TB-Profiler result

Run: SRR21658556
Summary

Run ID: SRR21658556

Sample name:

Date: 2024-10-04T02:33:17.765853

Number of reads: 1152127

Percentage reads mapped: 99.83

Median coverage: 51.0

Strain: lineage4.3.3;lineage4.8

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
lineage4.3 Euro-American (LAM) None 0.06
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.6
lineage4.3.3 Euro-American (LAM) RD115 0.11
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
dnaA 247 p.Thr83Ala missense_variant 0.52 isoniazid
gyrB 5076 c.-164_-163insT upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrB 5524 c.285C>A synonymous_variant 0.66 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13442 p.Leu39Phe missense_variant 0.49 isoniazid Uncertain significance
fgd1 491172 c.390C>A synonymous_variant 0.29 pretomanid
delamanid
clofazimine
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsA 1834836 p.Met432Thr missense_variant 0.22 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.16 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154980 c.1132C>T synonymous_variant 0.21 isoniazid Not assoc w R - Interim
katG 2156196 c.-85C>T upstream_gene_variant 0.11 isoniazid Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.52 pyrazinamide Not assoc w R
PPE35 2170811 c.-199C>T upstream_gene_variant 0.6 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 0.12 isoniazid
folC 2746735 c.864C>T synonymous_variant 0.28 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.57 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.24 para-aminosalicylic_acid
Rv3083 3448428 c.-76A>C upstream_gene_variant 0.28 ethionamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249354 c.2841G>C synonymous_variant 0.4 ethambutol Not assoc w R - Interim
aftB 4268076 p.Met254Ala missense_variant 0.25 ethambutol Uncertain significance
whiB6 4338590 c.-69A>T upstream_gene_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R