TB-Profiler result

Run: SRR6485082
Summary

Run ID: SRR6485082

Sample name:

Date: 2024-04-15T05:49:02.671583

Number of reads: 4228412

Percentage reads mapped: 99.59

Median coverage: 113.0

Strain: lineage2.2.1;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
lineage2 East-Asian RD105 0.06
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.08
lineage2.2 East-Asian (Beijing) RD105;RD207 0.14
lineage4 Euro-American None 0.86
lineage4.8 Euro-American (mainly T) RD219 0.88
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 7585 p.Ser95Thr missense_variant 0.11 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.17 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.15 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.18 ethionamide Uncertain significance
rpoC 764437 c.1068G>A synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoC 766645 p.Glu1092Asp missense_variant 0.11 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.14 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
embR 1417580 c.-233T>C upstream_gene_variant 0.92 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.95 capreomycin Not assoc w R
linezolid Not assoc w R
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15 ethionamide
isoniazid
rpsA 1834177 c.636A>C synonymous_variant 0.11 pyrazinamide Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156563 c.-452G>A upstream_gene_variant 0.86 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.11 pyrazinamide Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.12 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.12 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.84 capreomycin
Rv2681 2997923 c.1185G>T synonymous_variant 0.84 capreomycin Not assoc w R - Interim
Rv2752c 3066871 c.-680C>T upstream_gene_variant 0.89 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3073715 p.Pro253Ala missense_variant 0.1 para-aminosalicylic_acid
Rv3236c 3612813 p.Thr102Ala missense_variant 0.15 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.13 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267331 c.1506C>A synonymous_variant 0.68 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.14 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.11 capreomycin
amikacin
kanamycin