TB-Profiler result

Run: SRR15368948
Summary

Run ID: SRR15368948

Sample name:

Date: 2024-10-04T13:29:28.203264

Number of reads: 8001082

Percentage reads mapped: 99.22

Median coverage: 235.0

Strain: lineage4.4.2;lineage4.5

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.19
lineage4 Euro-American None 1.0
lineage4.4 Euro-American None 0.79
lineage4.4.2 Euro-American None 0.8
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 7892 c.591G>A synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 576690 p.Tyr448Cys missense_variant 0.22 isoniazid
ethionamide
ccsA 620029 c.139C>T synonymous_variant 0.25 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834803 p.Ala421Val missense_variant 0.2 pyrazinamide
tsnR 1853577 c.-29G>A upstream_gene_variant 0.82 linezolid Uncertain significance
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
bacA 2062923 c.1806G>A synonymous_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
PPE35 2168757 p.Gln619Arg missense_variant 0.81 pyrazinamide Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 0.2 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
eis 2714211 c.1122G>A synonymous_variant 0.14 kanamycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2752c 3066099 p.Met31Ile missense_variant 0.82 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.79 cycloserine
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.83 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 0.21 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.19 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.86 ethambutol Not assoc w R
embC 4242397 c.2535G>A synonymous_variant 0.22 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 0.78 ethambutol Not assoc w R
embB 4247249 p.Gly246Arg missense_variant 0.79 ethambutol Uncertain significance
ubiA 4268928 c.906C>T synonymous_variant 0.78 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.82 ethambutol Not assoc w R
ethA 4326009 p.Val489Phe missense_variant 0.21 ethionamide 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
whiB6 4338839 c.-318T>C upstream_gene_variant 0.27 kanamycin
capreomycin
amikacin
gid 4408090 p.Pro38Arg missense_variant 0.8 streptomycin