TB-Profiler result

Run: ERR11466061
Summary

Run ID: ERR11466061

Sample name:

Date: 2024-04-14T23:04:03.319608

Number of reads: 456315

Percentage reads mapped: 98.59

Median coverage: 9.0

Strain: lineage4.9.1

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.9.1 Euro-American (H37Rv-like) None 0.99
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7832 c.531G>T synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 7835 c.534A>C synonymous_variant 0.25 levofloxacin
moxifloxacin
gyrA 7841 c.540C>T synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7847 c.546G>A synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 8978 c.1677C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
rpoC 766484 c.3115_3117delGTAinsAT frameshift_variant&missense_variant 0.46 rifampicin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801207 c.399C>T synonymous_variant 0.55 linezolid
rplC 801210 c.402T>C synonymous_variant 0.46 linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833661 c.120A>G synonymous_variant 0.43 pyrazinamide
rpsA 1833664 c.123C>G synonymous_variant 0.4 pyrazinamide
rpsA 1833886 c.345C>G synonymous_variant 0.38 pyrazinamide
rpsA 1833892 c.351G>A synonymous_variant 0.43 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.43 pyrazinamide
rpsA 1834375 c.834G>C synonymous_variant 0.25 pyrazinamide
rpsA 1834498 c.957C>T synonymous_variant 0.38 pyrazinamide
Rv2477c 2782483 c.1560G>C synonymous_variant 0.31 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
clpC1 4040423 c.282A>G synonymous_variant 0.6 pyrazinamide Not assoc w R - Interim
clpC1 4040431 c.274T>C synonymous_variant 0.64 pyrazinamide
clpC1 4040441 c.264C>T synonymous_variant 0.54 pyrazinamide
clpC1 4040444 c.261C>G synonymous_variant 0.54 pyrazinamide
clpC1 4040450 c.255A>G synonymous_variant 0.5 pyrazinamide Not assoc w R - Interim
clpC1 4040456 c.249C>T synonymous_variant 0.53 pyrazinamide Not assoc w R - Interim
clpC1 4040459 c.246C>A synonymous_variant 0.53 pyrazinamide
clpC1 4040465 c.240T>C synonymous_variant 0.59 pyrazinamide
clpC1 4040471 c.234T>C synonymous_variant 0.39 pyrazinamide Not assoc w R - Interim
clpC1 4040522 c.183T>C synonymous_variant 0.36 pyrazinamide Not assoc w R - Interim
embB 4247428 c.915C>G synonymous_variant 0.43 ethambutol
embB 4247434 c.921C>G synonymous_variant 0.46 ethambutol
embB 4247437 c.924A>G synonymous_variant 0.46 ethambutol Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R