TB-Profiler result

Run: SRR1049959
Summary

Run ID: SRR1049959

Sample name:

Date: 2024-04-16T07:54:33.246552

Number of reads: 806678

Percentage reads mapped: 98.41

Median coverage: 17.0

Strain: lineage4.1;lineage6.3.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.87
lineage4 Euro-American None 0.84
lineage6.3.1 West-Africa 2 RD702 0.07
lineage6 West-Africa 2 RD702 0.12
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 6446 p.Ala403Ser missense_variant 0.32 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrB 6507 p.Ala423Val missense_variant 0.53 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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
gyrA 9656 c.2355C>G synonymous_variant 0.85 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.88 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.27 ethionamide
rpoC 765150 p.Gly594Glu missense_variant 0.8 rifampicin Not assoc w R
rpoC 765187 c.1818C>T synonymous_variant 0.71 rifampicin Not assoc w R - Interim
rpoC 766012 c.2643C>G synonymous_variant 0.76 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776411 c.2070T>C synonymous_variant 0.87 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mmpL5 776750 c.1731C>T synonymous_variant 0.61 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781421 c.-139C>A upstream_gene_variant 0.75 streptomycin Uncertain significance
atpE 1461251 c.207G>T synonymous_variant 0.25 bedaquiline Not assoc w R - Interim
rrs 1471627 n.-219C>T upstream_gene_variant 0.81 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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
katG 2156007 c.105C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.29 pyrazinamide 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627293 c.57G>A synonymous_variant 0.93 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
rpoA 3878652 c.-145C>T upstream_gene_variant 0.71 rifampicin Uncertain significance
clpC1 4039835 c.870C>T synonymous_variant 0.89 pyrazinamide Not assoc w R - Interim
embC 4242803 p.Val981Leu missense_variant 0.92 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