TB-Profiler result

Run: SRR8692905

Summary

Run ID: SRR8692905

Sample name:

Date: 2024-05-22T10:19:39.261192

Number of reads: 603286

Percentage reads mapped: 23.86

Median coverage: 14.0

Strain:

Spoligotype:

Drug-resistance: Sensitive


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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
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 0.69 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.64 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTC non_coding_transcript_exon_variant 0.64 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.56 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473814 n.157A>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473815 n.158T>G non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid
rrl 1473816 n.159C>G non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid
rrl 1473828 n.171G>C non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1473829 n.172G>C non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid
rrl 1473830 n.173T>G non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1473831 n.174G>T non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474709 n.1053delT non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1474714 n.1058delT non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475395 n.1738T>G non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1475396 n.1739C>G non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1475397 n.1740G>T non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.55 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.55 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.67 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid
tlyA 1917972 c.33A>G synonymous_variant 0.38 capreomycin Not assoc w R
clpC1 4038878 c.1827A>G synonymous_variant 0.3 pyrazinamide Not assoc w R - Interim
clpC1 4038881 c.1824C>G synonymous_variant 0.3 pyrazinamide
clpC1 4038890 c.1815G>A synonymous_variant 0.33 pyrazinamide
clpC1 4039733 c.972G>C synonymous_variant 0.38 pyrazinamide
clpC1 4039751 c.954A>G synonymous_variant 0.38 pyrazinamide
clpC1 4039757 c.948A>G synonymous_variant 0.4 pyrazinamide
clpC1 4039760 c.945T>C synonymous_variant 0.38 pyrazinamide
clpC1 4039766 c.939T>C synonymous_variant 0.38 pyrazinamide
clpC1 4039769 c.936C>G synonymous_variant 0.38 pyrazinamide
clpC1 4039775 c.930G>C synonymous_variant 0.35 pyrazinamide
clpC1 4039778 c.927A>G synonymous_variant 0.35 pyrazinamide
clpC1 4039817 c.888A>T synonymous_variant 0.46 pyrazinamide
clpC1 4039820 c.885T>C synonymous_variant 0.46 pyrazinamide Not assoc w R - Interim
clpC1 4039823 c.882T>A synonymous_variant 0.46 pyrazinamide
clpC1 4039831 c.874T>C synonymous_variant 0.46 pyrazinamide
clpC1 4039832 c.873C>G synonymous_variant 0.46 pyrazinamide
whiB6 4338595 c.-75delG upstream_gene_variant 0.32 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R