TB-Profiler result

Run: SRR5818405
Summary

Run ID: SRR5818405

Sample name:

Date: 2024-04-15T17:39:29.359794

Number of reads: 688056

Percentage reads mapped: 97.22

Median coverage: 0.0

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 mmpR5 c.442_444delAACinsCA Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.442_444delAACinsCA Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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
mmpR5 779431 c.442_444delAACinsCA frameshift_variant&missense_variant 0.79 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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 0.79 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6721 c.1482C>T synonymous_variant 0.8 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 779283 c.-803G>A upstream_gene_variant 0.84 clofazimine
bedaquiline
mmpL5 779295 c.-815A>G upstream_gene_variant 0.83 clofazimine
bedaquiline
mmpL5 779472 c.-992G>A upstream_gene_variant 0.79 clofazimine
bedaquiline
mmpS5 779523 c.-618T>A upstream_gene_variant 0.74 clofazimine
bedaquiline
mmpS5 779538 c.-633A>C upstream_gene_variant 0.66 clofazimine
bedaquiline
mmpS5 779539 c.-634C>A upstream_gene_variant 0.65 clofazimine
bedaquiline
rplC 801267 c.459A>G synonymous_variant 0.77 linezolid Not assoc w R - Interim
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.83 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.84 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.47 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
inhA 1674816 c.615T>C synonymous_variant 0.68 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
tlyA 1917812 c.-128G>A upstream_gene_variant 0.6 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
pncA 2289104 c.138A>G synonymous_variant 0.74 pyrazinamide Not assoc w R - Interim
embB 4247590 c.1077A>G synonymous_variant 0.86 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4247815 c.1302C>T synonymous_variant 0.88 ethambutol Not assoc w R - Interim
ethA 4326463 c.1011C>T synonymous_variant 0.87 ethionamide Not assoc w R - Interim
ethA 4326740 p.Arg245His missense_variant 0.86 ethionamide Uncertain significance
ethA 4326764 p.Ala237Val missense_variant 0.26 ethionamide
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407742 p.Arg154Pro missense_variant 0.29 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.28 streptomycin Not assoc w R
gid 4408185 c.18C>T synonymous_variant 0.71 streptomycin Not assoc w R - Interim