TB-Profiler result

Run: SRR28859799
Summary

Run ID: SRR28859799

Sample name:

Date: 2024-10-04T21:22:44.935329

Number of reads: 3360247

Percentage reads mapped: 99.48

Median coverage: 104.0

Strain: lineage4.1.1.2;lineage4.7

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.1.2 Euro-American (X-type) None 0.43
lineage4.1 Euro-American None 0.42
lineage4.7 Euro-American (mainly T) None 0.61
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.45
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 folC p.Ser150Gly Mutation from literature
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
folC 2747151 p.Ser150Gly missense_variant 0.48 para-aminosalicylic_acid Mutation from literature
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
dnaA 1509 p.Gln503His missense_variant 0.4 isoniazid Uncertain significance
gyrB 6950 p.Leu571Ile missense_variant 0.61 levofloxacin Uncertain significance
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.5 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.47 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13631 c.-73T>C upstream_gene_variant 0.59 isoniazid Uncertain significance
mshA 576453 p.Val369Gly missense_variant 0.25 isoniazid
ethionamide
Rv0565c 657269 p.Ser68Pro missense_variant 0.51 ethionamide Uncertain significance
mmaA3 738135 c.15A>G synonymous_variant 0.38 isoniazid
rpoC 764617 c.1248C>T synonymous_variant 0.45 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.47 rifampicin 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
rplC 800219 c.-590T>C upstream_gene_variant 0.32 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1854268 p.Ile221Met missense_variant 0.43 linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.38 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 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3066014 p.Ile60Val missense_variant 0.62 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 0.44 cycloserine
Rv3083 3449787 c.1284C>T synonymous_variant 0.43 ethionamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.43 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626305 c.309C>T synonymous_variant 0.41 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.4 ethambutol Not assoc w R
embA 4243833 p.Ala201Thr missense_variant 0.3 ethambutol Not assoc w R
embB 4246930 p.Gln139His missense_variant 0.31 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.28 ethambutol
embB 4247634 p.Gly374Glu missense_variant 0.45 ethambutol Uncertain significance
embB 4248562 c.2049G>A synonymous_variant 0.43 ethambutol
embB 4249408 c.2895G>A synonymous_variant 0.35 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.5 ethambutol Not assoc w R
aftB 4268135 c.702G>C synonymous_variant 0.48 ethambutol Not assoc w R - Interim
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 0.41 kanamycin
capreomycin
amikacin