TB-Profiler result

Run: SRR5073871
Summary

Run ID: SRR5073871

Sample name:

Date: 2024-10-04T22:21:28.657706

Number of reads: 2595054

Percentage reads mapped: 99.66

Median coverage: 85.0

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) RD219 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
dnaA 902 p.Val301Ala missense_variant 0.23 isoniazid Uncertain significance
gyrA 7321 p.Pro7Leu missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620375 p.Pro162Arg missense_variant 0.99 kanamycin
capreomycin
amikacin
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
fbiC 1303747 p.Thr273Ala missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1853943 p.Thr113Ile missense_variant 1.0 linezolid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2169063 p.Met517Thr missense_variant 0.57 pyrazinamide
PPE35 2169066 p.Ala516Val missense_variant 0.57 pyrazinamide
PPE35 2169071 c.1542A>G synonymous_variant 0.5 pyrazinamide Not assoc w R - Interim
PPE35 2169122 c.1491C>G synonymous_variant 0.71 pyrazinamide Not assoc w R - Interim
PPE35 2169125 p.Val496Ile missense_variant 0.73 pyrazinamide Uncertain significance
PPE35 2169131 c.1482C>T synonymous_variant 0.76 pyrazinamide Not assoc w R - Interim
PPE35 2169134 c.1479G>A synonymous_variant 0.76 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726687 c.495C>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.99 ethionamide Uncertain significance
embC 4242643 c.2781C>T synonymous_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