TB-Profiler result

Run: SRR5818430
Summary

Run ID: SRR5818430

Sample name:

Date: 2024-04-16T11:14:03.584540

Number of reads: 203047

Percentage reads mapped: 98.6

Median coverage: 0.0

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
gyrB 6454 c.1215C>T synonymous_variant 0.99 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6721 c.1482C>T synonymous_variant 0.98 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
mmpL5 779283 c.-803G>A upstream_gene_variant 0.85 clofazimine
bedaquiline
mmpL5 779295 c.-815A>G upstream_gene_variant 0.83 clofazimine
bedaquiline
rplC 801267 c.459A>G synonymous_variant 0.99 linezolid Not assoc w R - Interim
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.95 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.96 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.78 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.81 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472673 n.828_837delTTTCCTTCCTinsGGCCACCCG non_coding_transcript_exon_variant 0.67 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.65 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.69 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.63 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.68 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.61 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.77 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476164 n.2507A>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476194 n.2537A>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.41 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476207 n.2550T>C non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
pncA 2289104 c.138A>G synonymous_variant 0.95 pyrazinamide Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.93 ethambutol Not assoc w R
embB 4247815 c.1302C>T synonymous_variant 0.95 ethambutol Not assoc w R - Interim
ethA 4326740 p.Arg245His missense_variant 1.0 ethionamide Uncertain significance