TB-Profiler result

Run: SRR6442526
Summary

Run ID: SRR6442526

Sample name:

Date: 2024-10-04T13:43:34.950680

Number of reads: 458656

Percentage reads mapped: 99.3

Median coverage: 9.0

Strain: lineage1.2.2.2

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
lineage1.2.2 Indo-Oceanic RD239 1.0
lineage1.2.2.2 Indo-Oceanic RD239 1.0
lineage1 Indo-Oceanic RD239 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
gyrB 5075 c.-165C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620586 c.696C>T synonymous_variant 1.0 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 1.0 rifampicin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 1.0 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302948 c.18T>G synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrA 3627602 c.-253C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
bedaquiline Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 1.0 streptomycin Not assoc w R