TB-Profiler result

Run: SRR7535039
Summary

Run ID: SRR7535039

Sample name:

Date: 2024-10-04T12:03:31.336602

Number of reads: 5070461

Percentage reads mapped: 98.47

Median coverage: 105.0

Strain: lineage4.3.4.2.1;lineage4.6.1.2

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 0.75
lineage4.6 Euro-American None 0.28
lineage4.6.1.2 Euro-American RD724 0.26
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.76
lineage4.6.1 Euro-American (Uganda) RD724 0.25
lineage4.3.4 Euro-American (LAM) RD174 0.76
lineage4.3.4.2 Euro-American (LAM) RD174 0.75
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 6140 p.Val301Leu missense_variant 0.71 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7539 p.Thr80Ala missense_variant 0.23 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
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
fgd1 491331 p.Lys183Asn missense_variant 0.74 pretomanid
delamanid
clofazimine
rpoC 764995 c.1626C>G synonymous_variant 0.7 rifampicin Not assoc w R
rpoC 767083 c.3714C>T synonymous_variant 0.79 rifampicin Not assoc w R - Interim
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 1416410 p.Leu313Arg missense_variant 0.32 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
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
ndh 2101786 c.1257G>A synonymous_variant 0.22 isoniazid Not assoc w R - Interim
delamanid
ethionamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2519162 p.Val350Ile missense_variant 0.29 isoniazid
Rv2681 2996876 c.138A>C synonymous_variant 0.32 capreomycin Not assoc w R
Rv2752c 3065954 p.Thr80Ala missense_variant 0.3 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3066511 c.-320T>C upstream_gene_variant 0.75 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyA 3073868 p.Thr202Ala missense_variant 0.74 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.78 cycloserine
whiB7 3569029 c.-350A>G upstream_gene_variant 0.27 kanamycin Not assoc w R
amikacin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.81 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.68 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.74 cycloserine
alr 3840869 c.552C>G synonymous_variant 0.77 cycloserine
rpoA 3877896 c.612G>T synonymous_variant 0.75 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.76 pyrazinamide Not assoc w R
glpK 4139670 p.Cys29Tyr missense_variant 0.25 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4240572 p.Gly237Ala missense_variant 0.71 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245055 p.Thr608Asn missense_variant 0.35 ethambutol Uncertain significance
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
gid 4408156 p.Leu16Arg missense_variant 0.71 streptomycin Not assoc w R