TB-Profiler result

Run: SRR10851653
Summary

Run ID: SRR10851653

Sample name:

Date: 2024-04-16T07:55:55.886805

Number of reads: 867202

Percentage reads mapped: 69.64

Median coverage: 23.0

Strain: lineage4.1.2;lineage4.3.4

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.54
lineage4.1 Euro-American None 0.37
lineage4.1.2 Euro-American None 0.45
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.59
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.43 ethionamide Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.57 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777320 c.1161C>G synonymous_variant 0.54 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mmpL5 778001 c.480A>C synonymous_variant 0.35 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800200 c.-609C>G upstream_gene_variant 0.33 linezolid
Rv1129c 1254582 c.-48A>G upstream_gene_variant 0.5 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302736 c.-195A>G upstream_gene_variant 0.62 clofazimine
pretomanid
delamanid
rrs 1471644 n.-202T>C upstream_gene_variant 0.53 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1833952 c.411C>G synonymous_variant 0.43 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.45 isoniazid
eis 2714852 p.Ser161Arg missense_variant 0.52 amikacin
kanamycin
thyA 3073868 p.Thr202Ala missense_variant 0.55 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3611974 c.1143A>C synonymous_variant 0.47 pyrazinamide Not assoc w R - Interim
Rv3236c 3612009 p.Ala370Thr missense_variant 0.44 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626568 p.Ser16Pro missense_variant 0.77 bedaquiline
rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.53 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.52 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 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.64 streptomycin Not assoc w R