TB-Profiler result

Run: SRR13837458

Summary

Run ID: SRR13837458

Sample name:

Date: 2024-04-15T22:29:05.058550

Number of reads: 881502

Percentage reads mapped: 98.0

Median coverage: 30.0

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
gyrA 8827 p.Asp509Gly missense_variant 1.0 levofloxacin
moxifloxacin
nusG 734793 c.540C>G synonymous_variant 1.0 rifampicin
mmpR5 779201 p.Ala71Val missense_variant 1.0 clofazimine
bedaquiline
rplC 800119 c.-690G>C upstream_gene_variant 1.0 linezolid
rplC 800522 c.-287C>A upstream_gene_variant 1.0 linezolid
Rv1129c 1253232 p.Asp435His missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1253562 p.Gln325Lys missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1254726 c.-192C>T upstream_gene_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1305062 p.Gly711Glu missense_variant 1.0 clofazimine
pretomanid
delamanid
sigE 1364621 p.Ala70Val missense_variant 1.0 pyrazinamide
rrs 1472361 n.516C>G non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475981 n.2324G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rpsA 1834620 p.Leu360Ser missense_variant 1.0 pyrazinamide
tlyA 1918366 p.Ala143Pro missense_variant 1.0 capreomycin
bacA 2064408 c.321C>T synonymous_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
ndh 2101701 c.1341delG frameshift_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
ndh 2103327 c.-285C>A upstream_gene_variant 1.0 ethionamide
delamanid
isoniazid
PPE35 2170109 c.504C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
kasA 2518676 p.Gly188Cys missense_variant 1.0 isoniazid
eis 2714749 p.Val195Ala missense_variant 1.0 amikacin
kanamycin
eis 2715045 c.288G>A synonymous_variant 1.0 amikacin
kanamycin
Rv2752c 3067080 c.-889G>C upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
lpqB 3624325 p.Thr196Pro missense_variant 1.0 bedaquiline
rifampicin
mtrB 3625849 p.His255Gln missense_variant 1.0 bedaquiline
rifampicin
clpC1 4039055 p.Ile550Met missense_variant 1.0 pyrazinamide
embC 4242797 p.Asp979His missense_variant 1.0 ethambutol
embB 4247936 p.Thr475Ala missense_variant 1.0 ethambutol