TB-Profiler result

Run: SRR2101569
Summary

Run ID: SRR2101569

Sample name:

Date: 2024-10-05T09:04:28.388725

Number of reads: 938087

Percentage reads mapped: 99.09

Median coverage: 37.0

Strain: lineage4.8.1

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 0.82
lineage4.8.1 Euro-American (mainly T) RD219 0.84
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 9304 p.Gly668Asp missense_variant 0.18 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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
Rv1129c 1253968 c.567A>G synonymous_variant 0.85 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.72 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.33 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.14 isoniazid Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.79 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.97 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.16 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.27 cycloserine
fbiD 3339040 c.-78T>C upstream_gene_variant 0.9 pretomanid
delamanid
clofazimine
Rv3083 3448497 c.-6_*1408del transcript_ablation 0.92 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.31 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.13 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3642874 p.Leu447Arg missense_variant 0.75 pretomanid
delamanid Uncertain significance
clofazimine 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