid
pyrazinamide
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.75 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1674891 p.Trp230Cys missense_variant 1.0 ethionamide
isoniazid
Rv1979c 2222721 c.444G>C synonymous_variant 1.0 clofazimine
bedaquiline
ahpC 2726345 p.Phe51Leu missense_variant 1.0 isoniazid
Rv2477c 2783258 c.784delC frameshift_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
whiB7 3568676 p.Ser2Ala missense_variant 1.0 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
glpK 4138911 p.Gly282Val missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embA 4242250 c.-983C>G upstream_gene_variant 1.0 ethambutol
embB 4249328 p.Met939Leu missense_variant 1.0 ethambutol