TB-Profiler result

Run: SRR6855892
Summary

Run ID: SRR6855892

Sample name:

Date: 2024-10-03T16:37:55.597076

Number of reads: 567003

Percentage reads mapped: 99.62

Median coverage: 26.0

Strain: lineage4.1.2;lineage4.4.1.1.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.4.1.1.1 Euro-American None 0.62
lineage4.1 Euro-American None 0.34
lineage4.1.2 Euro-American None 0.25
lineage4.4.1 Euro-American (S-type) None 0.61
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.62
lineage4.4 Euro-American None 0.61
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 gid p.Ala200Glu Assoc w R
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
gid 4407604 p.Ala200Glu missense_variant 0.55 streptomycin Assoc w R
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
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
embR 1417140 p.Ala70Ser missense_variant 0.5 ethambutol Not assoc w R
embR 1418018 c.-671C>T upstream_gene_variant 0.41 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673249 c.-953C>T upstream_gene_variant 0.36 isoniazid
ethionamide
tsnR 1853674 c.69G>A synonymous_variant 0.76 linezolid Not assoc w R - Interim
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
ndh 2102990 p.Val18Ala missense_variant 0.7 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2169840 p.Gly258Asp missense_variant 0.59 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.62 ethionamide Not assoc w R - Interim
Rv3083 3448894 p.Tyr131Asp missense_variant 0.35 ethionamide Uncertain significance
Rv3083 3449642 p.Asn380Ser missense_variant 0.6 ethionamide Uncertain significance
whiB7 3568921 c.-242G>C upstream_gene_variant 0.47 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.75 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641164 p.Ile208Val missense_variant 0.31 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 0.71 ethambutol Not assoc w R
embC 4239274 c.-589C>G upstream_gene_variant 0.66 ethambutol Not assoc w R
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
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin